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Encyclopedia > Protein
A representation of the 3D structure of myoglobin showing coloured alpha helices. This protein was the first to have its structure solved by X-ray crystallography.

Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Although this genetic code specifies 20 "standard" amino acids plus selenocysteine and - in certain archaea - pyrrolysine, the residues in a protein are sometimes chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.[1] Download high resolution version (695x702, 67 KB)Image created by uploader from PDB file: Source: Sperm whale (Physeter catodon) Authors: S.E.V. Phillips Reference: Structure and refinement of oxymyoglobin at 1. ... Download high resolution version (695x702, 67 KB)Image created by uploader from PDB file: Source: Sperm whale (Physeter catodon) Authors: S.E.V. Phillips Reference: Structure and refinement of oxymyoglobin at 1. ... An X-ray diffraction image for the protein myoglobin. ... Side view of an α-helix of alanine residues in atomic detail. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Proteins are broken down in the stomach during digestion by enzymes known as proteases into smaller polypeptides to provide amino acids for the organism, including the essential amino acids that the organism cannot biosynthesize itself. ... Protein is a class of biomolecules. ... Benzene is the simplest of the arenes, a family of organic compounds An organic compound is any member of a large class of chemical compounds whose molecules contain carbon. ... This article is about the class of chemicals. ... A peptide bond is a chemical bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... A carboxyl or carboxylic group is a functional group consisting of a carbon atom and an oxygen atom doubly bonded to each other. ... In chemistry, especially in organic chemistry and biochemistry, an amino group is an ammonia-like functional group. ... For other uses, see Gene (disambiguation). ... For a non-technical introduction to the topic, see Introduction to Genetics. ... Skeletal formula of L-selenocysteine Space-filling model of L-selenocysteine Selenocysteine is an amino acid that is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5 deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases and some hydrogenases). ... Pyrrolysine is a naturally-occurring genetically-coded amino acid. ... Posttranslational modification means the chemical modification of a protein after its translation. ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell being used to describe the smallest unit of a living organism Cells in culture, stained for keratin (red) and DNA (green) The cell is the... A protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time. ...


Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. A macromolecule is a molecule composed of a very large number of atoms. ... Polysaccharides (sometimes called glycans) are relatively complex carbohydrates. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell being used to describe the smallest unit of a living organism Cells in culture, stained for keratin (red) and DNA (green) The cell is the... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Catalyst redirects here. ... Structure of the coenzyme adenosine triphosphate, a central intermediate in energy metabolism. ... G-Actin (PDB code: 1j6z). ... Myosin is a motor protein filament found in muscle tissue. ... The eukaryotic cytoskeleton. ... This article is about the temporary framework. ... Cell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. ... Each antibody binds to a specific antigen; an interaction similar to a lock and key. ... Schematic of cell adhesion The study of cell adhesion is part of cell biology. ... The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic cell leading to its replication. ... An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet. ... For the industrial process, see anaerobic digestion. ...


The word protein comes from the Greek word πρώτα ("prota"), meaning "of primary importance." Proteins were first described and named by the Swedish chemist Jöns Jakob Berzelius in 1838. However, central role of proteins in living organisms was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was a protein.[2] The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved included hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.[3][4] The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. Friherre Jöns Jakob Berzelius (August 20, 1779 – August 7, 1848) was a Swedish chemist. ... James Batcheller Sumner (November 19, 1887 – August 12, 1955) was an American chemist. ... Helicobacter Pylori Urease drawn from PDB 1E9Z. Urease (EC 3. ... Not to be confused with inulin. ... Frederick Sanger, OM, CH, CBE, FRS (born 13 August 1918) is an English biochemist and a two time Nobel laureate in chemistry. ... Structure of hemoglobin. ... An X-ray diffraction image for the protein myoglobin. ... Max Ferdinand Perutz, OM (May 19, 1914 – February 6, 2002) was an Austrian-British molecular biologist. ... This article or section does not cite its references or sources. ... This is a list of Nobel Prize laureates in Chemistry from 1901 to 2006. ...

Contents

Biochemistry

Main articles: Amino acid and peptide bond
Resonance structures of the peptide bond that links individual amino acids to form a protein polymer.
Section of a protein structure showing serine and alanine residues linked together by peptide bonds. Carbons are shown in white and hydrogens are omitted for clarity.

Proteins are linear polymers built from 20 different L-α-amino acids. All amino acids possess common structural features, including an α carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation.[5] The side chains of the standard amino acids, detailed in the list of standard amino acids, have different chemical properties that produce three-dimensional protein structure and are therefore critical to protein function. The amino acids in a polypeptide chain are linked by peptide bonds formed in a dehydration reaction. Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. This article is about the class of chemicals. ... A peptide bond is a chemical bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... Image File history File links Peptide_group_resonance. ... Image File history File links Peptide_group_resonance. ... For other uses, see Resonance (disambiguation). ... A peptide bond is a chemical bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... A polymer (from Greek: πολυ, polu, many; and μέρος, meros, part) is a substance composed of molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds. ... Image File history File links Download high-resolution version (873x614, 182 KB) Summary I created image Licensing I, the creator of this work, hereby release it into the public domain. ... Image File history File links Download high-resolution version (873x614, 182 KB) Summary I created image Licensing I, the creator of this work, hereby release it into the public domain. ... This article is about the class of chemicals. ... The Alpha carbon refers to the first carbon after the carbon that attaches to the functional group. ... In chemistry, especially in organic chemistry and biochemistry, an amino group is an ammonia-like functional group. ... A carboxyl or carboxylic group is a functional group consisting of a carbon atom and an oxygen atom doubly bonded to each other. ... The term Side chain can have different meanings depending on the context: In chemistry and biochemistry a side chain is a part of a molecule attached to a core structure. ... A chemical bond is the physical process responsible for the attractive interactions between atoms and molecules, and that which confers stability to diatomic and polyatomic chemical compounds. ... It has been suggested that this article or section be merged with Proteinogenic amino acid. ... A peptide bond is a chemical bond that is formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... In chemistry, a dehydration reaction is a chemical reaction that involves the loss of water from the reacting molecule. ... For other uses, see Resonance (disambiguation). ... Covalent bonding is a form of chemical bonding characterized by the sharing of one or more pairs of electrons between atoms, in order to produce a mutual attraction, which holds the resultant molecule together. ... A set of points is said to be coplanar if and only if they lie on the same geometric plane. ... In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ...


Due to the chemical structure of the individual amino acids, the protein chain has directionality. The end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus, whereas the end with a free amino group is known as the N-terminus or amino terminus. The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ... The N-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free amine group (NH2). ...


The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and usually lies near 20–30 residues.[6] Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined conformation. Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... Peptides (from the Greek πεπτος, digestible), are the family of short molecules formed from the linking, in a defined order, of various α-amino acids. ... In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. ... In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. ...


Synthesis

Main article: Protein biosynthesis
The DNA sequence of a gene encodes the amino acid sequence of a protein.

Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination stands for an amino acid, for example AUG stands for methionine. Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid. In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.[7] Protein biosynthesis (synthesis) is the process in which cells build proteins. ... Image File history File links This is a lossless scalable vector image. ... Image File history File links This is a lossless scalable vector image. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... For a non-technical introduction to the topic, see Introduction to Genetics. ... This article is about the class of chemicals. ... For other uses, see Gene (disambiguation). ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... For a non-technical introduction to the topic, see Introduction to Genetics. ... RNA codons. ... Methionine is an α-amino acid with the chemical formula HO2CCH(NH2)CH2CH2SCH3. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... The life cycle of an mRNA in a eukaryotic cell. ... This article does not cite any references or sources. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Prokaryotic bacteria cell structure Prokaryotes (IPA: //) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. ... It has been suggested that Genophore be merged into this article or section. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ... HeLa cells stained for DNA with the Blue Hoechst dye. ... The nuclear envelope refers to the double membrane of the nucleus that encloses genetic material in eukaryotic cells. ... Schematic showing the cytoplasm, with major components of a typical animal cell. ... Protein biosynthesis (synthesis) is the process in which cells build proteins. ...


The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus. Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ... Base pairs, of a DNA molecule. ... An anticodon is a unit made up of nucleotides that plays an important role in various DNA cycles, including DNA transcription. ... Transfer RNA Transfer RNA (abbreviated tRNA), first hypothesized by Francis Crick, is a small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... An aminoacyl tRNA synthetase (abbreviated aaRs) is an enzyme that catalyzes the binding of a specific amino acid to a tRNA to form an aminoacyl-tRNA. The synthetase hydrolyzes ATP to bind the appropriate amino acid to the 3 hydroxyl of the tRNA molecule. ... The N-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free amine group (NH2). ... The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ...


The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[6] The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.[8] The molecular mass (abbreviated Mr) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12). ... The unified atomic mass unit (u), or dalton (Da), is a small unit of mass used to express atomic and molecular masses. ... Typical divisions Ascomycota (sac fungi) Saccharomycotina (true yeasts) Taphrinomycotina Schizosaccharomycetes (fission yeasts) Basidiomycota (club fungi) Urediniomycetes Sporidiales Yeasts are a growth form of eukaryotic micro organisms classified in the kingdom Fungi, with about 1,500 species described;[1] they dominate fungal diversity in the oceans. ... Not to be confused with Tintin. ... For other uses of Muscle, see Muscle (disambiguation). ... Image of sarcomere A sarcomere is the basic unit of a cross striated muscles myofibril. ...


Chemical synthesis

Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis, which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield.[9] Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains.[10] These methods are useful in laboratory biochemistry and cell biology, though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. In organic chemistry, peptide synthesis is the creation of peptides, which are organic compounds in which multiple amino acids bind via peptide bonds which are also known as amide bonds. ... Organic synthesis is the construction of organic molecules via chemical processes. ... Chemical ligation is a set of techniques used for creating long peptide or protein chains. ... Fluorescence induced by exposure to ultraviolet light in vials containing various sized cadmium selenide (CdSe) quantum dots. ... Wöhler observes the synthesis of urea. ... Cell biology (also called cellular biology or formerly cytology, from the Greek kytos, container) is an academic discipline that studies cells. ... In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. ...


Structure of proteins

Main article: Protein structure
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: all-atom representation colored by atom type. Middle: simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).

Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state. Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. ... Image File history File links Proteinviews-1tim. ... Image File history File links Proteinviews-1tim. ... Triose phosphate isomerase is an enzyme which, during glycolysis, converts dihydroxyacetone phosphate to glyceraldehyde-3-phosphate. ... Protein before and after folding. ... In biochemistry, the native state of a protein is its operative or functional form. ...

NMR structures of the protein cytochrome c in solution show the constantly shifting dynamic structure of the protein. Larger version.

Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis. In solution all proteins also undergo variation in structure through thermal vibration and the collision with other molecules, see the animation on the right. A protein primary structure is a chain of amino acids. ... Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain. ... A representation of the 3D structure of the myoglobin protein. ... An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... Side view of an α-helix of alanine residues in atomic detail. ... Diagram of β-pleated sheet with H-bonding between protein strands The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins — the first is the alpha helix — consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. ... In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. ... The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. ... In protein chemistry, the term salt bridge or salt bond is used to denote chemical bonds between positively and negatively charged side-chains of proteins. ... In chemistry, a disulfide bond is a single covalent bond derived from the coupling of thiol groups. ... Posttranslational modification means the chemical modification of a protein after its translation. ... In biochemistry, many proteins are actually assemblies of more than one protein (polypeptide) molecule, which in the context of the larger assemblage are known as protein subunits. ... Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. ... In structural biology, a protein subunit or subunit protein is a double protein molecule that assembles (or coassembles) with other protein molecules to form a multimeric or oligomeric protein. ... A protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time. ... Image File history File links Protein_Dynamics_Cytochrome_C_2NEW_smaller. ... Cytochrome c with heme c. ... Image File history File links Protein_Dynamics_Cytochrome_C_2NEW_small. ... In chemistry, a chemical conformation is the spatial arrangement of atoms in a molecule. ... For other uses, see Substrate. ... The active site of an enzyme contains the catalytic and binding sites. ...

Molecular surface of several proteins showing their comparative sizes. From left to right are: Antibody (IgG), Hemoglobin, Insulin (a hormone), Adenylate kinase (an enzyme), and Glutamine synthetase (an enzyme).

Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural; membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane. Download high resolution version (2824x812, 301 KB) Wikipedia does not have an article with this exact name. ... Download high resolution version (2824x812, 301 KB) Wikipedia does not have an article with this exact name. ... Each antibody binds to a specific antigen; an interaction similar to a lock and key. ... Structure of hemoglobin. ... Not to be confused with inulin. ... Adenylate kinase (also known as ADK) is a phosphotransferase enzyme (EC 2. ... Glutamine synthetase ( 6. ... 3-dimensional structure of hemoglobin, a globular protein. ... Fibrous proteins, also called scleroproteins, are long filamentous protein molecules that form one of the two main classes of tertiary structure protein (the other being globular proteins). ... A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. ... It has been suggested that this article or section be merged with Solution. ... In biochemistry, a receptor is a protein on the cell membrane or within the cytoplasm or cell nucleus that binds to a specific molecule (a ligand), such as a neurotransmitter, hormone, or other substance, and initiates the cellular response to the ligand. ...


A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration, are called dehydrons. Dehydration (hypohydration) is the removal of water (hydro in ancient Greek) from an object. ... Intramolecular hydrogen bond poorly shielded from water attack, with a propensity to promote its own dehydration. ...


Structure determination

Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function. Common experimental methods of structure determination include X-ray crystallography and NMR spectroscopy, both of which can produce information at atomic resolution. Cryoelectron microscopy is used to produce lower-resolution structural information about very large protein complexes, including assembled viruses;[11] a variant known as electron crystallography can also produce high-resolution information in some cases, especially for two-dimensional crystals of membrane proteins.[12] Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein. X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... For other uses, see Atom (disambiguation). ... Electron cryomicroscopy (aka cryoelectron microscopy) is a developing method in structural biology. ... This article is about biological infectious particles. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format). ... Cartesian means relating to the French mathematician and philosopher Descartes, who, among other things, worked to merge algebra and Euclidean geometry. ...


Many more gene sequences are known than protein structures. Further, the set of solved structures is biased toward proteins that can be easily subjected to the conditions required in X-ray crystallography, one of the major structure determination methods. In particular, globular proteins are comparatively easy to crystallize in preparation for X-ray crystallography. Membrane proteins, by contrast, are difficult to crystallize and are underrepresented in the PDB.[13] Structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes. Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined. X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Crystal (disambiguation) Insulin crystals A crystal is a solid in which the constituent atoms, molecules, or ions are packed in a regularly ordered, repeating pattern extending in all three spatial dimensions. ... Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins. ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ...


Cellular functions

Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.[6] With the exception of certain types of RNA, most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively.[14] The set of proteins expressed in a particular cell or cell type is known as its proteome. Image File history File links This is a lossless scalable vector image. ... For other uses, see RNA (disambiguation). ... E. coli redirects here. ... The term proteome was coined by Mark Wilkins in 1995 (1) and is used to describe the entire complement of proteins in a given biological organism or system at a given time, i. ...

The enzyme hexokinase is shown as a simple ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.

The chief characteristic of proteins that allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10-15 M) but does not bind at all to its amphibian homolog onconase (>1 M). Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine. Image File history File links Download high-resolution version (897x640, 189 KB) Summary I am author. ... Image File history File links Download high-resolution version (897x640, 189 KB) Summary I am author. ... A hexokinase is an enzyme that phosphorylates a six-carbon sugar, a hexose, to a hexose phosphate. ... Adenosine 5-triphosphate (ATP) is a multifunctional nucleotide that is most important as a molecular currency of intracellular energy transfer. ... Glucose (Glc), a monosaccharide (or simple sugar), is an important carbohydrate in biology. ... A binding site is a region on a protein to which specific ligands bind. ... Top view of porcine ribonuclease inhibitor (PDB accesion code 2BNH), showing its horseshoe shape. ... Angiogenin (Ang) is a small polypeptide that is implicated in angiogenesis (formation of new blood vessels) in tumor growth . ... In chemistry and biochemistry, a dissociation constant or an ionization constant is a specific type of equilibrium constant used for reversible reactions or processes. ... Ranpirnase is a ribonuclease enzyme found in Rana pipiens oocytes. ... An aminoacyl tRNA synthetase (abbreviated aaRs) is an enzyme that catalyzes the binding of a specific amino acid to a tRNA to form an aminoacyl-tRNA. The synthetase hydrolyzes ATP to bind the appropriate amino acid to the 3 hydroxyl of the tRNA molecule. ... Valine is an amino acid that cannot be synthesized by humans, so it is considered an essential amino acid for human life. ... Isoleucine is an α-amino acid with the chemical formula HO2CCH(NH2)CH(CH3)CH2CH3. ...


Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of the same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein-protein interactions also regulate enzymatic activity, control progression through the cell cycle, and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks. In chemistry, an oligomer consists of a finite number of monomer units (oligo is Greek for a few), in contrast to a polymer which, at least in principle, consists of an infinite number of monomers. ... Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. ... The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic cell leading to its replication. ... A protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time. ... Cell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. ...


Enzymes

Main article: Enzyme

The best-known role of proteins in the cell is their duty as enzymes, which catalyze chemical reactions. Enzymes are usually highly specific catalysts that accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism and catabolism, as well as DNA replication, DNA repair, and RNA synthesis. Some enzymes act on other proteins to add or remove chemical groups in a process known as post-translational modification. About 4,000 reactions are known to be catalyzed by enzymes.[15] The rate acceleration conferred by enzymatic catalysis is often enormous - as much as 1017-fold increase in rate over the uncatalyzed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme).[16] Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Catalyst redirects here. ... Structure of the coenzyme adenosine triphosphate, a central intermediate in energy metabolism. ... Anabolism is the aspect of metabolism that contributes to growth. ... DNA replication. ... DNA damage resulting in multiple broken chromosomes DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. ... In genetics, transcription is the first of the two-step protein biosynthesis process. ... Posttranslational modification means the chemical modification of a protein after its translation. ... Orotidine 5-phosphate decarboxylase is an enzyme involved in pyrimidine metabolism. ...


The molecules bound and acted upon by enzymes are known as substrates. Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with the substrate, and an even smaller fraction - 3-4 residues on average - that are directly involved in catalysis.[17] The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site. For other uses, see Substrate. ... The active site of an enzyme contains the catalytic and binding sites. ...


Cell signaling and ligand transport

A mouse antibody against cholera that binds a carbohydrate antigen.

Many proteins are involved in the process of cell signaling and signal transduction. Some proteins, such as insulin, are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues. Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell. Many receptors have a binding site exposed on the cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell. Image File history File links Download high-resolution version (471x702, 218 KB) Summary Licensing File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Protein ... Image File history File links Download high-resolution version (471x702, 218 KB) Summary Licensing File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Protein ... Distribution of cholera Cholera, sometimes known as Asiatic cholera or epidemic cholera, is an infectious gastroenteritis caused by the bacterium Vibrio cholerae. ... Lactose is a disaccharide found in milk. ... Cell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. ... In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another, most often involving ordered sequences of biochemical reactions inside the cell, that are carried out by enzymes and linked through second messengers resulting in what is thought of as... Not to be confused with inulin. ... Biological tissue is a collection of interconnected cells that perform a similar function within an organism. ... A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. ... In biochemistry, a receptor is a protein on the cell membrane or within the cytoplasm or cell nucleus that binds to a specific molecule (a ligand), such as a neurotransmitter, hormone, or other substance, and initiates the cellular response to the ligand. ... In molecular biology, a protein may change its shape in order to undertake a new function; each possible shape is called a conformation, and a transition between them is called a conformational change. ...


Antibodies are protein components of adaptive immune system whose main function is to bind antigens, or foreign substances in the body, and target them for destruction. Antibodies can be secreted into the extracellular environment or anchored in the membranes of specialized B cells known as plasma cells. Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high. Wikipedia does not yet have an article with this exact name. ... The immune system is the collection of organs and tissues involved in the adaptive defense of a body against foreign biological material. ... An antigen or immunogen is a molecule that stimulates an immune response. ... Secretion is the process of segregating, elaborating, and releasing chemicals from a cell, or a secreted chemical substance or amount of substance. ... B cells are lymphocytes that play a large role in the humoral immune response (as opposed to the cell-mediated immune response). ... Plasma cells (also called plasma B cells or plasmocytes) are cells of the immune system that secrete large amounts of antibodies. ...


Many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is hemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom. In chemistry, a ligand is an atom, ion, or molecule (see also: functional group) that generally donates one or more of its electrons through a coordinate covalent bond to, or shares its electrons through a covalent bond with, one or more central atoms or ions (these ligands act as a... Structure of hemoglobin. ... This article is about the chemical element and its most stable form, or dioxygen. ... For the village in Tibet, see Lung, Tibet. ... This article does not cite any references or sources. ... In biology, homology is any similarity between structures that is due to their shared ancestry. ... The hierarchy of scientific classifications major eight taxonomic ranks. ...


Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. A transmembrane protein is a protein that spans the entire biological membrane. ... Scheme of semipermeable membrane during hemodialysis, where red is blood, blue is the dialysing fluid, and yellow is the membrane. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... A commonly-used example of a polar compound is water (H2O). ... diffusion (disambiguation). ... Ion channels are pore-forming proteins that help to establish and control the small voltage gradient that exists across the plasma membrane of all living cells (see cell potential) by allowing the flow of ions down their electrochemical gradient. ... General Name, symbol, number potassium, K, 19 Chemical series alkali metals Group, period, block 1, 4, s Appearance silvery white Standard atomic weight 39. ... For sodium in the diet, see Salt. ...


Structural proteins

Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins; for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that comprise the cytoskeleton, which allows the cell to maintain its shape and size. Collagen and elastin are critical components of connective tissue such as cartilage, and keratin is found in hard or filamentous structures such as hair, nails, feathers, hooves, and some animal shells. Fibrous proteins, also called scleroproteins, are long filamentous protein molecules that form one of the two main classes of tertiary structure protein (the other being globular proteins). ... G-Actin (PDB code: 1j6z). ... Tubulin is the protein which makes up microtubules. ... A polymer (from Greek: πολυ, polu, many; and μέρος, meros, part) is a substance composed of molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds. ... The eukaryotic cytoskeleton. ... Tropocollagen triple helix. ... Elastin is a protein in connective tissue that is elastic and allows many tissues in the body to resume their shape after stretching or contracting. ... Connective tissue is one of the four types of tissue in traditional classifications (the others being epithelial, muscle, and nervous tissue. ... Cartilage is a type of dense connective tissue. ... Not to be confused with kerogen or carotene. ... This article is about the body feature. ... For other uses, see Nail. ... For other uses, see Feather (disambiguation). ... Rear hooves of a horse Rear hoof of a giraffe A hoof (plural: hooves) is the foot of an ungulate, all of which walk more or less on their toes and have toes with a horny (keratin) covering. ... Various seashells Danielle A shell is the hard, rigid outer covering, or integument, allanimals. ...


Other proteins that serve structural functions are motor proteins such as myosin, kinesin, and dynein, which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and the sperm of many sexually reproducing multicellular organisms. They also generate the forces exerted by contracting muscles. This is a list of gene families or gene complexes, that is sets of genes which occur across a number of different species which often serve similar biological functions. ... Myosin is a motor protein filament found in muscle tissue. ... The kinesin dimer attaches to, and moves along, microtubules. ... Dynein is a motor protein (also called molecular motor or motor molecule) in cells which converts the chemical energy contained in ATP into the mechanical energy of movement. ... Motility is a biological term which refers to the ability to move spontaneously and independently. ... A spermatozoon or spermatozoan ( spermatozoa), from the ancient Greek σπέρμα (seed) and (living being) and more commonly known as a sperm cell, is the haploid cell that is the male gamete. ... For other uses of Muscle, see Muscle (disambiguation). ...


Methods of study

Main article: Protein methods

As some of the most commonly studied biological molecules, the activities and structures of proteins are examined both in vitro and in vivo. In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments on proteins' activities within cells or even within whole organisms can provide complementary information about where a protein functions and how it is regulated. Protein methods are the techniques used to study proteins. ... In vitro (Latin: within the glass) refers to the technique of performing a given experiment in a test tube, or, generally, in a controlled environment outside a living organism. ... In vivo (Latin for (with)in the living). ... Dihydrofolate reductase from with its two substrates, dihydrofolate (right) and NADPH (left), bound in the active site. ... In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. ...


Protein purification

Main article: Protein purification

In order to perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate. The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids. Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity. The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according their charge[18] using electrofocusing.-1... In vitro (Latin: within the glass) refers to the technique of performing a given experiment in a test tube, or, generally, in a controlled environment outside a living organism. ... Cytolysis is the lysis, or death, of cells due to the rupture of the cell membrane. ... A crude lysate is the solution produced when cells are destroyed by disrupting their cell membranes in a process known as cytolysis. ... Differential centrifugation is a procedure in which the homogenate is subjected to repeated centrifugations each time increasing the centrifugal force. ... Some common lipids. ... In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is separately enclosed within its own lipid membrane. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Salting out is a method of separating proteins based on the principle that proteins are less soluble at high salt concentrations. ... For the Second Person album, see Chromatography (album). ... Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid, ribonucleic acid, or protein molecules using an electric current applied to a gel matrix. ... The isoelectric point (pI) is the pH at which a molecule or surface carries no net electrical charge. ... Animation of the dispersion of light as it travels through a triangular prism. ... Enzyme assays are laboratory methods for measuring enzymatic activity. ... Electrofocusing, or isoelectric focusing, is a technique for separating different molecules by their electric charge differences (if they have any charge). ...


For natural proteins, a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a "His-tag"), is attached to one terminus of the protein. As a result, when the lysate is passed over a chromatography column containing nickel, the histidine residues ligate the nickel and attach to the column while the untagged components of the lysate pass unimpeded. Elements of genetic engineering Genetic engineering, recombinant DNA technology, genetic modification/manipulation (GM) and gene splicing are terms that are applied to the direct manipulation of an organisms genes. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... A His-tag is an amino acid motif in proteins that consists of six histidine (His) residues, often at the N- or C-terminus of the protein. ... For other uses, see Nickel (disambiguation). ...


Cellular localization

Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white).

The study of proteins in vivo is often concerned with the synthesis and localization of the protein within the cell. Although many intracellular proteins are synthesized in the cytoplasm and membrane-bound or secreted proteins in the endoplasmic reticulum, the specifics of how proteins are targeted to specific organelles or cellular structures is often unclear. A useful technique for assessing cellular localization uses genetic engineering to express in a cell a fusion protein or chimera consisting of the natural protein of interest linked to a "reporter" such as green fluorescent protein (GFP). The fused protein's position within the cell can be cleanly and efficiently visualized using microscopy, as shown in the figure opposite. In these cases, additional fluorescent chimeric proteins are generally required to prove the inferred localization. Image File history File linksMetadata Download high-resolution version (469x618, 71 KB) Summary Licensing File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Protein Gfp-cdna Metadata This file contains additional information, probably added from the digital camera or... Image File history File linksMetadata Download high-resolution version (469x618, 71 KB) Summary Licensing File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Protein Gfp-cdna Metadata This file contains additional information, probably added from the digital camera or... Cellular compartments in cell biology comprise all closed parts within a cell whose lumen is usually surrounded by a single or double lipid layer membrane. ... It has been suggested that mGFP be merged into this article or section. ... Schematic showing the cytoplasm, with major components of a typical animal cell. ... The endoplasmic reticulum or ER is an organelle found in all eukaryotic cells that is an interconnected network of tubules, vesicles and cisternae that is responsible for several specialized functions: Protein translation, folding, and transport of proteins to be used in the cell membrane (e. ... Protein targeting a. ... A fusion protein is a protein created through genetic engineering from two or more proteins/peptides. ... A Chimera (or chimeric protein) is a human-engineered or in vivo mutated protein that is encoded by a nucleotide sequence made by a splicing together of two or more complete or partial genes or cDNA. The pieces used may be from different species. ... In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to another gene of interest in cell culture, animals or plants. ... It has been suggested that mGFP be merged into this article or section. ... Microscopy is any technique for producing visible images of structures or details too small to otherwise be seen by the human eye, using a microscope or other magnification tool. ...


Other methods for elucidating the cellular location of proteins requires the use of known compartmental markers for regions such as the ER, the Golgi, lysosomes/vacuoles, mitochondria, chloroplasts, plasma membrane, etc. With the use of fluorescently-tagged versions of these markers or of antibodies to known markers, it becomes much simpler to identify the localization of a protein of interest. For example, indirect immunofluorescence will allow for fluorescence colocalization and demonstration of location. Fluorescent dyes are used to label cellular compartments for a similar purpose.


Other possibilities exist, as well. For example, immunohistochemistry usually utilizes an antibody to one or more proteins of interest that are conjugated to enzymes yielding either luminescent or chromogenic signals that can be compared between samples, allowing for localization information. Immunohistochemistry or IHC refers to the process of localizing proteins in cells of a tissue section exploiting the principle of antibodies binding specifically to antigens in biological tissues. ...


Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation. While this technique does not prove colocalization of a compartment of known density and the protein of interest, it does increase the likelihood, and is more amenable to large-scale studies. Isopycnic centrifugation or equilibrium centrifugation is a process used to isolate nucleic acids such as DNA. To begin the analysis a mixture of cesium chloride and DNA is placed in a centrifuge for several hours at high speed to generate a force of about 10^5 x g (earths...


Finally, the gold-standard method of cellular localization is immunoelectron microscopy. This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques. The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest.


Through another genetic engineering application known as site-directed mutagenesis, researchers can alter the protein sequence and hence its structure, cellular localization, and susceptibility to regulation, which can be followed in vivo by GFP tagging or in vitro by enzyme kinetics and binding studies. Site-directed mutagenesis is a molecular biology technique in which a mutation is created at a defined site in a DNA molecule, usually a circular molecule known as a plasmid. ... Dihydrofolate reductase from with its two substrates, dihydrofolate (right) and NADPH (left), bound in the active site. ...


Proteomics and bioinformatics

Main articles: Proteomics and Bioinformatics

The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis, which allows the separation of a large number of proteins, mass spectrometry, which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow the detection of the relative levels of a large number of proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein-protein interactions. The total complement of biologically possible such interactions is known as the interactome. A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics. For the journal Proteomics, see Proteomics (journal). ... Map of the human X chromosome (from the NCBI website). ... The term proteome was coined by Mark Wilkins in 1995 (1) and is used to describe the entire complement of proteins in a given biological organism or system at a given time, i. ... For the journal Proteomics, see Proteomics (journal). ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... Two-dimensional gel electrophoresis, commonly abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. ... Mass spectrometry (previously called mass spectroscopy (deprecated) or informally, mass-spec and MS) is an analytical technique that measures the mass-to-charge ratio of ions. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Overview of two-hybrid assay as follows. ... Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. ... Interactome is the whole set of molecular interactions in cells. ... Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins. ...


The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment. Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction. From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express. The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics. A graphical representation of the normal human karyotype. ... In biology, homology is any similarity between structures that is due to their shared ancestry. ... In bioinformatics, a sequence alignment is a way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. ... Sequence profiling Tools in bioinformatics refer to all those software tools (web-based/downloadable) that provide a brief overview on all related information about an input sequence. ... A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the sugar-phosphate backbones (i. ... An open reading frame or ORF is any sequence of DNA or RNA that can be translated into a protein. ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... A representation of the 3D structure of the myoglobin protein. ... Fig. ... This article is about evolution in biology. ... Clustal is a widely used multiple sequence alignment computer program. ... Map of the human X chromosome (from the NCBI website). ... Computer science, or computing science, is the study of the theoretical foundations of information and computation and their implementation and application in computer systems. ... Gene finding is the area of computational biology that is concerned with algorithmically identifying stretches of sequence, usually genomic DNA, that are biologically functional. ... It has been suggested that Clade be merged into this article or section. ...


Structure prediction and simulation

Complementary to the field of structural genomics, protein structure prediction seeks to develop efficient ways to provide plausible models for proteins whose structures have not yet been determined experimentally. The most successful type of structure prediction, known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain. Although producing accurate models remains a challenge when only distantly related template structures are available, it has been suggested that sequence alignment is the bottleneck in this process, as quite accurate models can be produced if a "perfect" sequence alignment is known.[19] Many structure prediction methods have served to inform the emerging field of protein engineering, in which novel protein folds have already been designed.[20] A more complex computational problem is the prediction of intermolecular interactions, such as in molecular docking and protein-protein interaction prediction. Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ... Homology modeling, also known as comparative modeling, is a class of techniques in protein structure prediction that seek to construct a model of a proteins tertiary structure based on its amino acid sequence. ... Protein engineering is the application of science, mathematics, and economics to the process of developing useful or valuable proteins. ... In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. ... This article is being considered for deletion in accordance with Wikipedias deletion policy. ...


The processes of protein folding and binding can be simulated using techniques derived from molecular dynamics, which increasingly take advantage of distributed computing as in the [email protected] project. The folding of small alpha-helical protein domains such as the villin headpiece[21] and the HIV accessory protein[22] have been successfully simulated in silico, and hybrid methods that combine standard molecular dynamics with quantum mechanics calculations have allowed exploration of the electronic states of rhodopsins.[23] Molecular dynamics (MD) is a form of computer simulation wherein atoms and molecules are allowed to interact for a period of time under known laws of physics, giving a view of the motion of the atoms. ... Distributed computing is a method of computer processing in which different parts of a program are run simultaneously on two or more computers that are communicating with each other over a network. ... [email protected] (also known as FAH or [email protected]) is a distributed computing project designed to perform computationally intensive simulations of protein folding and other molecular dynamics. ... Villin is an actin-binding protein that contains gelsolin domains capped by a headpiece consisting of a fast- and independently-folding three-helix bundle that is stabilized by hydrophobic interactions. ... Species Human immunodeficiency virus 1 Human immunodeficiency virus 2 Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS, a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections). ... For a generally accessible and less technical introduction to the topic, see Introduction to quantum mechanics. ... A rhodopsin molecule (yellow) with bound retinal (orange), embedded in a cell membrane (lipids shown as green, head groups as red/blue). ...


Nutrition

Further information: Protein in nutrition

Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals, (including humans) must obtain some of the amino acids from the diet.[14] Key enzymes in the biosynthetic pathways that synthesize certain amino acids - such as aspartokinase, which catalyzes the first step in the synthesis of lysine, methionine, and threonine from aspartate - are not present in animals. The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids. If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways. Proteins are broken down in the stomach during digestion by enzymes known as proteases into smaller polypeptides to provide amino acids for the organism, including the essential amino acids that the organism cannot biosynthesize itself. ... A cluster of Escherichia coli bacteria magnified 10,000 times. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... In nutrition, the diet is the sum of food consumed by a person or other organism. ... Aspartokinase is an enzyme that catalyzes the phosphorylation of the amino acid aspartate. ... Lysine is one of the 20 amino acids normally found in proteins. ... Methionine is an α-amino acid with the chemical formula HO2CCH(NH2)CH2CH2SCH3. ... Threonine is one of the 20 natural amino acids. ... Aspartic acid, also known as aspartate, the name of its anion, is one of the 20 natural proteinogenic amino acids which are the building blocks of proteins. ... First, what is an amino acid? Amino Acids are chemical substances that make up protein. ...


In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are broken down through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases. Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle. This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle.[24] Amino acids are also an important dietary source of nitrogen. For the industrial process, see anaerobic digestion. ... Irreversible egg protein denaturation and loss of solubility, caused by the high temperature (while cooking it) Denaturation is the alteration of a protein or nucleic acids shape through some form of external stress (for example, by applying heat, acid or alkali), in such a way that it will no... For other uses, see acid (disambiguation). ... Hydrolysis is a chemical reaction or process in which a chemical compound is broken down by reaction with water. ... Proteases (proteinases, peptidases, or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. ... Glucose (Glc), a monosaccharide (or simple sugar), is an important carbohydrate in biology. ... Pyruvic acid Oxaloacetic acid Phosphoenolpyruvate Fructose 1,6-bisphosphate Fructose 6-phosphate Glucose-6-phosphate Glucose Gluconeogenesis is the generation of glucose from non-sugar carbon substrates like pyruvate, lactate, glycerol, and amino acids (primarily alanine and glutamine). ... Overview of the citric acid cycle The citric acid cycle (also known as the tricarboxylic acid cycle, the TCA cycle, or the Krebs cycle, after Hans Adolf Krebs who identified the cycle) is a series of chemical reactions of central importance in all living cells that use oxygen as part... This article is about extreme malnutrition. ... For other uses of Muscle, see Muscle (disambiguation). ... General Name, symbol, number nitrogen, N, 7 Chemical series nonmetals Group, period, block 15, 2, p Appearance colorless gas Standard atomic weight 14. ...


History

Further information: History of molecular biology

Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid. Noted examples at the time included albumin from egg whites, blood, serum albumin, fibrin, and wheat gluten. Dutch chemist Gerhardus Johannes Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula. The term "protein" to describe these molecules was proposed in 1838 by Mulder's associate Jöns Jakob Berzelius. Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da. The history of molecular biology begins in the 1930s with the convergence of various, previously distinct biological disciplines: biochemistry, genetics, microbiology, and virology. ... Antoine François, comte de Fourcroy (June 15, 1755 – December 16, 1809), French chemist, the son of an apothecary in the household of the duke of Orleans, was born at Paris. ... This page is a candidate to be moved to Wiktionary. ... This article needs additional references or sources for verification. ... Albumen redirects here. ... For other uses, see Blood (disambiguation). ... You may be looking for albumen, or egg white. ... Fibrin is a protein involved in the clotting of blood. ... Wheat - a prime source of gluten Gluten is an amorphous mixture of ergastic (i. ... Gerhardus Johannes Mulder (1802 - 1880) was a organic chemist who described the chemical composition of proteins and after correspondence with Jöns Jacob Berzelius named them in his paper On the composition of some animal substances. In the same publication he also proposed that animals draw most of their protein... Elemental analysis is a process where a sample of some material (eg. ... In chemistry, the empirical formula of a chemical compound is a simple expression of the relative number of each type of atom in it. ... Friherre Jöns Jakob Berzelius (August 20, 1779 – August 7, 1848) was a Swedish chemist. ... This article is about the class of chemicals. ... Leucine is one of the 20 most common amino acids and coded for by DNA. It is isomeric with isoleucine. ... The unified atomic mass unit (u), or dalton (Da), is a small unit of mass used to express atomic and molecular masses. ...


The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, e.g., those of blood, egg white, various toxins, and digestive/metabolic enzymes obtained from slaughterhouses. In the late 1950s, the Armour Hot Dog Co. purified 1 kg (= one million milligrams) of pure bovine pancreatic ribonuclease A and made it freely available to scientists around the world. For other uses, see Blood (disambiguation). ... Albumen redirects here. ... For other uses, see Toxin (disambiguation). ... For the Batman villain, see Abattoir (comics). ... Armour and Company was an American slaughterhouse and meatpacking company founded in Chicago, Illinois in 1867 by the Armour brothers led by Philip Danforth Armour (1832–1901). ... Structure of RNase A Ribonuclease A (RNase A) is an endonuclease that cleaves single-stranded RNA. Bovine pancreatic RNase A is one of the classic model systems of protein science. ...


Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding, an idea first put forth by William Astbury in 1933. Later work by Walter Kauzmann on denaturation, based partly on previous studies by Kaj Linderstrøm-Lang, contributed an understanding of protein folding and structure mediated by hydrophobic interactions. In 1949 Fred Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids, or cyclols. The first atomic-resolution structures of proteins were solved by X-ray crystallography in the 1960s and by NMR in the 1980s. As of 2006, the Protein Data Bank has nearly 40,000 atomic-resolution structures of proteins. In more recent times, cryo-electron microscopy of large macromolecular assemblies and computational protein structure prediction of small protein domains are two methods approaching atomic resolution. Linus Carl Pauling (February 28, 1901 – August 19, 1994) was an American scientist, peace activist, author and educator of German ancestry. ... A representation of the 3D structure of the myoglobin protein. ... In chemistry, a hydrogen bond is a type of attractive intermolecular force that exists between two partial electric charges of opposite polarity. ... William Astbury (1898-1961) was an English biochemist who made X-ray diffraction studies of nucleic acid in 1937. ... Irreversible egg protein denaturation and loss of solubility, caused by the high temperature (while cooking it) Denaturation is the alteration of a protein or nucleic acids shape through some form of external stress (for example, by applying heat, acid or alkali), in such a way that it will no... Protein before and after folding. ... The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. ... This article or section should be merged with Frederick Sanger Fred Sanger (born 1918), is an English biochemist, the winner of two Nobel prizes in Chemistry. ... Not to be confused with inulin. ... A Colloid or colloidal dispersion is a type of homogeneous mixture. ... Figure 1: In the classic cyclol reaction, two peptide groups are linked by a N-C’ bond, converting the carbonyl oxygen into a hydroxyl group. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format). ... Cryo-electron microscopy (sometimes called cryoEM or electron cryomicroscopy) is a form of electron microscopy (EM) where the sample is studied at cryogenic temperatures (generally liquid nitrogen temperatures). ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ... Within a protein, a structural domain (domain) is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. ...


See also

This article is about the class of chemicals. ... An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet. ... Protein design is the design of new protein molecules from scratch. ... The isoelectric point (pI) is the pH at which a molecule or surface carries no net electrical charge. ... An intein is a segment of a protein that is able to excise itself and rejoin the remaining portions (the exteins) with a peptide bond. ... Since human recombinants have replaced the animal version in human therapeutics, the prefix of rh for human recombinant appears less and less in the literature // Human growth hormone (rhGH) Humatrope® from Lilly; and Serostim® from Serono replaced cadaver harvested human growth hormone Human insulin (rhI) Humulin® from Lilly replaced bovine... A list of proteins (and protein complexes). ... For the bird, see Prion (bird). ... Edible protein per unit area of land is a measure of agricultural productivity. ... There are very few or no other articles that link to this one. ... Proteopathy (Proteo- [pref. ... Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, QM - Quantum mechanics. ...

References

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  2. ^ Sumner, JB (1926). "The Isolation and Crystallization of the Enzyme Urease. Preliminary Paper". J Biol Chem 69: 435-41. 
  3. ^ Muirhead H, Perutz M (1963). "Structure of hemoglobin. A three-dimensional fourier synthesis of reduced human hemoglobin at 5.5 A resolution". Nature 199 (4894): 633-8. PMID 14074546. 
  4. ^ Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H, Phillips D (1958). "A three-dimensional model of the myoglobin molecule obtained by x-ray analysis". Nature 181 (4610): 662-6. doi:10.1038/181662a0. PMID 13517261. 
  5. ^ Nelson, D. L. and Cox, M. M. (2005) Lehninger's Principles of Biochemistry, 4th Edition, W. H. Freeman and Company, New York.
  6. ^ a b c Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J. (2004). Molecular Cell Biology 5th ed. WH Freeman and Company: New York, NY.
  7. ^ Dobson CM. (2000). The nature and significance of protein folding. In Mechanisms of Protein Folding 2nd ed. Ed. RH Pain. Frontiers in Molecular Biology series. Oxford University Press: New York, NY.
  8. ^ Fulton A, Isaacs W (1991). "Titin, a huge, elastic sarcomeric protein with a probable role in morphogenesis". Bioessays 13 (4): 157-61. doi:10.1002/bies.950130403. PMID 1859393. 
  9. ^ Bruckdorfer T, Marder O, Albericio F (2004). "From production of peptides in milligram amounts for research to multi-tons quantities for drugs of the future". Curr Pharm Biotechnol 5 (1): 29-43. doi:10.2174/1389201043489620. PMID 14965208. 
  10. ^ Schwarzer D, Cole P (2005). "Protein semisynthesis and expressed protein ligation: chasing a protein's tail". Curr Opin Chem Biol 9 (6): 561-9. doi:10.1016/j.cbpa.2005.09.018. PMID 16226484. 
  11. ^ a b Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY
  12. ^ Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T. (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438(7068):633-8.
  13. ^ Walian P, Cross TA, Jap BK. (2004). Structural genomics of membrane proteins Genome Biol 5(4): 215.
  14. ^ a b Voet D, Voet JG. (2004). Biochemistry Vol 1 3rd ed. Wiley: Hoboken, NJ.
  15. ^ Bairoch A. (2000). "The ENZYME database in 2000". Nucleic Acids Res 28: 304-305. doi:10.1093/nar/28.1.304. PMID 10592255. 
  16. ^ Radzicka A, Wolfenden R. (1995). "A proficient enzyme.". Science 6 (267): 90-3. PMID 7809611. 
  17. ^ The Catalytic Site Atlas at The European Bioinformatics Institute
  18. ^ Calculating protein charge (isoelectric point)
  19. ^ Zhang Y, Skolnick J. (2005). The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102(4):1029-34.
  20. ^ Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. (2003). Design of a novel globular protein fold with atomic-level accuracy. Science 302(5649):1364-8.
  21. ^ Zagrovic B, Snow CD, Shirts MR, Pande VS. (2002). Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol 323(5):927-37.
  22. ^ Herges T, Wenzel W. (2005). In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. Phys Rev Let 94(1):018101.
  23. ^ Hoffmann M, Wanko M, Strodel P, Konig PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M. (2006). Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 128(33):10808-18.
  24. ^ Brosnan J (2003). "Interorgan amino acid transport and its regulation". J Nutr 133 (6 Suppl 1): 2068S-72S. PMID 12771367. 

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ...

External links

  • Proteins (the journal), also called "Proteins: Structure, Function, and Bioinformatics" and previously "Proteins: Structure, Function, and Genetics" (1986-1995).

Databases and projects

Tutorials and educational websites

Structure of the coenzyme adenosine triphosphate, a central intermediate in energy metabolism. ... Protein metabolism denotes the various biochemical processes responsible for the synthesis of proteins and amino acids, and the breakdown of proteins (catabolism). ... Protein biosynthesis (synthesis) is the process in which cells build proteins. ... For the non-biological synthesis of amino acids see: Strecker amino acid synthesis Amino acid synthesis is the set of biochemical processes (metabolic pathways) by which the various amino acids are produced from other compounds. ... Protein catabolism is the breakdown of proteins into amino acids and simple derivative compounds, for transport into the cell through the plasma membrane and ultimately for the polymerisation into new proteins via the use of ribonucleic acids (RNA) and ribosomes. ... Many organisms have metabolic pathways to synthesise and break down purines. ... A salvage pathway is a pathway in which nucleotides (purine and pyrimidine) are synthesized from intermediates in the degradative pathway for nucleotides. ... Pyrimidine biosynthesis occurs both in the body and through organic synthesis. ...


  Results from FactBites:
 
The Protein Society: www.proteinsociety.org (445 words)
The Protein Society welcomes individuals devoted to furthering research and development in protein science to apply for a regular or corporate membership.
Members have an opportunity to actively participate in the emerging fields of protein science including proteomics, bioinformatics, structural biology, and computational biology as they pertain to proteins at the molecular and cellular level.
Protein Science is dedicated to research on all scientific aspects of protein molecules.
Protein Information Sheet (1177 words)
Proteins are broken down into their constituent amino acids during digestion which are then absorbed and used to make new proteins in the body.
Dietary proteins with all the essential amino acids in the proportions required by the body are said to be a high quality protein.
Protein quality is usually defined according to the amino acid pattern of egg protein, which is regarded as the ideal.
  More results at FactBites »

 
 

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