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Encyclopedia > Protein 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. All proteins are polymers of amino acids. The polymers, also known as polypeptides consist of a sequence of 20 different L-α-amino acids, also referred to as residues. For chains under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van der Waals' forces and hydrophobic packing. In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... A macromolecule is a molecule composed of a very large number of atoms. ... The periodic table of the chemical elements A chemical element, or element, is a type of atom that is defined by its atomic number; that is, by the number of protons in its nucleus. ... For other uses, see Carbon (disambiguation). ... General Name, Symbol, Number hydrogen, H, 1 Chemical series nonmetals Group, Period, Block 1, 1, s Appearance colorless Atomic mass 1. ... General Name, symbol, number nitrogen, N, 7 Chemical series nonmetals Group, period, block 15, 2, p Appearance colorless gas Standard atomic weight 14. ... General Name, symbol, number oxygen, O, 8 Chemical series nonmetals, chalcogens Group, period, block 16, 2, p Appearance colorless (gas) pale blue (liquid) Standard atomic weight 15. ... This article is about the chemical element. ... A polymer is a long, repeating chain of atoms, formed through the linkage of many molecules called monomers. ... This article is about the class of chemicals. ... 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. ... 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. ... In chemistry, a hydrogen bond is a type of attractive intermolecular force that exists between two partial electric charges of opposite polarity. ... Electron configurations of lithium and fluorine. ... In chemistry, the term van der Waals forces (sometimes called London dispersion forces) refers to a particular class of intermolecular forces. ... 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. ... Structural biology is a branch of molecular biology concerned with the study of the architecture and shape of biological macromolecules--proteins and nucleic acids in particular—and what causes them to have the structures they have. ... 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. ...


A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a collagen filament. Biochemistry is the study of the chemical processes in living organisms. ... --RAG 01:54, 16 March 2007 (UTC) The concept of the domain was first proposed in 1973 by Wetlaufer after X-ray crystallographic studies of hen lysozyme (Phillips, 1966), papain (Drenth et al. ... 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. ... G-Actin (PDB code: 1j6z). ...

Contents

Levels of protein structure

Protein structure, from primary to quaternary structure.

Biochemistry refers to four distinct aspects of a protein's structure: Image File history File links Description: This image shows the structure hierarchy of Proteins Source: [1] (file) License: All of the illustrations in the Talking Glossary of Genetics are freely available and may be used without special permission. ... Image File history File links Description: This image shows the structure hierarchy of Proteins Source: [1] (file) License: All of the illustrations in the Talking Glossary of Genetics are freely available and may be used without special permission. ...

  • Primary structure - the amino acid sequence of the peptide chains.
  • Secondary structure - highly regular sub-structures (alpha helix and strands of beta sheet) which are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule.
  • Tertiary structure - Three-dimensional structure of a single protein molecule; a spatial arrangement of the secondary structures.
  • Quaternary structure - complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.

In addition to these levels of structure, a protein may shift between several similar structures in performing its biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as chemical conformation, and transitions between them are called conformational changes. In chemistry, a chemical conformation is the spatial arrangement of atoms in a molecule. ...


The primary structure is held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or translation. The two ends of the amino acid chain are referred to as the C-terminal end or carboxyl terminus (C-terminus) and the N-terminal end or amino terminus (N-terminus) based on the nature of the free group on each extremity. Covalent redirects here. ... 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). ... An overview of protein synthesis. ...


The various types of secondary structure are defined by their patterns of hydrogen bonds between the main-chain peptide groups. However, these hydrogen bonds are generally not stable by themselves, since the water-amide hydrogen bond is generally more favorable than the amide-amide hydrogen bond. Thus, secondary structure is stable only when the local concentration of water is sufficiently low, e.g., in the molten globule or fully folded states. In protein structure, the DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. ... Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ...


Similarly, the formation of molten globules and tertiary structure is driven mainly by structurally non-specific interactions, such as the rough propensities of the amino acids and hydrophobic interactions. However, the tertiary structure is fixed only when the parts of a protein domain are locked into place by structurally specific interactions, such as ionic interactions (salt bridges), hydrogen bonds and the tight packing of side chains. The tertiary structure of extracellular proteins can also be stabilized by disulfide bonds, which reduce the entropy of the unfolded state; disulfide bonds are extremely rare in cytosolic proteins, since the cytosol is generally a reducing environment. In chemistry, a disulfide bond is a single covalent bond derived from the coupling of thiol groups. ...


Structure of the amino acids

An α-amino acid

An α-amino acid consists of a part that is present in all the amino acid types, and a side chain that is unique to each type of residue. The Cα atom is bound to 4 different molecules (the H is omitted in the diagram); an amino group, a carboxyl group, a hydrogen and a side chain, specific for this type of amino acid. An exception from this rule is proline, where the hydrogen atom is replaced by a bond to the side chain. Because the carbon atom is bound to four different groups it is chiral, however only one of the isomers occur in biological proteins. Glycine however, is not chiral since its side chain is a hydrogen atom. A simple mnemonic for correct L-form is "CORN": when the Cα atom is viewed with the H in front, the residues read "CO-R-N" in a clockwise direction. Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Proline is an α-amino acid with the chemical formula HO2CCH(NH[CH2)3]. L-Proline is one of the twenty DNA-encoded amino acids. ... The term chiral (pronounced ) is used to describe an object which is non-superimposable on its mirror image. ... In chemistry, isomers are molecules with the same chemical formula and often with the same kinds of chemical bonds between atoms, but in which the atoms are arranged differently (analogous to a chemical anagram). ... For other uses, see Mnemonic (disambiguation). ...

CO-R-N rule

The side chain determines the chemical properties of the α-amino acid and may be any one of the 20 different side chains: Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ...

Name  (Residue) 3-letter
code
Single
code
Relative
abundance
(%) E.C.
MW pK VdW volume
(ų)
Charged,
Polar,
Hydrophobic,
Neutral
Alanine ALA A 13.0 71   67 H
Arginine ARG R 5.3 157 12.5 148 C+
Asparagine ASN N 9.9 114   96 P
Aspartate ASP D 9.9 114 3.9 91 C-
Cysteine CYS C 1.8 103   86 P
Glutamate GLU E 10.8 128 4.3 109 C-
Glutamine GLN Q 10.8 128   114 P
Glycine GLY G 7.8 57   48 N
Histidine HIS H 0.7 137 6.0 118 P,C+
Isoleucine ILE I 4.4 113   124 H
Leucine LEU L 7.8 113   124 H
Lysine LYS K 7.0 129 10.5 135 C+
Methionine MET M 3.8 131   124 H
Phenylalanine PHE F 3.3 147   135 H
Proline PRO P 4.6 97   90 H
Serine SER S 6.0 87   73 P
Threonine THR T 4.6 101   93 P
Tryptophan TRP W 1.0 186   163 P
Tyrosine TYR Y 2.2 163 10.1 141 P
Valine VAL V 6.0 99   105 H

The 20 naturally occurring amino acids can be divided into several groups based on their chemical proporties. Important factors are charge, hydrophobicity/hydrophilicity, size and functional groups. The nature of the interaction of the different side chains with the aqueous environment plays a major role in molding protein structure. Hydrophobic side chains tends to be buried in the middle of the protein, whereas hydrophilic side chains are exposed to the solvent. Examples of hydrophobic residues are: Leucine, isoleucine, phenylalanine, and valine, and to a lesser extent tyrosine, alanine and tryptophan. The charge of the side chains plays an important role in protein structures, since ion bonding can stabilize proteins structures, and an unpaired charge in the middle of a protein can disrupt structures. Charged residues are strongly hydrophilic, and are usually found on the out side of proteins. Positively charged side chains are found in lysine and arginine, and in some cases in histidine. Negative charges are found in glutamate and aspartate. The rest of the amino acids have smaller generally hydrophilic side chains with various functional groups. Serine and threonine have hydroxylgroups, and aspargine and glutamine have amide groups. Some amino acids have special properties such as cysteine, that can form covalent disulphide bonds to other cysteines, proline that is cyclical, and glycine that is small, and more flexible than the other amino acids. Alanine (Ala, A) also 2-aminopropanoic acid is a non-essential α-amino acid. ... Arginine (abbreviated as Arg or R)[1] is an α-amino acid. ... For other articles using the abbreviation or acronym asn see ASN. Asparagine is one of the 20 most common natural amino acids on Earth. ... 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. ... Cysteine is a naturally occurring, sulfur-containing amino acid that is found in most proteins, although only in small quantities. ... Glutamate is the anion of glutamic acid. ... Glutamine is one of the 20 amino acids encoded by the standard genetic code. ... For the plant, see Glycine (plant). ... Histidine is one of the 20 most common natural amino acids present in proteins. ... Isoleucine is an α-amino acid with the chemical formula HO2CCH(NH2)CH(CH3)CH2CH3. ... Leucine is one of the 20 most common amino acids and coded for by DNA. It is isomeric with isoleucine. ... 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. ... Phenyl alanine is an α-amino acid with the formula HO2CCH(NH2)CH2C6H5. ... Proline is an α-amino acid with the chemical formula HO2CCH(NH[CH2)3]. L-Proline is one of the twenty DNA-encoded amino acids. ... Serine (IPA ), organic compound, one of the 20 amino acids commonly found in animal proteins. ... Threonine is one of the 20 natural amino acids. ... Tryptophan is an essential amino acid involved in human nutrition. ... Tyrosine (from the Greek tyros, meaning cheese, as it was first discovered in 1846 by German chemist Justus von Liebig in the protein casein from cheese[1][2]), 4-hydroxyphenylalanine, or 2-amino-3(4-hydroxyphenyl)-propanoic acid, is one of the 20 amino acids that are used by cells... Valine is an amino acid that cannot be synthesized by humans, so it is considered an essential amino acid for human life. ... A disulfide bond (SS-bond), also called a disulfide bridge, is a strong covalent bond between two sulfhydryl groups. ...


The peptide bond

Two amino acids
Bond angles for ψ and ω

Two amino acids can be combined in a condensation reaction. By repeating this reaction, long chains of residues (amino acids in a peptide bond) can be generated. This reaction is catalysed by the ribosome in a process known as translation. The peptide bond is in fact planar due to the delocalization of the electrons from the double bond. The rigid peptide dihedral angle, ω (the bond between C1 and N) is always close to 180 degrees. The dihedral angles φ (the bond between N and Cα) and psi ψ (the bond between Cα and C1) can have a certain range of possible values. These angles are the degrees of freedom of a protein, they control the protein's three dimensional structure. They are restrained by geometry to allowed ranges typical for particular secondary structure elements, and represented in a Ramachandran plot. A few important bond lengths are given in the table below. Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source: [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... A condensation reaction is a chemical reaction in which two molecules or moieties combine to form one single molecule, together with the loss of a small molecule. ... In chemistry and biology, catalysis is the acceleration (increase in rate) of a chemical reaction by means of a substance, called a catalyst, that is itself not consumed by the overall reaction. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Protein biosynthesis (Synthesis) is the process in which cells build proteins. ... 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). ... For other uses, see Electron (disambiguation). ... In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ... A Ramachandran plot generated from the protein PCNA, a human DNA clamp protein that is composed of both beta sheets and alpha helices (PDB ID 1AXC). ... In molecular geometry, bond length or bond distance is the distance between two bonded atoms in a molecule. ...

Peptide bond Average length Single bond Average length Hydrogen bond Average (±30)
Ca - C 153 pm C - C 154 pm O-H --- O-H 280 pm
C - N 133 pm C - N 148 pm N-H --- O=C 290 pm
N - Ca 146 pm C - O 143 pm O-H --- O=C 280 pm

Picometre (American spelling: picometer) is an SI measure of length that is equal to 10−12 of a metre. ...

Primary structure

Main article: Primary structure

The sequence of the different amino acids is called the primary structure of the peptide or protein. Counting of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often however, it is read directly from the sequence of the gene using the genetic code. Post-transcriptional modifications such as disulfide formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene. A protein primary structure is a chain of amino acids. ... A protein primary structure is a chain of amino acids. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... 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 interaction of mRNA in a eukaryote cell. ... Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. ... Mass spectrometry (previously called mass spectroscopy (deprecated)[1] or informally, mass-spec and MS) is an analytical technique used to measure the mass-to-charge ratio of ions. ... For a non-technical introduction to the topic, see Introduction to Genetics. ...


Secondary structure

Main article: Secondary structure

By building models of peptides using known information about bond lengths and angles, the first elements of secondary structure, the alpha helix and the beta sheet, were suggested in 1951 by Linus Pauling and coworkers.[1] Both the alpha helix and the beta-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. These secondary structure elements only depend on properties that all the residues have in common, explaining why they occur frequently in most proteins. Since then other elements of secondary structure have been discovered such as various loops and other forms of helices. The part of the backbone that is not in a regular secondary structure is said to be random coil. Each of these two secondary structure elements have a regular geometry, meaning they are constrained to specific values of the dihedral angles ψ and φ. Thus they can be found in a specific region of the Ramachandran plot. A representation of the 3D structure of the Myoglobin protein. ... 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. ... Linus Carl Pauling (February 28, 1901 – August 19, 1994) was an American quantum chemist and biochemist. ... Illustration of a 3-dimensional polypeptide A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. ...

The left panel shows the hydrogen bonding in an actual α-helix backbone. Note that the nth residue O (Lys 153) bonds to the (n+4)th following residue's N (Arg 147). The actual values of some displayed H-bond distances give you some idea about the variations to expect within a helix. The center panel includes the side chains which were omitted in the left panel for clarity. You see the side chains pointing towards the N-terminal of the chain (lower residue numbers) and thus it is usually possible to determine the direction of the helix quite well during initial model building. A 0.2 nm electron density is shown in the right panel
Here are some more representation of the same helix.
Ball and stick model
Backbone
Secondary structure cartoon ("ribbon" or "linguini diagram")
The hydrogen bond network in a 2-stranded, antiparallel β-sheet. The side chains are sticking out above or below the plane of the picture. It less clear cut than in the case of the helix, in which direction to initially trace a beta sheet strand. The beta sheet can be infinitely extended due to the repeatable H-bonding pattern to either side of a strand.


Turns, loops and a few other secondary structure elements such as a 3-10 helix complete the picture. We have now enough pieces to assemble a complete protein, displaying its typical tertiary structure. Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links source [1] File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ...


Tertiary structure

Main article: tertiary structure

The elements of secondary structure are usually folded into a compact shape using a variety of loops and turns. The formation of tertiary structure is usually driven by the burial of hydrophobic residues, but other interactions such as hydrogen bonding, ionic interactions and disulfide bonds can also stabilize the tertiary structure. The tertiary structure encompasses all the noncovalent interactions that are not considered secondary structure, and is what defines the overall fold of the protein, and is usually indispensable for the function of the protein. In biochemistry, the tertiary structure of a protein is its overall shape. ...


Quarternary structure

Main article: quarternary structure

The quarternary structure is the interaction between several chains of peptide bonds. The individual chains are called subunits. The individual subunits are not necessarily covalently connected, but might be connected by a disulfide bond. Not all proteins have quarternary structure, since they might be functional as monomers. The quarternary structure is stabilized by the same range of interactions as the tertiary structure. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, and a tetramer if it contains four subunits. Multimers made up of identical subunits may be referred to with a prefix of "homo-" (e.g. a homotetramer) and those made up of different subunits may be referred to with a prefix of "hetero-" (e.g. a heterodimer). Tertiary structures vary greatly from one protein to another. They are held together by glycosydic and covalent bonds. In biochemistry, many proteins are actually assemblies of more than one protein molecule, which in the context of the larger assemblage are known as protein subunits. ...


Side chain conformation

The atoms along the side chain are named with Greek letters in Greek alphabetical order: α, β, γ, δ, є and so on. Cα refers to the carbon atom closest to the carbonyl group of that amino acid, Cβ the second closest and so on. The Cα is usually considered a part of the backbone. The dihedral angles around the bonds between these atoms are named χ1, χ2, χ3 etc. E.g. the first and second carbon atom in the side chain of lysine is named α and β, and the dihedral angle around the α-β bond is named χ1. Side chains can be in different conformations called gauche(-), trans and gauche(+). Side chains generally tend to try to come into a staggered conformation around χ2, driven by the minimization of the overlap between the electron orbitals of the hydrogen atoms. staggered conformation left, eclipsed conformation right in Newman projection Main article: Alkane stereochemistry A staggered conformation is a chemical conformation that exists in any open chain single chemical bond connecting two sp3 hybridised atoms as a conformational energy minimum. ... Electron atomic and molecular orbitals In atomic physics, an electron orbital (or simply orbital) is the description of the behavior of an electron in an atom or molecule according to quantum mechanics. ...


Domains, motifs, and folds in protein structure

Many proteins are organised into several units. A structural domain is an element of the proteins overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding domain of calmodulin". Because they are self-stabilizing, domains can be "swapped" by genetic engineering between one protein and another to make chimeras. A motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). These elements are often called supersecondary structures. Fold refers to a global type of arrangement, like helix-bundle or beta-barrel. Structure motifs usually consist of just a few elements, e.g. the 'helix-turn-helix' has just three. Note that while the spatial sequence of elements is the same in all instances of a motif, they may be encoded in any order within the underlying gene. Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene. Note also that even when two genes encode secondary structural elements of a motif in the same order, nevertheless they may specify somewhat different sequences of amino acids. This is true not only because of the complicated relationship between tertiary and primary structure, but because the size of the elements varies from one protein and the next. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are much fewer different domains, structural motifs and folds. This is partly a consequence of evolution, since genes or parts of genes can be doubled or moved around within the genome. This means that, for example, a protein domain might be moved from one protein to another thus giving the protein a new function. Because of these mechanisms pathways and mechanisms tends to be reused in several different proteins. 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. ... Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ... For other uses, see Gene (disambiguation). ... A gene family is a set of genes defined by presumed homology, i. ... oommen sir is a fool. ... Kenyans examining insect-resistant transgenic Bt corn. ... 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. ... The λ repressor of bacteriophage lambda employs a helix-turn-helix to bind DNA. In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many... In 1976 only 56 protein structures were available in the PDB cite(bernstein1977), yet tertiary structure had already been generally classified into four secondary structure classes cite(levitt1976) and three different folding units or supersecondary structures cite(lesk2001), speculated to be the building blocks of tertiary structure cite(levitt1976,chothia1977). ... A beta barrel is a protein fold containing a series of beta sheets, typically arranged in an antiparallel fashion. ... For other uses, see Gene (disambiguation). ... part of a DNA sequence A DNA sequence (sometimes genetic sequence) is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand (adenine, cytosine, guanine... This article is about the class of chemicals. ... 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. ... This article is about evolution in biology. ...


Protein folding

Main article: Protein folding

The process by which the higher structures form is called protein folding and is a consequence of the primary structure. A unique polypeptide may have more than one stable folded conformation, which could have a different biological activity, but usually, only one conformation is considered to be the active, or native conformation. Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ...


Structure classification

Several methods have been developed for the structural classification of proteins. These seek to classify the data in the Protein Data Bank in a structured order. Several databases exist which classify proteins using different methods. SCOP, CATH and FSSP are the largest ones. The methods used are purely manual, manual and automated, and purely automated. Work is being done to better integrate the current data. The classification is consistent between SCOP, CATH and FSSP for the majority of proteins which have been classified, but there are still some differences and inconsistencies. The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... SCOP can refer to Structural Classification of Proteins A scop was an Old English poet, the Anglo-Saxon counterpart of the Old Norse skald. ... CATH Protein Structure Classification is a way to classify proteins. ... Pope Benedict XVI (then Cardinal Joseph Ratzinger) at an ordination of FSSP priests in Wigratzbad, Germany in 1990. ...


Protein structure determination

Around 90% of the protein structures available in the Protein Data Bank have been determined by X-ray crystallography. This method allows one to measure the 3D density distribution of electrons in the protein (in the crystallized state) and thereby infer the 3D coordinates of all the atoms to be determined to a certain resolution. Roughly 9% of the known protein structures have been obtained by Nuclear Magnetic Resonance techniques, which can also be used to determine secondary structure. Note that aspects of the secondary structure as whole can be determined via other biochemical techniques such as circular dichroism. Secondary structure can also be predicted with a high degree of accuracy (see next section). Cryo-electron microscopy has recently become a means of determining protein structures to low resolution (less than 5 angstroms or 0.5 nanometer) and is anticipated to increase in power as a tool for high resolution work in the next decade. This technique is still a valuable resource for researchers working with very large protein complexes such as virus coat proteins and amyloid fibers. The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... 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. ... To infer is to draw a conclusion based on what one already knows and on that alone. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... Circular dichroism (CD) is a form of spectroscopy based on the differential absorption of left- and right-handed circularly polarized light. ... 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). ...

A rough guide to the resolution of protein structures
Resolution Meaning
>4.0 Individual coordinates meaningless
3.0 - 4.0 Fold possibly correct, but errors are very likely. Many sidechains placed with wrong rotamer.
2.5 - 3.0 Fold likely correct except that some surface loops might be mismodelled. Several long, thin sidechains (lys, glu, gln, etc) and small sidechains (ser, val, thr, etc) likely to have wrong rotamers.
2.0 - 2.5 As 2.5 - 3.0, but number of sidechains in wrong rotamer is considerably less. Many small errors can normally be detected. Fold normally correct and number of errors in surface loops is small. Water molecules and small ligands become visible.
1.5 - 2.0 Few residues have wrong rotamer. Many small errors can normally be detected. Folds are extremely rarely incorrect, even in surface loops.
0.5 - 1.5 In general, structures have almost no errors at this resolution. Rotamer libraries and geometry studies are made from these structures.

Computational prediction of protein structure

The generation of a protein sequence is much simpler than the generation of a protein structure. However, the structure of a protein gives much more insight in the function of the protein than its sequence. Therefore, a number of methods for the computational prediction of protein structure from its sequence have been proposed. Ab initio prediction methods use just the sequence of the protein. Threading uses existing protein structures. Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain. ... Threading is a method for the computational prediction of protein structure from protein sequence. ...


Rosetta@home is a distributed computing project which tries to predict the structures of proteins with massive sampling on thousands of home computers. Rosetta@home (website) is a distributed computing project, run by the Baker Laboratory at the University of Washington, aiming to solve the protein structure prediction problem. ... Distributed computing is a method of computer processing in which different parts of a program run simultaneously on two or more computers that are communicating with each other over a network. ...


Software

There are many available software packages, such as free web-based STING, used to visualize and analyze protein structures. Another example is the FeatureMap3D web-server which can visualize the quality of a protein-protein alignment in 3D and be used to map sequence feature annotation such as the underlying Intron/Exon structure onto a protein structure. This article is about the musician. ... Diagram of the location of introns and exons within a gene. ... An exon is any region of DNA within a gene, that is transcribed to the final messenger RNA (mRNA) molecule, rather than being spliced out from the transcribed RNA molecule. ...


Several packages, such as Quantum Pharmaceuticals software[2], can be used to predict conformational changes of proteins and its influence on protein's functions.


Several methods have been developed to compare structures of different proteins. Please see structural alignment. Structural alignment of thioredoxins from humans and the fly Drosophila melanogaster. ...


Computational tools are also frequently employed to check experimental and theoretical models of protein structures for errors (examples: ProSA, NQ-Flipper, Verify3D, ANOLEA, WHAT_CHECK).


References

  1. ^ PAULING L, COREY RB, BRANSON HR. Proc Natl Acad Sci U S A. 1951 Apr;37(4):205-11. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. PMID 14816373
  2. ^ Quantum Pharmaceuticals software

External links

  • Habeck M, Nilges M, Rieping W (2005). "Bayesian inference applied to macromolecular structure determination". Physical review. E, Statistical, nonlinear, and soft matter physics 72 (3 Pt 1): 031912. PMID 16241487.  (Bayesian computational methods for the structure determination from NMR data)
  • ProSA-web Web service for the recognition of errors in experimentally or theoretically determined protein structures
  • NQ-Flipper Check for unfavorable rotamers of Asn and Gln residues in protein structures

  Results from FactBites:
 
Protein structure - definition of Protein structure in Encyclopedia (1663 words)
Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures.
Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene.
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.
  More results at FactBites »

 
 

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