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Encyclopedia > Tertiary structure

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.[1] Biochemistry is the study of the chemical processes in living organisms. ... For other uses, see Chemistry (disambiguation). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Illustration of a polypeptide macromolecule Structure of a polyphenylene dendrimer macromolecule reported by Müllen and coworkers in Chem. ...

Contents

Relationship to primary sequence

Tertiary structure is considered to be largely determined by the protein's primary sequence, or the sequence of amino acids of which it is composed. Efforts to predict tertiary structure from the primary sequence are known generally as protein structure prediction. However, the environment in which a protein is synthesized and allowed to fold are significant determinants of its final shape and are usually not directly taken into account by current prediction methods. (Most such methods do rely on comparisons between the sequence to be predicted and sequences of known structure in the Protein Data Bank and thus account for environment indirectly, assuming the target and template sequences share similar cellular contexts.) A large-scale experiment known as CASP directly compares the performance of state-of-the-art prediction methods and is run once every two years. A protein primary structure is a chain of amino acids. ... This article is about the class of chemicals. ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ...


Determinants of tertiary structure

In globular proteins, tertiary interactions are frequently stabilized by the sequestration of hydrophobic amino acid residues in the protein core, from which water is excluded, and by the consequent enrichment of charged or hydrophilic residues on the protein's water-exposed surface. In secreted proteins that do not spend time in the cytoplasm, disulfide bonds between cysteine residues help to maintain the protein's tertiary structure. A variety of common and stable tertiary structures appear in a large number of proteins that are unrelated in both function and evolution - for example, many proteins are shaped like a TIM barrel, named for the enzyme triosephosphateisomerase. Another common structure is a highly stable dimeric coiled-coil structure composed of four alpha helices. Proteins are classified by the folds they represent in databases like SCOP and CATH. 3-dimensional structure of hemoglobin, a globular protein. ... 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. ... Secretion is the process of segregating, elaborating, and releasing chemicals from a cell, or a secreted chemical substance or amount of substance. ... Organelles. ... In chemistry, a disulfide bond is a single covalent bond derived from the coupling of thiol groups. ... Cysteine is a naturally occurring, sulfur-containing amino acid that is found in most proteins, although only in small quantities. ... Top view of a triosephosphateisomerase (TIM) barrel (PDB accession code 8TIM), colored from blue (N-terminus) to red (C-terminus). ... Triose-phosphate isomerase (TIM), is an enzyme (EC 5. ... Side view of an α-helix of alanine residues in atomic detail. ...


Not every polypeptide chain has a well-defined tertiary structure. Some proteins, especially short proteins, are natively disordered and exist as random coils under standard physiological conditions. Disordered regions can also occur in otherwise well-structured proteins, especially at the termini and in loop or linker regions connecting domains whose relative orientation can change depending on the environment. 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. ... It has been suggested that Structural domain be merged into this article or section. ...


Stability of native states

The most typical conformation of a protein in its cellular environment is generally referred to as the native state or native conformation. It is commonly assumed that this most-populated state is also the most thermodynamically stable conformation attainable for a given primary sequence; this is a reasonable first approximation but the claim assumes that the reaction is not under kinetic control - that is, that the time required for the protein to attain its native conformation after being translated is small. 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... In biochemistry, the native state of a protein is its operative or functional form. ... In chemistry, a chemical conformation is the spatial arrangement of atoms in a molecule. ... Thermodynamics (from the Greek θερμη, therme, meaning heat and δυναμις, dynamis, meaning power) is a branch of physics that studies the effects of changes in temperature, pressure, and volume on physical systems at the macroscopic scale by analyzing the collective motion of their particles using statistics. ... In physical chemistry, chemical kinetics or reaction kinetics is the study of reaction rates in a chemical reaction. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ...


In the cell, a variety of protein chaperones assist a newly synthesized polypeptide in attaining its native conformation. Some such proteins are highly specific in their function, such as protein disulfide isomerase; others are very general and can be of assistance to most globular proteins - the prokaryotic GroEL/GroES system and the homologous eukaryotic Heat shock proteins Hsp60/Hsp10 system fall into this category. In biology, chaperones are proteins whose function is to assist other proteins in achieving proper folding. ... Protein disulfide isomerase or PDI (EC 5. ... GroEL is a protein chaperone required for the proper folding of many proteins in prokaryotes. ... GroES is a chaperonin which usually works in conjunction with GroEL. In eurkaryotes, it is very similar to Heat Shock Protein 10 or Hsp10. ... Heat shock proteins (HSP) are a group of proteins whose expression is increased when the cells are exposed to elevated temperatures. ...


Some proteins explicitly take advantage of the fact that they can become kinetically trapped in a relatively high-energy conformation due to folding kinetics. Influenza hemagglutinin, for example, is synthesized as a single polypeptide chain that acts as a kinetic trap. The "mature" activated protein is proteolytically cleaved to form two polypeptide chains that are trapped in a high-energy conformation. Upon encountering a drop in pH, the protein undergoes an energetically favorable conformational rearrangement that enables it to penetrate a host cell membrane. Hemagglutinin, as depicted in a simplified molecular model. ... Proteolysis is the directed degradation (digestion) of proteins by cellular enzymes called proteases or by intramolecular digestion. ... For other uses, see PH (disambiguation). ...


Experimental determination

The majority of protein structures known to date have been solved with the experimental technique of X-ray crystallography, which typically provides data of high resolution but provides no time-dependent information on the protein's conformational flexibility. A second common way of solving protein structures uses NMR, which provides somewhat lower-resolution data in general and is limited to relatively small proteins, but can provide time-dependent information about the motion of a protein in solution. More is known about the tertiary structural features of soluble globular proteins than about membrane proteins because the latter class is extremely difficult to study using these methods. Crystallography (from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and graphein = write) is the experimental science of determining the arrangement of atoms in solids. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. ...


History

Since the tertiary structure of proteins is an important problem in biochemistry, and since structure determination is relatively difficult, protein structure prediction has been a long-standing problem. The first predicted structure of globular proteins was the cyclol model of Dorothy Wrinch, but this was quickly discounted as being inconsistent with experimental data. Modern methods are sometimes able to predict the tertiary structure de novo to within 5 Šfor small proteins (<120 residues) and under favorable conditions, e.g., confident secondary structure predictions. [citation needed] Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ... 3-dimensional structure of hemoglobin, a globular protein. ... 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. ... Dorothy Maud Wrinch (September 12, 1894 - February 11, 1976; married names Nicholson, Glaser) was a mathematician and biochemical theorist best known for her attempt to explain protein structure using mathematical principles. ... An angstrom, angström, or ångström (symbol Å) is a unit of length. ... A representation of the 3D structure of the myoglobin protein. ...


See also

Crystal structure of a foldamer reported by Lehn and coworkers in Helv. ... A protein primary structure is a chain of amino acids. ... A representation of the 3D structure of the myoglobin protein. ... 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. ... 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. ...

References

  1. ^ International Union of Pure and Applied Chemistry. "tertiary structure". Compendium of Chemical Terminology Internet edition.

IUPAC logo The International Union of Pure and Applied Chemistry (IUPAC) (Pronounced as eye-you-pack) is an international non-governmental organization established in 1919 devoted to the advancement of chemistry. ... Compendium of Chemical Terminology (ISBN 0-86542-684-8) is a book published by IUPAC containing internationally accepted definitions for terms in chemistry. ...

External links


  Results from FactBites:
 
Tertiary structure - Wikipedia, the free encyclopedia (164 words)
In biochemistry, the tertiary structure of a protein is its overall shape.
The tertiary structure that a protein assumes to carry out its physiological role inside a cell is known as the native state or sometimes the native conformation.
The study of protein tertiary structure is known as structural biology.
TERTIARY STRUCTURE (993 words)
Tertiary Structure is the folding of the total chain, the combination of the elements of secondary structure linked by turns and loops.
The tertiary structure of proteins is characterized by tightly folded structure with polar groups on the surface and non-polar groups buried.
There are a number of ways to represent the folding of a protein and the arrangement of secondary structure elements within the tertiary structure.
  More results at FactBites »

 
 

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