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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. Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as Chemistry (from Egyptian kēme (chem meaning "earth") is the Science concerned with the composition structure and properties Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl The term macromolecule by definition implies "large Molecule " [1]

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. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Efforts to predict tertiary structure from the primary sequence are known generally as protein structure prediction. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. 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. The Protein Data Bank ( PDB) is a repository for 3-D structural data of Proteins and Nucleic acids These data typically obtained by X-ray crystallography ) A large-scale experiment known as CASP directly compares the performance of state-of-the-art prediction methods and is run once every two and a half years. CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide experiment (though it is commonly referred to as a competition

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. Globular proteins, or spheroproteins are one of the two main Protein classes comprising "globe" -like proteins that are more or less soluble in In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of In secreted proteins that do not spend time in the cytoplasm, disulfide bonds between cysteine residues help to maintain the protein's tertiary structure. Secretion is the process of segregating elaborating and releasing chemicals from a cell, or a secreted Chemical substance or amount of substance The cytoplasm is the contents of a cell that is enclosed within the Plasma membrane. In Chemistry, a disulfide bond is a single Covalent bond derived from the coupling of Thiol groups Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with 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. The TIM barrel is a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone Triose-phosphate isomerase (TPI or TIM is an Enzyme ( that catalyzes the reversible interconversion of the Triose phosphate Isomers Another common structure is a highly stable dimeric coiled coil structure composed of 2-7 alpha helices. For the coiled coil shape in general see Coil. A coiled coil is a Structural motif in Proteins in which 2-7 A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which Proteins are classified by the folds they represent in databases like SCOP and CATH. The Structural Classification of Proteins (SCOP database is a largely manual classification of protein Structural domains based on similarities of their Amino acid The CATH Protein Structure Classification is a semi-automatic hierarchical classification of protein domains published in 1997 by Christine Orengo Janet Thornton and their colleagues

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. The cell is the structural and functional unit of all known living Organisms It is the smallest unit of an organism that is classified as living and is often called In Biochemistry, the native state of a Protein is its operative or functional form In Chemistry, conformational isomerism is a form of Stereoisomerism in which Molecules with the same Structural formula (same connectivity 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. In Physics, thermodynamics (from the Greek θερμη therme meaning " Heat " and δυναμις dynamis meaning " Chemical kinetics, also known as reaction kinetics is the study of rates of chemical processes Translation is the first stage 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. This article is about the protein For other uses see Chaperone, a disambiguation page 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. Protein disulfide isomerase or PDI ( is an Enzyme in the Endoplasmic reticulum in eukaryotes or Periplasmic space of prokaryotes that catalyzes GroEL belongs to the Chaperonin family of Molecular chaperones, and is found in a large number of bacteria Heat shock 10kDa protein 1 (chaperonin 10, also known as HSPE1 or GroES, is a Chaperonin which usually works in conjunction with GroEL. Heat shock proteins ( HSP) are a group of Proteins whose expression is increased when the cells are exposed to elevated temperatures or other stress

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. Hemagglutinin (HA or haemagglutinin ( British English) is an Antigenic Glycoprotein found on the surface of the Influenza Viruses The "mature" activated protein is proteolytically cleaved to form two polypeptide chains that are trapped in a high-energy conformation. Proteolysis is the directed degradation ( digestion) of Proteins by cellular Enzymes called Proteases or by intramolecular digestion Upon encountering a drop in pH, the protein undergoes an energetically favorable conformational rearrangement that enables it to penetrate a host cell membrane. pH is the measure of the acidity or alkalinity of a Solution.

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. Crystallography is the experimental science of determining the arrangement of Atoms in Solids In older usage it is the scientific study of Crystals The 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. Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used 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. Also see Transmembrane protein. A membrane protein is a Protein molecule that is attached to or associated with the membrane

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. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. 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. Globular proteins, or spheroproteins are one of the two main Protein classes comprising "globe" -like proteins that are more or less soluble in The cyclol hypothesis is the first structural model of a folded, globular Protein. Dorothy Maud Wrinch ( September 12, 1894 - February 11, 1976; married names Nicholson Glaser was a Mathematician and biochemical Modern methods are sometimes able to predict the tertiary structure de novo to within 5 Å for small proteins (<120 residues) and under favorable conditions, e. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal g. , confident secondary structure predictions. In Biochemistry and Structural biology, secondary structure is the general three-dimensional form of local segments of Biopolymers such as

See also

References

  1. ^ International Union of Pure and Applied Chemistry. The International Union of Pure and Applied Chemistry ( IUPAC) (aɪjuːpæk or ay-yoo-pec) is an international Non-governmental organization "tertiary structure". Compendium of Chemical Terminology Internet edition. 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

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