Quaternary structure prediction, protein

Visualizing Folded Protein Structures Primary Structure Determines Tertiary Structure Secondary Valence Forces Are the Glue That Holds Polypeptide Chains Together Domains Are Functional Units of Tertiary Structure Predicting Protein Tertiary Structure Quaternary Structure Involves the Interaction of Two or More Proteins... 

Over the last decade, using reduced protein models, considerable progress has been made towards understanding the nature of the protein folding process as well as in the development of techniques to predict low resolution tertiary and in some ca.ses quaternary structure from protein sequence. Becau.se they reduce the number of degrees of freedom, reduced or simplified protein models can address aspects of... 

Considering that rough recognition of interacting sites is provided by distribution of hydrophobic groups on the surface, a tentative approach for predicting quaternary structure of proteins was proposed by Wodak and Janin (1978) and Rashin and Yudman (1979). 

Primary structure is determined, as we ve seen, by sequencing the pTotein. Secondary, tertiary, and quaternary structures are determined by X-ray crystallography (Chapter 22 Focus On) because it s not yet possible to predict computationally how a given protein sequence will fold. 

In order to imderstand tertiary and quaternary structure, we need to explore briefly the secondary structural possibilities of protein molecules. The a-helix was predicted in 1951 by Linus Pauling. The peptide chain forms a compact core with the residues pointing outwards. The pitch is formed by 3.6 amino acid residues, with a helical period of 5.4 A. The structure is stabilised by a very-effective network of hydrogen bonds. 

The crystal structure of CJueF from B. suhtilis was solved to 2.25 A, the protein exhibited a quaternary structure consisting of a dimer of hexamers (a dodecamer) belonging to the tunnel-fold superfamily, where substrate binding is believed to be at the subunit interface. To confirm the role of the enzyme in vitro, the genes from B. suhtilis and E. coli were cloned and expressed. After determining that the predicted GTP cyclohydrolase activity was not exhibited by CJiieF from these two species, alternative roles were explored. 

One of the important elements of protein function is the ability of a protein to interact with and bind various ligands. This ability is closely related to the three-dimensional structure of the protein. Because the quality of theoretical strucmre prediction methods has recently improved considerably, we are developing a docking procedure that will utilize these relatively low-quality models of proteins for the prediction of plausible conformations of receptor-small ligand complexes as well as for the prediction of interactions between particular subunits of a protein in the quaternary structures. 

Support for the aromatic h> othesis comes from model studies and protein crystal structure analysis. In biomimetic model studies, Dougherty has shown that cation-x interactions can stabilize both ground and transition states (44), and has used these results to predict the involvement of aromatic sidechains in receptors and enzymes that operate on cationic species (45,46). In the structural realm, the widespread occurrence of amino-aromatic interactions have been noted (47). In addition, a cocrystal structure shows that the myeloma protein McPC603 interacts with tile quaternary ammonium ion of its ligand phosphorylcholine through the... 

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