Prediction of Tertiary Structure

The basic thesis has served as the stimulus for a large number of studies directed towards the prediction of protein three-dimensional structures from their amino-acid sequences alone. Implicit in most of the predictive methods investigated are two concepts (i) that there is in the protein the clearly-observed hierarchical structural arrangement (primary structure - secondary structure - secondary aggregates or super-secondary structure - domains - total structure) which has already been discussed in the previous section and (ii) that the folding process of a random chain to give the stable native structure is kinetically-controlled and that it proceeds via a characteristic and predictable pathway. This pathway is visualized as requiring nucleation at various sites around which the subsequent 

Chou and Fasman have continued their studies of known structures with a detailed examination of -turns. In their definition tetrapeptides whose a-C )— a-C i+3) distances were less than 7 A and which were not in a helical region were characterized as -turns ( being the residue number in the sequence). They concluded that the most frequently occurring bend residues are Asn, Cys, Asp in the first position. Pro, Ser, Lys in the second, Asn, Asp, Gly in the third, and Trp, Gly, Tyr in the fourth. Residues with the highest /9-turn potential in all four positions were Pro, Gly, Asn, and Ser, with Val, He, and Leu appearing least in bends. However, they also observed that hydrophobic residues occurred wth high frequency just beyond -turns. Clearly consistent with these results are the 

Rose and Seltzer also considered turns but identified them rather less restrictively. Their analysis treated the peptide chain as a curve in space with a discrete radius of curvature at any point. They defined a turn as occurring at a point whau the chain direction was changing rapidly and where there was a local minimum in the radius of curvature. Subsequently Rose developed an approach 

Levitt and Greer characterized three main features which constitute secondary structure, viz, -helix, -strand, and reverse turns, using objective data relating to structural criteria including torsion angle, hydrogen bonds, and C -C - distances. 

Continuing this idea a number of groups have extended the studies to medium-and long-range interactions and considered the extent to which side chain groups, in particular hydrophobic groups, associate in pairs or clusters within the molecule.  

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Knowledge of secondary structure is necessary for prediction of tertiary structure... 

Galaktionov, S.G., Marshall, G.R. Properties of intraglobular contacts in proteins an approach to prediction of tertiary structure. Proceedings of the 27th Hawaii International Conference on System Sciences. IEEE Computational Society, Washington, DC, 1994,... 

H. Kawai, T. Kikuchi, and Y. Okamoto, Protein Engin., 3, 85 (1989). A Prediction of Tertiary Structures of Peptide by the Monte Carlo Simulated Annealing Method. 

In this chapter, some methods currently employed in the prediction of tertiary structure from the protein sequence will be highlighted This is not intended to be a comprehensive review of the literature, a goal that would require an entire book of this size and would quickly become outdated. Instead, the aim is to provide some of the basic tenets of the theories and methods utilized with a few select references to the original literature. Hopefully this will serve as a starting point to delve into this very exciting and ongoing field of research. 

Method for Prediction of Tertiary Structure from Predicted Secondary Structure and Tertiary Restraints... 

Unfortunately, the approach of determining empirical potentials from equilibrium data is intrinsically limited, even if we assume complete knowledge of all equilibrium geometries and their energies. It is obvious that statistical potentials cannot define an energy scale, since multiplication of a potential by a positive, constant factor does not alter its global minimizers. But for the purpose of tertiary structure prediction by global optimization, this does not not matter. 

EE Cohen, ID Kuntz. Tertiary stiaicture prediction. In CD Easman, ed. Prediction of Protein Structure and the Principles of Protein Conformation. New York Plenum Press, 1989, pp 647-705. 

Using CD spectroscopy and published data it is possible to predict the tertiary structure of ODN compounds similar to a reference ODN (e.g., DIMS0400 which forms a type of structure called parallel tetramer of G-quadruplex (24) (Fig. 3)), whose structural characteristics had been determined previously by NMR and/or XRC techniques (see Notes 9-15). 

A heuristic approach to predicting the tertiary structure of hovine somatotropin PDB ID IBST... 

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... 

Since the different domains often have quite different types of tertiary structure, they need to be described and classified separately and, if possible, should be predicted separately. Multiple domains should be considered for any sequence that suggests an internal repeat or that is longer than about 200 residues (250 for a/P structures or 100 for a disulfide-rich sequence). 

Tertiary Structure - Attempts to predict tertiary structure of proteins have not been as successful as those for predicting secondary structure. Folding of sequences depends critically on specific side chain interactions, often far removed from one another in the amino acid sequence. Attempts to predict tertiary structure include efforts to recognize overall patterns in tertiary folding combined with the prediction of secondary structure. These efforts have led to the successful prediction of an ot//f-barrel structure for tryptophan synthase, which is in excellent agreement with the structure determined by x-ray diffraction. 

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