Tertiary structure prediction, protein folding

As noted above, the recent CASP3 results suggest that for small proteins, current tertiary structure prediction schemes can often (but far from always) create inexact protein models of the global fold. Are these structures useftil for identifying functional sites in proteins To explore this issue, using the ab initio structure prediction program MONSSTER [191,193], the tertiary stmcture of the... 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

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... 

M.J. Sippl, S. Weitckus, and H. Flockner. In search of protein folds. In Merz and LeGrand, eds., The Protein Folding Problem and Tertiary Structure Prediction, 353-407. Birkhaeuser, 1994. 

Le-Grand SM, Merz KM Jr (1994) The protein folding problem and tertiary structure prediction the genetic algorithm and protein tertiary structure prediction. Birkhauser, Boston, p 109... 

Table 10.1 summarizes neural network applications for protein structure prediction. Protein secondary structure prediction is often used as the first step toward understanding and predicting tertiary structure because secondary structure elements constitute the building blocks of the folding units. An estimated 90% or so of the residues in most proteins are involved in three classes of secondary structures, the a-helices, p-strands or reverse turns. Related to the secondary structure prediction are also the prediction of solvent accessibility, transmembrane helices, and secondary structure content (10.2). Neural networks have also been applied to protein tertiary structure prediction, such as the prediction of the backbones or side-chain packing, and to structural class prediction (10.3). 

In tertiary structure prediction, there are three distinct scenarios. The sequence to be modeled may be closely related to a protein whose structure has been determined experimentally. Here, there is the prospect of developing a relatively accurate structural model through comparative modeling. This prospect drops markedly with the strength of the relationship between the sequence to be modeled and known structures. As this relationship weakens, one moves from the realm of comparative modeling to an approach known as fold recognition. Here, one attempts to utilize... 

Le Grand, S. M., and Merz, K. M. 1994. The genetic algorithm and protein structme prediction. In The Protein Folding Problem and Tertiary Structure Prediction. Eds. K. M. Merz and S. M. Le Grand. Birkhauser, Boston. 

T. N. Hart and R. J. Read, Multiple-start Monte Carlo docking of flexible ligands, in The Protein Folding Problem and Tertiary Structure Prediction, Birkhauser, 1994, pp. 71-108. 

Highly simplified models of protein structure embedded into low coordination lattices have been used for tertiary structure prediction for almost 20 years [65, 66, 75]. For example, Covell and Jemigan [64] enumerated all possible conformations of five small proteins restricted to fee and bcc lattices. They found that the nativelike conformation always has an energy within 2% of the lowest energy. Virtually simultaneously. Hinds and Levitt [28] used a diamond lattice model where a single lattice unit represents several residues. While such a representation cannot reproduce the geometric details of helices or P-sheets, the topology of native folds could be recovered with moderate accuracy. 

Improvements in the ability to predict tertiary structure will allow these techniques to assist in the rapid determination of protein structures. Such tools are necessary if structural genomics, which is designed to determine the tertiary structure of all proteins [220-222], is to make major progress. By suggesting proteins of novel fold and/or function, tertiary structure prediction can be used to prioritize the selection of proteins whose structure will determined by experiment. It will also assist in the rapid determination of the structure of... 

What can be done by predictive methods if the sequence search fails to reveal any homology with a protein of known tertiary structure Is it possible to model a tertiary structure from the amino acid sequence alone There are no methods available today to do this and obtain a model detailed enough to be of any use, for example, in drug design and protein engineering. This is, however, a very active area of research and quite promising results are being obtained in some cases it is possible to predict correctly the type of protein, a, p, or a/p, and even to derive approximations to the correct fold. 

Approaches of de novo predictions, which try to calculate how the structural elements are folded into the 3D-stmcture (tertiary structure) of complete proteins are nowadays far away from reliable large-scale applications. On the other, hand this topic is under strong development indicated by recent successful results at the contest for structural prediction methods CASP4. With the fast growing number of experimentally solved 3D-stmctures of protein and new promising approaches like threading tools combined with experimental structural constraints, one can expect more reliable de novo predictions for 3D-protein structures in the future. 

Secondary structural predictions about NPAs, and direct biophysical measurements, have demonstrated that the NPAs are rich in a-helix, with no p-structure either predicted from secondary structure prediction algorithms, or detected by circular dichroism (Kennedy et al, 1995b). In this they are the antithesis of the similarly sized cLBPs and lipocalins. The predictions are that each individual NPA unit protein will fold into four main regions of helix, and it has been speculated that the tertiary structure is as a four-bundle helix protein, similar to other invertebrate carrier proteins (Sheriff et al., 1987). 

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