computer modeling in molecular biology.pdf

24 Tim 1 F! Hubbard and Arthur M. Leskof the VH domain (H2). The size of the residue at site 71, a site in the conserved0-sheet of the VH domain, is a major determinant of the conformation and positionof this loop [58].Several general methods have been developed for prediction of the conformationsof loops in proteins. The antigen-binding loops of antibodies have received specialattention, and some special methods have been developed for them [52].Prediction of Loop Conformations by Energy Calculations. The main chain conformationof a loop attached to a given framework must obey the constraint that thechain must connect two fixed endpoints using a specified number of residues. Forloops of fewer than about six residues, it is possible to enumerate a fairly completeset of main chain and side chain conformations that bridge the given endpoints anddo not make steric collisions within the loop or between the loop and the rest of themolecule. The search procedure can be fine enough to be sure to produce a loop closeto the correct one.However, there are in general many possible loops of different internal conformationsthat bridge a given pair of endpoints. To choose one of them as the predictedconformation, it is possible to estimate conformational energies and evaluate the accessiblesurface areas of each loop - in the context of the remainder of the protein- and set criteria for selecting the one that appears the most favourable. Typicalconformational energy calculations include terms representing hydrogen bonding,van der Waals, and electrostatic interactions. Accessible surface area calculationsgive estimates of the interaction between the protein and the solvent. This is in principlea completely general, automatic and objective procedure.Procedures for conformation generation and evaluation have been implementedin a number of computer programs, of which the best known is CONGEN, by Bruccoleriand Karplus [59]. (Other similar procedures have been developed by Fine etal. [60], and by Moult and James [61].) An application to predicting all six antigenbindingloops of McPC603 and HyHELS, based on the program CONGEN, hasbeen described by Bruccoleri, Haber and Novotny [62]. The CONGEN proceduregenerates conformations for a single loop, and calculates energies of that loop in thecontext of the fixed portion of the structure. To apply this procedure to the predictionof several loops - for instance the six loops of an antigen-binding site - a protocolmust be used that involves a sequential prediction of the loops, starting withthe loops that interact primarily with the known parts of the molecule, and then proceedingto the loops that interact with each other.Prediction of Loop Conformations by Data Base Screening. Jones and Thirup [44]developed a method of building loops, based on selecting from proteins in thedatabase of known structures loops that span the given endpoints and overlap withpeptides at the loop termini. Vpically, a user selects the endpoints and initiates adata base search. The results are displayed interactively at a graphics terminal.