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TURN A N D LOOP PREDICTION The recognition of turns as distinct structural elements was first described by Venkatachalam (260) in 1968. Recently, Rose et al. (261) presented an extensive review of turns, and Milner-White and Poet (262) have also discussed turns and other related structural elements such as loops, bulges, and hairpins. Because turns on average constitute about 25% of the residues of globular proteins (202, 261), they undoubtedly play an important role in determining their overall 3D structure.
These include free diffusion of individual proteins, diffusional encounters between proteins and between an enzyme and its substrate, certain activated-rate processes, and long-term dynamics of polypeptide chains. An interesting variant of the SD approach is the use of stochastic boundary conditions. Localized regions of proteins are treated by traditional MD methods while the effects of the remainder of the protein and the surrounding solvent are incorporated implicitly. Excellent overviews of SD methodology and its application to proteins are given by McCammon and Harvey (14) and Brooks et al.
It is therefore necessary to study packing of helices in terms of their interaction energies. 3 kcal/mol (Table 11). Several distinct values ofthe orientation angles have been found, but the three lowest-energy packing arrangements are nearly antiparallel (occurring within k35" of 52, = -+ 180"). The orientation angle for the energetically most favorable packing is Q, = -154" (Fig. lo), which is the arrangement found in most proteins. The second most frequent 43 PROTEIN- STRUCTURE PREDICTION AND ANALYSIS TABLE 11.