期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 66, 期 4, 页码 877-888出版社
WILEY
DOI: 10.1002/prot.21234
关键词
folding search principle; HP lattice model; effective contact order; topology-dependent folding rates; topologically local; fast conformational search algorithm; folding mechanism
It has been proposed that proteins fold by a process called Zipping and Assembly (Z&A). Zipping refers to the growth of local substructures within the chain, and assembly refers to the coming together of already-formed pieces. Our interest here is in whether Z&A is a general method that can fold most of sequence space, to global minima, efficiently. Using the HP model, we can address this question by enumerating full conformation and sequence spaces. We find that Z&A reaches the global energy minimum native states, even though it searches only a very small fraction of conformational space, for most sequences in the full sequence space. We find that Z&A, a mechanism-based search, is more efficient in our tests than the replica exchange search method. Folding efficiency is increased for chains having: (a) small loop-closure steps, consistent with observations by Plaxco et al. 1998;277;985-994 that folding rates correlate with contact order, (b) neither too few nor too many nucleation sites per chain, and (c) assembly steps that do not occur too early in the folding process. We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms.
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