Paper Citing NAMD - Abstract
Raman, E. Prabhu; Barsegov, Valeri; Klimov, Dmitri K.
Folding of tandem-linked domains
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67:795-810, JUN 2007
One of the factors, which influences protein folding in vivo, is a linkage of protein domains into multidomain tandems. However, relatively little is known about the impact of domain connectivity on protein folding mechanisms. In this article, we use coarse grained models of proteins to explore folding of tandem-linked domains (TLD). We found TLD folding to follow two scenarios. In the first, the tandem connectivity produces relatively minor impact on folding and the mechanisms of folding of tandem-linked and single domains remain similar. The second scenario involves qualitative changes in folding mechanism because of tandem linkage. As a result, protein domains, which fold via two-state mechanism as single isolated domains, may form new stable intermediates when inserted into tandems. The new intermediates are created by topological constraints imposed by the linkers between domains. In both cases tandem linkage slows down folding. We propose that the impact of tandem connectivity can be minimized, if the terminal secondary structure elements (SSEs) are flexible. In particular, two factors appear to facilitate TLD folding: (1) the interactions between terminal SSE are poorly ordered in the folding transition state, whereas nonterminal. SSE are better structured, (2) the interactions between terminal SSE are weak in the native state. We apply these findings to wild-type proteins by examining experimental (D-value data and by performing all-atom molecular dynamics simulations. We show that immunoglobulin-like domains appear to utilize the factors, which minimize the impact of tandem connectivity on their folding. Several single domain proteins, which are likely to misfold in tandems, are also identified. Proteins 2007;67:795-810. (C) 2007 Wiley-Liss, Inc.
