Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

ABSTRACT: Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of "chimera proteins." In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We furth

SUBMITTER: Chikenji G 

PROVIDER: S-EPMC1413881 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature