Nonlinearities in protein space limit the utility of informatics in protein biophysics.

ABSTRACT: We examine the utility of informatic-based methods in computational protein biophysics. To do so, we use newly developed metric functions to define completely independent sequence and structure spaces for a large database of proteins. By investigating the relationship between these spaces, we demonstrate quantitatively the limits of knowledge-based correlation between the sequences and structures of proteins. It is shown that there are well-defined, nonlinear regions of protein space in which dissimilar structures map onto similar sequences (the conformational switch), and dissimilar sequences map onto similar structures (remote homology). These nonlinearities are shown to be quite common-almost half the proteins in our database fall into one or the other of these two regions. They are not

SUBMITTER: Rackovsky S 

PROVIDER: S-EPMC4609284 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature