Sampling Realistic Protein Conformations Using Local Structural Bias

Open Access
Publisher Website
Google Scholar
Abstract
The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design. Protein structure prediction is one of the main unsolved problems in computational biology today. A common way to tackle the problem is to generate plausible protein conformations using a fairly inaccurate but fast method, and to evaluate the conformations using an accurate but slow method. The main bottleneck lies in the first step, that is, efficiently exploring protein conformational space. Currently, the best way to do this is to construct plausible structures by stringing together fragments from experimentally determined protein structures, a method called fragment assembly. Hamelryck, Kent, and Krogh present a new method that can efficiently generate protein conformations that are compatible with a given protein sequence. Unlike for existing methods, the generated conformations cover a continuous range and come with an associated probability. The method shows great promise for use in protein structure prediction, determination, simulation, and design.