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Attenuating dependence on structural data in computing protein energy landscapes.

Abstract：

BACKGROUND:Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. In principle, reconstructing a protein's energy landscape holds the key to characterizing the structural dynamics and its regulation of protein function. In practice, the disparate spatio-temporal scales spanned by the slow dynamics challenge both wet and dry laboratories. However, the growing number of deposited structures for proteins central to human biology presents an opportunity to infer the relevant dynamics via exploitation of the information encoded in such structures about equilibrium dynamics. RESULTS:Recent computational efforts using extrinsic modes of motion as variables have successfully reconstructed detailed energy landscapes of several medium-size proteins. Here we investigate the extent to which one can reconstruct the energy landscape of a protein in the absence of sufficient, wet-laboratory structural data. We do so by integrating intrinsic modes of motion extracted off a single structure in a stochastic optimization framework that supports the plug-and-play of different variable selection strategies. We demonstrate that, while knowledge of more wet-laboratory structures yields better-reconstructed landscapes, precious information can be obtained even when only one structural model is available. CONCLUSIONS:The presented work shows that it is possible to reconstruct the energy landscape of a protein with reasonable detail and accuracy even when the structural information about the protein is limited to one structure. By attenuating the dependence on structural data of methods designed to compute protein energy landscapes, the work opens up interesting venues of research on structure-based inference of dynamics. Of particular interest are directions of research that will extend such inference to proteins with no experimentally-characterized structures.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Morris D,Maximova T,Plaku E,Shehu A

doi

10.1186/s12859-019-2822-5

subject

Has Abstract

pub_date

2019-06-06 00:00:00

pages

280

issue

Suppl 11

issn

1471-2105

pii

10.1186/s12859-019-2822-5

journal_volume

pub_type

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Attenuating dependence on structural data in computing protein energy landscapes.