Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 106, Issue 36, Pages 15302-15307Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0907002106
Keywords
fragment assembly; associative memory Hamiltonian; protein folding; annealing; molecular dynamics
Categories
Funding
- National Science Foundation [PHY-0822283, NSF-Career CHE0349303,, NSF-CCF-0523908, NSF-CDI CHE-0835824]
- National Institutes of Health [R01GM44557]
- Welch Foundation [C-1570]
- NSF [CNS-0421109, CNS-0454333, EIA0216467]
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0835824] Funding Source: National Science Foundation
- Division Of Computer and Network Systems
- Direct For Computer & Info Scie & Enginr [0821727] Funding Source: National Science Foundation
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Conformational restriction by fragment assembly and guidance in molecular dynamics are alternate conformational search strategies in protein structure prediction. We examine both approaches using a version of the associative memory Hamiltonian that incorporates the influence of water-mediated interactions (AMW). For short proteins (<70 residues), fragment assembly, while searching a restricted space, compares well to molecular dynamics and is often sufficient to fold such proteins to near-native conformations (4 angstrom) via simulated annealing. Longer proteins encounter kinetic sampling limitations in fragment assembly not seen in molecular dynamics which generally samples more native-like conformations. We also present a fragment enriched version of the standard AMW energy function, AMW-FME, which incorporates the local sequence alignment derived fragment libraries from fragment assembly directly into the energy function. This energy function, in which fragment information acts as a guide not a restriction, is found by molecular dynamics to improve on both previous approaches.
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