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An efficient conformational sampling method for homology modeling
Author(s) -
Han Rongsheng,
LeoMacias Alejandra,
Zerbino Daniel,
Bastolla Ugo,
ContrerasMoreira Bruno,
Ortiz Angel R.
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21672
Subject(s) - subspace topology , algorithm , computer science , statistical physics , monte carlo method , protein structure prediction , sampling (signal processing) , curvature , replica , casp , energy landscape , protein structure , mathematics , physics , artificial intelligence , geometry , statistics , filter (signal processing) , nuclear magnetic resonance , visual arts , computer vision , thermodynamics , art
The structural refinement of protein models is a challenging problem in protein structure prediction (Moult et al., Proteins 2003;53(Suppl 6):334–339). Most attempts to refine comparative models lead to degradation rather than improvement in model quality, so most current comparative modeling procedures omit the refinement step. However, it has been shown that even in the absence of alignment errors and using optimal templates, methods based on a single template have intrinsic limitations, and that refinement is needed to improve model accuracy. It is thought that failure of current methods originates on one hand from the inaccuracy of the effective free energy functions adopted, which do not represent properly the energetic balance in the native state, and on the other hand from the difficulty to sample the high dimensional and rugged free energy landscape of protein folding, in the search for the global minimum. Here, we address this second issue. We define the evolutionary and vibrational armonics subspace (EVA), a reduced sampling subspace that consists of a combination of evolutionarily favored directions, defined by the principal components of the structural variation within a homologous family, plus topologically favored directions, derived from the low frequency normal modes of the vibrational dynamics, up to 50 dimensions. This subspace is accurate enough so that the cores of most proteins can be represented within 1 Å accuracy, and reduced enough so that Replica Exchange Monte Carlo (Hukushima and Nemoto, J Phys Soc Jpn 1996;65:1604–1608; Hukushima et al., Int J Mod Phys C: Phys Comput 1996;7:337–344; Mitsutake et al., J Chem Phys 2003;118:6664–6675; Mitsutake et al., J Chem Phys 2003;118:6676–6688) (REMC) can be applied. REMC is one of the best sampling methods currently available, but its applicability is restricted to spaces of small dimensionality. We show that the combination of the EVA subspace and REMC can essentially solve the optimization problem for backbone atoms in the reduced sampling subspace, even for rather rugged free energy landscapes. Applications and limitations of this methodology are finally discussed. Proteins 2008. © 2007 Wiley‐Liss, Inc.