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Folding and stability of helical bundle proteins from coarse‐grained models
Author(s) -
Kapoor Abhijeet,
Travesset Alex
Publication year - 2013
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.24269
Subject(s) - folding (dsp implementation) , molecular dynamics , bundle , protein folding , native state , random coil , hydrogen bond , electrostatics , chemical physics , stability (learning theory) , side chain , downhill folding , chain (unit) , chemistry , phi value analysis , crystallography , biological system , topology (electrical circuits) , computer science , physics , computational chemistry , materials science , molecule , mathematics , biology , circular dichroism , engineering , combinatorics , composite material , polymer , biochemistry , machine learning , organic chemistry , astronomy , electrical engineering
We develop a coarse‐grained model where solvent is considered implicitly, electrostatics are included as short‐range interactions, and side‐chains are coarse‐grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side‐chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Proteins 2013; 81:1200–1211. © 2013 Wiley Periodicals, Inc.