A generic coarse-grained (CG) protein model is presented. The intermediate level of resolution (four beads per amino acid, implicit solvent) allows for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. The thermodynamics and kinetics of a three-helix bundle are studied. We check that the CG model is able to fold proteins with tertiary structures and amino acid sequences different from the one used for parameter tuning. By studying both helical and extended conformations we make sure the force field is not biased toward any particular secondary structure. The accuracy involved in folding not only the test protein but also other ones show strong evidence for amino acid cooperativity embedded in the model. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed.
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21 June 2009
Research Article|
June 18 2009
Generic coarse-grained model for protein folding and aggregation
Tristan Bereau;
Tristan Bereau
a)
Department of Physics,
Carnegie Mellon University
, 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, USA
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Markus Deserno
Markus Deserno
b)
Department of Physics,
Carnegie Mellon University
, 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, USA
Search for other works by this author on:
a)
Electronic mail: bereau@cmu.edu.
b)
Electronic mail: bereau@cmu.edu.
J. Chem. Phys. 130, 235106 (2009)
Article history
Received:
January 21 2009
Accepted:
May 19 2009
Citation
Tristan Bereau, Markus Deserno; Generic coarse-grained model for protein folding and aggregation. J. Chem. Phys. 21 June 2009; 130 (23): 235106. https://doi.org/10.1063/1.3152842
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