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Influence of temperature, friction, and random forces on folding of the B‐domain of staphylococcal protein A: All‐atom molecular dynamics in implicit solvent
Author(s) -
Jagielska Anna,
Scheraga Harold A.
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20631
Subject(s) - molecular dynamics , thermostat , chemistry , folding (dsp implementation) , protein folding , langevin dynamics , downhill folding , thermodynamics , contact order , helix (gastropod) , atom (system on chip) , chemical physics , solvation , crystallography , statistical physics , computational chemistry , physics , phi value analysis , solvent , computer science , organic chemistry , ecology , biochemistry , biology , snail , electrical engineering , embedded system , engineering
The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all‐atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007