Abstract：
:Many proteins exhibit strong binding affinities to surfaces, with binding energies much greater than thermal fluctuations. When modelling these protein-surface systems with classical molecular dynamics (MD) simulations, the large forces that exist at the protein/surface interface generally confine the system to a single free energy minimum. Exploring the full conformational space of the protein, especially finding other stable structures, becomes prohibitively expensive. Coupling MD simulations with metadynamics (enhanced sampling) has fast become a common method for sampling the adsorption of such proteins. In this paper, we compare three different flavors of metadynamics, specifically well-tempered, parallel-bias, and parallel-tempering in the well-tempered ensemble, to exhaustively sample the conformational surface-binding landscape of model peptide GGKGG. We investigate the effect of mobile ions and ion charge, as well as the choice of collective variable (CV), on the binding free energy of the peptide. We make the case for explicitly biasing ions to sample the true binding free energy of biomolecules when the ion concentration is high and the binding free energies of the solute and ions are similar. We also make the case for choosing CVs that apply bias to all atoms of the solute to speed up calculations and obtain the maximum possible amount of information about the system.
journal_name
Biochem Biophys Res Communjournal_title
Biochemical and biophysical research communicationsauthors
Prakash A,Sprenger KG,Pfaendtner Jdoi
10.1016/j.bbrc.2017.07.066subject
Has Abstractpub_date
2018-03-29 00:00:00pages
274-281issue
2eissn
0006-291Xissn
1090-2104pii
S0006-291X(17)31408-0journal_volume
498pub_type
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journal_title：Biochemical and biophysical research communications
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doi：10.1006/bbrc.1994.1282
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journal_title：Biochemical and biophysical research communications
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journal_title：Biochemical and biophysical research communications
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journal_title：Biochemical and biophysical research communications
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更新日期：1984-07-31 00:00:00
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更新日期：2004-09-24 00:00:00
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journal_title：Biochemical and biophysical research communications
pub_type： 杂志文章
doi：10.1006/bbrc.1993.1411
更新日期：1993-04-15 00:00:00
