Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions.
Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions.
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DOI：
10.1021/la904415d
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发表时间：
2010-05-18
期刊：
影响因子：
--
通讯作者：
Stuart SJ
中科院分区：
文献类型：
--
作者：
Vellore NA;Yancey JA;Collier G;Latour RA;Stuart SJ
In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (ΔGads) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. ΔGads was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent ΔGads within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.
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影响因子：
3
作者：
KUMAR, S;ROSENBERG, JM;KOLLMAN, PA
通讯作者：
KOLLMAN, PA
DOI：
10.1016/s0165-022x(03)00150-7
发表时间：
2004-01-30
影响因子：
--
作者：
Frederix, F;Bonroy, K;Maes, G
通讯作者：
Maes, G
影响因子：
15
作者：
Kim, J;Somorjai, GA
通讯作者：
Somorjai, GA
影响因子：
3.9
作者：
Fears, Kenan P.;Creager, Stephen E.;Latour, Robert A.
通讯作者：
Latour, Robert A.
DOI：
10.1111/j.1749-6632.1986.tb20933.x
发表时间：
1986-01-01
影响因子：
5.2
作者：
Mezei, M;Beveridge, D L
通讯作者：
Beveridge, D L