ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent

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• 作者：Daria B. Kokh ; Stefano Corni ; Peter J. Winn ; Martin Hoefling ; Kay E. Gottschalk ; Rebecca C. Wade
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2010
• 出版时间：May 11, 2010
• 年：2010
• 卷：6
• 期：5
• 页码：1753-1768
• 全文大小：384K
• 年卷期：v.6,no.5(May 11, 2010)
• ISSN：1549-9626

文摘

In order to study protein−inorganic surface association processes, we have developed a physics-based energy model, the ProMetCS model, which describes protein−surface interactions at the atomistic level while treating the solvent as a continuum. Here, we present an approach to modeling the interaction of a protein with an atomically flat Au(111) surface in an aqueous solvent. Protein−gold interactions are modeled as the sum of van der Waals, weak chemisorption, and electrostatic interactions, as well as the change in free energy due to partial desolvation of the protein and the metal surface upon association. This desolvation energy includes the effects of water−protein, water−surface, and water−water interactions and has been parametrized using molecular dynamics (MD) simulations of water molecules and a test atom at a gold−water interface. The proposed procedure for computing the energy terms is mostly grid-based and is therefore efficient for application to long-time simulations of protein binding processes. The approach was tested for capped amino acid residues whose potentials of mean force for binding to a gold surface were computed and compared with those obtained previously in MD simulations with water treated explicitly. Calculations show good quantitative agreement with the results from MD simulations for all but one amino acid (Trp), as well as correspondence with available experimental data on the adhesion properties of amino acids.