title: Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations.
abstract: In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.
authors.affiliation: Laboratoire de Physique de la Matière Condensé et Nanostructures, Université Claude Bernard Lyon 1, CNRS, UMR 5586, Domaine scientifique de la Doua, F-69622 Villeurbanne Cedex, France. micael@fis.uc.pt
authors.forename: Micael J T
authors.initials: MJ
authors.lastname: Oliveira
authors.forename: Silvana
authors.initials: S
authors.lastname: Botti
authors.forename: Miguel A L
authors.initials: MA
authors.lastname: Marques
mesh_terms: D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012825:Silicon / Q000737:chemistry*; D012822:Silicon Dioxide / Q000737:chemistry*; D013499:Surface Properties; D013997:Time Factors
chemical_list: D011506:Proteins; D012822:Silicon Dioxide; D012825:Silicon