title: Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites.
abstract: The effects of solvation on molecular recognition are investigated from different perspectives, ranging from methods to analyse explicit solvent dynamical behaviour at the protein surface to methods for the implicit treatment of solvent effects associated with the conformational behaviour of biomolecules. The here presented implicit solvation method is based on an analytical approximation of the Solvent Accessible Surface Area (SASA) of solute molecules, which is computationally efficient and easy to parametrise. The parametrised SASA solvation method is discussed in the light of protein design and ligand binding studies. The POPS program for the SASA computation on single molecules and complex interfaces is described in detail. Explicit solvent behaviour is described here in the form of solvent density maps at the protein surface. We highlight the usefulness of that approach in defining the organisation of specific water molecules at functional sites and in determining hydrophobicity scores for the identification of potential interaction patches.
authors.affiliation: Randall Division for Cellular and Molecular Biophysics, King's College London, London, UK.
authors.forename: Arianna
authors.initials: A
authors.lastname: Fornili
authors.forename: Flavia
authors.initials: F
authors.lastname: Autore
authors.forename: Nesrine
authors.initials: N
authors.lastname: Chakroun
authors.forename: Pierre
authors.initials: P
authors.lastname: Martinez
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000378:metabolism*; D012984:Software; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000378:metabolism*
chemical_list: D050505:Mutant Proteins; D011506:Proteins; D012997:Solvents; D014867:Water