title: Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.
abstract: Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X-ray crystallographic data are insufficient for analyzing a series of ligand-protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand-antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand-antibody interaction. Our results indicate the fact that d-fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Chemistry Section, Center for Natural Sciences, College of Liberal Arts and Sciences, Kitasato University, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan. noto@kitasato-u.ac.jp.
authors.forename: Kaori
authors.initials: K
authors.lastname: Ueno-Noto
authors.affiliation: Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-Ku, Tokyo, 112-8610, Japan.
authors.forename: Keiko
authors.initials: K
authors.lastname: Takano
mesh_terms: D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000378:metabolism*; D000080908:Broadly Neutralizing Antibodies; D015483:HIV Antibodies; D015497:HIV-1 / Q000737:chemistry; D006801:Humans; D009005:Monosaccharides / Q000737:chemistry / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism*; D014867:Water / Q000737:chemistry*
chemical_list: C529157:2G12 monoclonal antibody; D000911:Antibodies, Monoclonal; D000080908:Broadly Neutralizing Antibodies; D015483:HIV Antibodies; D009005:Monosaccharides; D014764:Viral Proteins; D014867:Water
keywords: HIV-1; a large scale quantum mechanical calculation; molecular dynamics; saccharide; water molecules