{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T12:12:12Z","timestamp":1763640732636},"reference-count":47,"publisher":"Proceedings of the National Academy of Sciences","issue":"3","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2003,2,4]]},"abstract":"<jats:p>\n            F\n            <jats:sub>1<\/jats:sub>\n            F\n            <jats:sub>o<\/jats:sub>\n            -ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F\n            <jats:sub>1<\/jats:sub>\n            of the F\n            <jats:sub>1<\/jats:sub>\n            F\n            <jats:sub>o<\/jats:sub>\n            complex, F\n            <jats:sub>1<\/jats:sub>\n            -ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic \u03b2 subunits (\u03b2\n            <jats:sub>TP<\/jats:sub>\n            , \u03b2\n            <jats:sub>DP<\/jats:sub>\n            , \u03b2\n            <jats:sub>E<\/jats:sub>\n            ) observed in the crystal structures of the mitochondrial enzyme, MF\n            <jats:sub>1<\/jats:sub>\n            . Using free energy difference simulations for the hydrolysis reaction ATP+H\n            <jats:sub>2<\/jats:sub>\n            O \u2192 ADP+P\n            <jats:sub>i<\/jats:sub>\n            in the \u03b2\n            <jats:sub>TP<\/jats:sub>\n            and \u03b2\n            <jats:sub>DP<\/jats:sub>\n            sites and unisite hydrolysis data, we are able to identify \u03b2\n            <jats:sub>TP<\/jats:sub>\n            as the \u201ctight\u201d (\n            <jats:italic>K<\/jats:italic>\n            <jats:sub>D<\/jats:sub>\n            = 10\n            <jats:sup>\u221212<\/jats:sup>\n            M, MF\n            <jats:sub>1<\/jats:sub>\n            ) binding site for ATP and \u03b2\n            <jats:sub>DP<\/jats:sub>\n            as the \u201cloose\u201d site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the \u03b2\n            <jats:sub>TP<\/jats:sub>\n            and \u03b2\n            <jats:sub>DP<\/jats:sub>\n            sites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of F\n            <jats:sub>1<\/jats:sub>\n            -ATPase, the present results make possible a consistent description of the binding change mechanism of F\n            <jats:sub>1<\/jats:sub>\n            -ATPase at an atomic level of detail.\n          <\/jats:p>","DOI":"10.1073\/pnas.0337432100","type":"journal-article","created":{"date-parts":[[2003,2,4]],"date-time":"2003-02-04T17:24:41Z","timestamp":1044379481000},"page":"874-879","update-policy":"http:\/\/dx.doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":101,"title":["The missing link between thermodynamics and structure in F\n            <sub>1<\/sub>\n            -ATPase"],"prefix":"10.1073","volume":"100","author":[{"given":"W.","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706; Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030; and Laboratoire de Chimie Biophysique, Institut de Science et d'Ing\u00e9nierie Supramol\u00e9culaires, Universit\u00e9 Louis Pasteur, 67000 Strasbourg, France"}]},{"given":"Y. Q.","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706; Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030; and Laboratoire de Chimie Biophysique, Institut de Science et d'Ing\u00e9nierie Supramol\u00e9culaires, Universit\u00e9 Louis Pasteur, 67000 Strasbourg, France"}]},{"given":"Q.","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706; Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030; and Laboratoire de Chimie Biophysique, Institut de Science et d'Ing\u00e9nierie Supramol\u00e9culaires, Universit\u00e9 Louis Pasteur, 67000 Strasbourg, France"}]},{"given":"J.","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706; Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030; and Laboratoire de Chimie Biophysique, Institut de Science et d'Ing\u00e9nierie Supramol\u00e9culaires, Universit\u00e9 Louis Pasteur, 67000 Strasbourg, France"}]},{"given":"M.","family":"Karplus","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; Department of Chemistry, California Institute of Technology, Pasadena, CA 91125; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706; Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030; and Laboratoire de Chimie Biophysique, Institut de Science et d'Ing\u00e9nierie Supramol\u00e9culaires, Universit\u00e9 Louis Pasteur, 67000 Strasbourg, 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