title: Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening.
abstract: Describing biological macromolecular energetics from computer simulations can pose major challenges, and often necessitates enhanced conformational sampling. We describe the calculation of conformational free-energy profiles along carefully chosen collective coordinates: "consensus" normal modes, developed recently as robust alternatives to conventional normal modes. In an application to the HIV-1 protease, we obtain efficient sampling of significant flap opening movements governing inhibitor binding from relatively short simulations, in close correspondence with experimental results.
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.|CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.|CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France.
authors.forename: Paulo R
authors.initials: PR
authors.lastname: Batista
authors.affiliation: Indian Institute of Technology , Roorkee, 247667, India.|CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Pandey
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.
authors.forename: Pedro G
authors.initials: PG
authors.lastname: Pascutti
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.
authors.forename: Paulo M
authors.initials: PM
authors.lastname: Bisch
authors.affiliation: CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.|CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France.
authors.forename: David
authors.initials: D
authors.lastname: Perahia
authors.affiliation: CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.|CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico Chimique, Université Paris Diderot, Sorbonne Paris Cité , 75005 Paris, France.
authors.forename: Charles H
authors.initials: CH
authors.lastname: Robert