title: Dataset showing the impact of the protonation states on molecular dynamics of HIV protease.
abstract: The data described here supports the research article "Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations" (Soares et al., 2016) [1]. The data involves both standard Molecular Dynamics (MD) and Constant pH Molecular Dynamics (CpHMD) to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation. The data obtained from MD simulation demonstrate that the protonation state of the two aspartic acids (Asp25/Asp25') has a strong influence on the dynamics of the HIV-PR. Regarding the CpHMD simulation, we performed pka calculations for HIV-PR and the data indicate that only one catalytic aspartate should be protonated.
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil.
authors.forename: Rosemberg O
authors.initials: RO
authors.lastname: Soares
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
authors.forename: Pedro H M
authors.initials: PH
authors.lastname: Torres
authors.affiliation: Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil.
authors.forename: Manuela L
authors.initials: ML
authors.lastname: da Silva
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil.
authors.forename: Pedro G
authors.initials: PG
authors.lastname: Pascutti