title: Human Cytomegalovirus Protease:  Why is the Dimer Required for Catalytic Activity?
abstract: Human cytomegalovirus (HCMV) is a pathogenic agent responsible for morbidity and mortality in immunocompromised and immunosuppressed individuals. HCMV encodes a serine protease that is essential for the production of infectious virions. In this work, we applied molecular dynamics (MD) simulations on HCMV protease models in order to investigate the experimentally observed (i) catalytic activity of the enzyme homodimer and (ii) induced-fit mechanism upon the binding of substrates and peptidyl inhibitors. Long and stable trajectories were obtained for models of the monomeric and dimeric states, free in solution and bound covalently and noncovalently to a peptidyl-activated carbonyl inhibitor, with very good agreement between theoretical and experimental results. The MD results suggest that HCMV protease indeed operates by an induced-fit mechanism. Also, our analysis indicates that the catalytic activity of the dimer is a result of more favorable interactions between the oxyanion in the covalently bound state and the backbone nitrogen of Arg165, resulting in a reaction that is 7.0 kcal/mol more exergonic and a more significant thermodynamic driving force. The incipient oxyanion in the transition state should also benefit from the stronger interactions with Arg165, reducing in this manner the intrinsic activation barrier for the reaction in the dimeric state.
authors.affiliation: Physical Organic Chemistry Group, Departamento de Química Organica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, lab. 609, Rio de Janeiro, RJ 21949-900, Brazil, and Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520-8107.
authors.forename: César Augusto Fernandes
authors.initials: CA
authors.lastname: de Oliveira
authors.affiliation: Physical Organic Chemistry Group, Departamento de Química Organica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, lab. 609, Rio de Janeiro, RJ 21949-900, Brazil, and Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520-8107.
authors.forename: Cristiano Ruch Werneck
authors.initials: CR
authors.lastname: Guimarães
authors.affiliation: Physical Organic Chemistry Group, Departamento de Química Organica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, lab. 609, Rio de Janeiro, RJ 21949-900, Brazil, and Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520-8107.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Barreiro
authors.affiliation: Physical Organic Chemistry Group, Departamento de Química Organica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, lab. 609, Rio de Janeiro, RJ 21949-900, Brazil, and Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520-8107.
authors.forename: Ricardo Bicca
authors.initials: RB
authors.lastname: de Alencastro