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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches

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Author(s):
Piccirillo, Erika [1] ; Alegria, Thiago G. P. [2] ; Discola, Karen F. [2] ; Cussiol, Jose A. R. R. [3, 2] ; Domingos, Renato M. [2] ; de Oliveira, Marcos A. [4] ; de Rezende, Leandro [1] ; Netto, Luis E. S. [2] ; Amaral, Antonia T-do [1]
Total Authors: 9
Affiliation:
[1] Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Sao Paulo, SP - Brazil
[2] Univ Sao Paulo, Inst Biociencias, Dept Genet & Biol Evolut, Sao Paulo, SP - Brazil
[3] Univ Fed Sao Paulo, Dept Bioquim, Sao Paulo, SP - Brazil
[4] Univ Estadual Paulista, Inst Biociencias, Campus Litoral Paulista, Sao Vicente, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: PLoS One; v. 13, n. 5 MAY 21 2018.
Web of Science Citations: 2
Abstract

Organic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (C-p) toward hydroperoxides. In the closed state, the thiolate of C-p is in close proximity to the guanidinium group of Arg19. Ohr enzymes can also assume an open state, where the loop containing the catalytic Arg is far away from C-p and Glu51. Here, we aimed to gain insights into the putative structural switches of the Ohr catalytic cycle. First, we describe the crystal structure of Ohr from Xylella fastidiosa (XfOhr) in the open state that, together with the previously described XfOhr structure in the closed state, may represent two snapshots along the coordinate of the enzyme-catalyzed reaction. These two structures were used for the experimental validation of molecular dynamics (MD) simulations. MD simulations employing distinct protonation states and in silico mutagenesis indicated that the polar interactions of Arg19 with Glu51 and C-p contributed to the stabilization of XfOhr in the closed state. Indeed, C-p oxidation to the disulfide state facilitated the switching of the Arg19 loop from the closed to the open state. In addition to the Arg19 loop, other portions of XfOhr displayed high mobility, such as a loop rich in Gly residues. In summary, we obtained a high correlation between crystallographic data, MD simulations and biochemical/enzymatic assays. The dynamics of the Ohr enzymes are unique among the Cys-based peroxidases, in which the active site Arg undergoes structural switches throughout the catalytic cycle, while C-p remains relatively static. (AU)

FAPESP's process: 16/12392-9 - 21st European Symposium on Quantitative Structure-Activity Relationship Where Molecular Simulations Meet Drug Discovery
Grantee:Antonia Tavares Do Amaral
Support Opportunities: Research Grants - Meeting - Abroad
FAPESP's process: 12/06633-2 - Rational search for inhibitors of Dengue and Foot-and-Mouth Disease proteases
Grantee:Erika Piccirillo
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 08/07971-3 - Kinetic characterization and search for inhibitors of Ohr (Organic Hydroperoxide Resistance Protein) from Xylella fastidiosa
Grantee:Thiago Geronimo Pires Alegria
Support Opportunities: Scholarships in Brazil - Master
FAPESP's process: 14/01614-5 - Use of MD simulations to improve DENV NS2B/NS3 protease pharmacophore models, considering protease conformational flexibility, and to validate different serotype proteases homology models
Grantee:Erika Piccirillo
Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
FAPESP's process: 05/50056-6 - Functional characterization of a new antioxidant protein: Ohr (Organic Hydroperoxide Resistance Protein): pathways of reduction and expression in Xylella fastidiosa
Grantee:José Renato Rosa Cussiol
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 13/07937-8 - Redoxome - Redox Processes in Biomedicine
Grantee:Ohara Augusto
Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC