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Ramírez, C.L.; Petruk, A.; Bringas, M.; Estrin, D.A.; Roitberg, A.E.; Marti, M.A.; Capece, L. "Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions" (2016) Journal of Chemical Theory and Computation. 12(7):3390-3397
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Abstract:

Heme proteins are ubiquitous in nature and perform many diverse functions in all kingdoms of life. Many of these functions are related to large-scale conformational transitions and allosteric processes. Sampling of these large conformational changes is computationally very challenging. In this context, coarse-grain simulations emerge as an efficient approach to explore the conformational landscape. In this work, we present a coarse-grained model of the heme group and thoroughly validate this model in different benchmark examples, which include the monomeric heme proteins myoglobin and neuroglobin and the tetrameric human hemoglobin where we evaluated the method's ability to explore conformational changes (as the formation of hexacoordinated species) and allosteric transitions (as the well-known R → T transition). The obtained results are compared with atomistic molecular dynamics simulations. Overall, the results indicate that this approach conserves the essential dynamical information on different allosteric processes. © 2016 American Chemical Society.

Registro:

Documento: Artículo
Título:Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
Autor:Ramírez, C.L.; Petruk, A.; Bringas, M.; Estrin, D.A.; Roitberg, A.E.; Marti, M.A.; Capece, L.
Filiación:Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
Dto. de Química Biologica, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, United States
Palabras clave:heme; protein; chemistry; human; molecular model; protein conformation; reproducibility; Heme; Humans; Models, Molecular; Protein Conformation; Proteins; Reproducibility of Results
Año:2016
Volumen:12
Número:7
Página de inicio:3390
Página de fin:3397
DOI: http://dx.doi.org/10.1021/acs.jctc.6b00278
Título revista:Journal of Chemical Theory and Computation
Título revista abreviado:J. Chem. Theory Comput.
ISSN:15499618
CODEN:JCTCC
CAS:heme, 14875-96-8; protein, 67254-75-5; Heme; Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v12_n7_p3390_Ramirez

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Citas:

---------- APA ----------
Ramírez, C.L., Petruk, A., Bringas, M., Estrin, D.A., Roitberg, A.E., Marti, M.A. & Capece, L. (2016) . Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions. Journal of Chemical Theory and Computation, 12(7), 3390-3397.
http://dx.doi.org/10.1021/acs.jctc.6b00278
---------- CHICAGO ----------
Ramírez, C.L., Petruk, A., Bringas, M., Estrin, D.A., Roitberg, A.E., Marti, M.A., et al. "Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions" . Journal of Chemical Theory and Computation 12, no. 7 (2016) : 3390-3397.
http://dx.doi.org/10.1021/acs.jctc.6b00278
---------- MLA ----------
Ramírez, C.L., Petruk, A., Bringas, M., Estrin, D.A., Roitberg, A.E., Marti, M.A., et al. "Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions" . Journal of Chemical Theory and Computation, vol. 12, no. 7, 2016, pp. 3390-3397.
http://dx.doi.org/10.1021/acs.jctc.6b00278
---------- VANCOUVER ----------
Ramírez, C.L., Petruk, A., Bringas, M., Estrin, D.A., Roitberg, A.E., Marti, M.A., et al. Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions. J. Chem. Theory Comput. 2016;12(7):3390-3397.
http://dx.doi.org/10.1021/acs.jctc.6b00278