Artículo
Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
Ramírez, Claudia Lilián
; Petruk, Ariel Alcides
; Bringas, Mauro
; Estrin, Dario Ariel
; Roitberg, Adrián; Marti, Marcelo Adrian
; Capece, Luciana
Fecha de publicación:
07/2016
Editorial:
American Chemical Society
Revista:
Journal of Chemical Theory and Computation
ISSN:
1549-9618
Idioma:
Inglés
Tipo de recurso:
Artículo publicado
Clasificación temática:
Resumen
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.
Palabras clave:
Coarse-Grained Simulations
,
Heme Proteins
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Articulos(INQUIMAE)
Articulos de INST.D/QUIM FIS D/L MATERIALES MEDIOAMB Y ENERGIA
Articulos de INST.D/QUIM FIS D/L MATERIALES MEDIOAMB Y ENERGIA
Articulos(IQUIBICEN)
Articulos de INSTITUTO DE QUIMICA BIOLOGICA DE LA FACULTAD DE CS. EXACTAS Y NATURALES
Articulos de INSTITUTO DE QUIMICA BIOLOGICA DE LA FACULTAD DE CS. EXACTAS Y NATURALES
Citación
Ramírez, Claudia Lilián; Petruk, Ariel Alcides; Bringas, Mauro; Estrin, Dario Ariel; Roitberg, Adrián; et al.; Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions; American Chemical Society; Journal of Chemical Theory and Computation; 12; 7; 7-2016; 3390-3397
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