Artículos de revistas
Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
Fecha
2016-07Registro en:
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
1549-9618
CONICET Digital
CONICET
Autor
Ramírez, Claudia Lilián
Petruk, Ariel Alcides
Bringas, Mauro
Estrin, Dario Ariel
Roitberg, Adrián
Marti, Marcelo Adrian
Capece, Luciana
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.