Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions

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 conte...

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Autores principales:	Ramírez, C.L., Petruk, A., Bringas, M., Estrin, D.A., Roitberg, A.E., Marti, M.A., Capece, L.
Formato:	JOUR
Materias:	heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_15499618_v12_n7_p3390_Ramirez
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_15499618_v12_n7_p3390_Ramirez
record_format	dspace
spelling	todo:paper_15499618_v12_n7_p3390_Ramirez2023-10-03T16:23:17Z Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions Ramírez, C.L. Petruk, A. Bringas, M. Estrin, D.A. Roitberg, A.E. Marti, M.A. Capece, L. heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results 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. Fil:Ramírez, C.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Petruk, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marti, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Capece, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15499618_v12_n7_p3390_Ramirez
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results
spellingShingle	heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results 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
topic_facet	heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results
description	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.
format	JOUR
author	Ramírez, C.L. Petruk, A. Bringas, M. Estrin, D.A. Roitberg, A.E. Marti, M.A. Capece, L.
author_facet	Ramírez, C.L. Petruk, A. Bringas, M. Estrin, D.A. Roitberg, A.E. Marti, M.A. Capece, L.
author_sort	Ramírez, C.L.
title	Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
title_short	Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
title_full	Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
title_fullStr	Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
title_full_unstemmed	Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions
title_sort	coarse-grained simulations of heme proteins: validation and study of large conformational transitions
url	http://hdl.handle.net/20.500.12110/paper_15499618_v12_n7_p3390_Ramirez
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_version_	1782029297978966016

Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions

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