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:	Ramirez, Claudia Lilian, Petruk, Ariel Alcides, Estrin, Dario Ariel, Martí, Marcelo Adrián, Capece, Luciana
Publicado:	2016
Materias:	heme protein chemistry human molecular model protein conformation reproducibility Heme Humans Models, Molecular Protein Conformation Proteins Reproducibility of Results
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v12_n7_p3390_Ramirez 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	paper:paper_15499618_v12_n7_p3390_Ramirez
record_format	dspace
spelling	paper:paper_15499618_v12_n7_p3390_Ramirez2023-06-08T16:21:25Z Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions Ramirez, Claudia Lilian Petruk, Ariel Alcides Estrin, Dario Ariel Martí, Marcelo Adrián Capece, Luciana 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. 2016 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v12_n7_p3390_Ramirez 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 Ramirez, Claudia Lilian Petruk, Ariel Alcides Estrin, Dario Ariel Martí, Marcelo Adrián Capece, Luciana 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.
author	Ramirez, Claudia Lilian Petruk, Ariel Alcides Estrin, Dario Ariel Martí, Marcelo Adrián Capece, Luciana
author_facet	Ramirez, Claudia Lilian Petruk, Ariel Alcides Estrin, Dario Ariel Martí, Marcelo Adrián Capece, Luciana
author_sort	Ramirez, Claudia Lilian
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
publishDate	2016
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v12_n7_p3390_Ramirez http://hdl.handle.net/20.500.12110/paper_15499618_v12_n7_p3390_Ramirez
work_keys_str_mv	AT ramirezclaudialilian coarsegrainedsimulationsofhemeproteinsvalidationandstudyoflargeconformationaltransitions AT petrukarielalcides coarsegrainedsimulationsofhemeproteinsvalidationandstudyoflargeconformationaltransitions AT estrindarioariel coarsegrainedsimulationsofhemeproteinsvalidationandstudyoflargeconformationaltransitions AT martimarceloadrian coarsegrainedsimulationsofhemeproteinsvalidationandstudyoflargeconformationaltransitions AT capeceluciana coarsegrainedsimulationsofhemeproteinsvalidationandstudyoflargeconformationaltransitions
_version_	1768544197059543040

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

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