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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| Formato: | Capítulo de libro |
| Lenguaje: | Inglés |
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American Chemical Society
2016
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| Acceso en línea: | Registro en Scopus DOI Handle Registro en la Biblioteca Digital |
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| LEADER | 09728caa a22009137a 4500 | ||
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| 001 | PAPER-15860 | ||
| 003 | AR-BaUEN | ||
| 005 | 20230518204641.0 | ||
| 008 | 190411s2016 xx ||||fo|||| 00| 0 eng|d | ||
| 024 | 7 | |2 scopus |a 2-s2.0-84978872446 | |
| 024 | 7 | |2 cas |a heme, 14875-96-8; protein, 67254-75-5; Heme; Proteins | |
| 040 | |a Scopus |b spa |c AR-BaUEN |d AR-BaUEN | ||
| 030 | |a JCTCC | ||
| 100 | 1 | |a Ramírez, C.L. | |
| 245 | 1 | 0 | |a Coarse-grained simulations of heme proteins: Validation and study of large conformational transitions |
| 260 | |b American Chemical Society |c 2016 | ||
| 270 | 1 | 0 | |m Capece, L.; Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICETArgentina; email: lula@qi.fcen.uba.ar |
| 506 | |2 openaire |e Política editorial | ||
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| 520 | 3 | |a 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. |l eng | |
| 593 | |a Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina | ||
| 593 | |a Dto. de Química Biologica, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina | ||
| 593 | |a Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, United States | ||
| 690 | 1 | 0 | |a HEME |
| 690 | 1 | 0 | |a PROTEIN |
| 690 | 1 | 0 | |a CHEMISTRY |
| 690 | 1 | 0 | |a HUMAN |
| 690 | 1 | 0 | |a MOLECULAR MODEL |
| 690 | 1 | 0 | |a PROTEIN CONFORMATION |
| 690 | 1 | 0 | |a REPRODUCIBILITY |
| 690 | 1 | 0 | |a HEME |
| 690 | 1 | 0 | |a HUMANS |
| 690 | 1 | 0 | |a MODELS, MOLECULAR |
| 690 | 1 | 0 | |a PROTEIN CONFORMATION |
| 690 | 1 | 0 | |a PROTEINS |
| 690 | 1 | 0 | |a REPRODUCIBILITY OF RESULTS |
| 700 | 1 | |a Petruk, A. | |
| 700 | 1 | |a Bringas, M. | |
| 700 | 1 | |a Estrin, D.A. | |
| 700 | 1 | |a Roitberg, A.E. | |
| 700 | 1 | |a Marti, M.A. | |
| 700 | 1 | |a Capece, L. | |
| 773 | 0 | |d American Chemical Society, 2016 |g v. 12 |h pp. 3390-3397 |k n. 7 |p J. Chem. Theory Comput. |x 15499618 |t Journal of Chemical Theory and Computation | |
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| 856 | 4 | 0 | |u https://doi.org/10.1021/acs.jctc.6b00278 |y DOI |
| 856 | 4 | 0 | |u https://hdl.handle.net/20.500.12110/paper_15499618_v12_n7_p3390_Ramirez |y Handle |
| 856 | 4 | 0 | |u https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499618_v12_n7_p3390_Ramirez |y Registro en la Biblioteca Digital |
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