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Marcos-Alcalde Í, Mendieta-Moreno JI, Puisac B, Gil-Rodríguez MC, Hernández-Marcos M, Soler-Polo D, Ramos FJ, Ortega J, Pié J, Mendieta J, Gómez-Puertas P. Two-step ATP-driven opening of cohesin head. Sci Rep 2017; 7:3266. [PMID: 28607419 PMCID: PMC5468275 DOI: 10.1038/s41598-017-03118-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.
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Affiliation(s)
| | - Jesús I Mendieta-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Beatriz Puisac
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Concepción Gil-Rodríguez
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Hernández-Marcos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Feliciano J Ramos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Pié
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Departamento de Biotecnología, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223, Madrid, Spain
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Mendieta-Moreno JI, Trabada DG, Mendieta J, Lewis JP, Gómez-Puertas P, Ortega J. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer. J Phys Chem Lett 2016; 7:4391-4397. [PMID: 27768300 DOI: 10.1021/acs.jpclett.6b02168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.
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Affiliation(s)
- Jesús I Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain
- Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain
| | - Daniel G Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain
| | - Jesús Mendieta
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain
- Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain
- Departamento de Biotecnología, Universidad Francisco de Vitoria , ctra. Pozuelo-Majadahonda, km 1,800, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - James P Lewis
- Department of Physics, West Virginia University , Morgantown, West Virginia 26506-6315, United States
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain
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Marcos-Alcalde I, Setoain J, Mendieta-Moreno JI, Mendieta J, Gómez-Puertas P. MEPSA: minimum energy pathway analysis for energy landscapes. Bioinformatics 2015; 31:3853-5. [PMID: 26231428 DOI: 10.1093/bioinformatics/btv453] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/24/2015] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. AVAILABILITY AND IMPLEMENTATION MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Javier Setoain
- Departamento de Arquitectura de Computadores y Automática, UCM, ES-28040 Madrid, Spain
| | - Jesús I Mendieta-Moreno
- Molecular Modelling Group, CBMSO (CSIC-UAM), ES-28049 Madrid, Spain, Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), UAM and
| | - Jesús Mendieta
- Molecular Modelling Group, CBMSO (CSIC-UAM), ES-28049 Madrid, Spain, Biomol-Informatics SL, Campus UAM, ES-28049 Madrid, Spain
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