Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State
The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynami...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090 http://www.ncbi.nlm.nih.gov/pubmed/22356468 https://doi.org/10.1021/jp212148x |
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ftpubmed:oai:pubmedcentral.nih.gov:3319090 2023-05-15T18:26:45+02:00 Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State Cottone, Grazia Lattanzi, Gianluca Ciccotti, Giovanni Elber, Ron 2012-03-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090 http://www.ncbi.nlm.nih.gov/pubmed/22356468 https://doi.org/10.1021/jp212148x en eng http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090 http://www.ncbi.nlm.nih.gov/pubmed/22356468 http://dx.doi.org/10.1021/jp212148x Article Text 2012 ftpubmed https://doi.org/10.1021/jp212148x 2013-09-04T05:08:13Z The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to Non Equilibrium Molecular Dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment provide hints to allostery. In particular a pathway of energy flow between the heme and the FG loop is illustrated. Although the simulations were conducted for myoglobin only, the thermal fluctuations of the FG corner are in agreement with the large structural shifts of FG during the allosteric transition of tetrameric hemoglobin. Text Sperm whale PubMed Central (PMC) The Journal of Physical Chemistry B 116 10 3397 3410 |
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Article Cottone, Grazia Lattanzi, Gianluca Ciccotti, Giovanni Elber, Ron Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
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description |
The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to Non Equilibrium Molecular Dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment provide hints to allostery. In particular a pathway of energy flow between the heme and the FG loop is illustrated. Although the simulations were conducted for myoglobin only, the thermal fluctuations of the FG corner are in agreement with the large structural shifts of FG during the allosteric transition of tetrameric hemoglobin. |
format |
Text |
author |
Cottone, Grazia Lattanzi, Gianluca Ciccotti, Giovanni Elber, Ron |
author_facet |
Cottone, Grazia Lattanzi, Gianluca Ciccotti, Giovanni Elber, Ron |
author_sort |
Cottone, Grazia |
title |
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
title_short |
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
title_full |
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
title_fullStr |
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
title_full_unstemmed |
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State |
title_sort |
multiphoton absorption of myoglobin nitric-oxide complex: relaxation by d-nemd of a stationary state |
publishDate |
2012 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090 http://www.ncbi.nlm.nih.gov/pubmed/22356468 https://doi.org/10.1021/jp212148x |
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Sperm whale |
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Sperm whale |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090 http://www.ncbi.nlm.nih.gov/pubmed/22356468 http://dx.doi.org/10.1021/jp212148x |
op_doi |
https://doi.org/10.1021/jp212148x |
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The Journal of Physical Chemistry B |
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116 |
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10 |
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3397 |
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3410 |
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1766208713619668992 |