Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities
The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/clos...
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Biophysical Society
2005
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Online Access: | http://hdl.handle.net/2108/35255 https://doi.org/10.1529/biophysj.104.055020 |
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ftunivromatorver:oai:art.torvergata.it:2108/35255 2024-02-27T08:45:41+00:00 Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities Bossa, C. Daidone, I. Anselmi, M. Vallone, B. Brunori, M. Nola, AD AMADEI, ANDREA Bossa, C Amadei, A Daidone, I Anselmi, M Vallone, B Brunori, M Nola, A 2005 http://hdl.handle.net/2108/35255 https://doi.org/10.1529/biophysj.104.055020 eng eng Biophysical Society country:US place:BETHESDA info:eu-repo/semantics/altIdentifier/pmid/15849248 info:eu-repo/semantics/altIdentifier/wos/WOS:000230114500049 volume:89 issue:1 firstpage:465 lastpage:474 journal:BIOPHYSICAL JOURNAL http://hdl.handle.net/2108/35255 doi:10.1529/biophysj.104.055020 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-23244457434 carbon monoxide deoxymyoglobin glutamine heme histidine iron mutant protein myoglobin pyrrole derivative solvent tyrosine unclassified drug water YQR deoxymyoglobin article dissociation hydrogen bond molecular dynamic mutation nonhuman photodissociation photoreactivity protein structure simulation sperm whale whale Animal Biophysic Crystallography X-Ray Ligand Light Models Molecular Statistical Molecular Conformation Oxygen Photolysi Protein Binding Protein Conformation Secondary info:eu-repo/semantics/article 2005 ftunivromatorver https://doi.org/10.1529/biophysj.104.055020 2024-01-31T00:01:41Z The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and the presence of the photolyzed CO in the proximity of the passage; here we show that in wild-type deoxy myoglobin, opening is almost random. In wild-type deoxy myoglobin, the passage between the distal pocket and the solvent is strictly correlated to the presence/absence of a water molecule that simultaneously interacts with the distal histidine side chain and the heme iron; conversely, in the photodissociated myoglobin, the connection with the bulk solvent is always open when CO is in the vicinity of the A pyrrole ring. In YQR deoxy myoglobin, the mutated Gln(E7)64 is stably H-bonded with the mutated Tyr(B10)29. The essential dynamics analysis unveils a different behavior for the three systems. The motion amplitude is progressively restricted in going from wild-type to YQR deoxy myoglobin and to wild-type myoglobin photoproduct. In all cases, the principal motions involve mainly the same regions, but their directions are different. Analysis of the dynamics of the preexisting cavities indicates large fluctuations and frequent connections with the solvent, in agreement with the earlier hypothesis that some of the ligand may escape from the protein through these pathways. Article in Journal/Newspaper Sperm whale Universitá degli Studi di Roma "Tor Vergata": ART - Archivio Istituzionale della Ricerca Biophysical Journal 89 1 465 474 |
institution |
Open Polar |
collection |
Universitá degli Studi di Roma "Tor Vergata": ART - Archivio Istituzionale della Ricerca |
op_collection_id |
ftunivromatorver |
language |
English |
topic |
carbon monoxide deoxymyoglobin glutamine heme histidine iron mutant protein myoglobin pyrrole derivative solvent tyrosine unclassified drug water YQR deoxymyoglobin article dissociation hydrogen bond molecular dynamic mutation nonhuman photodissociation photoreactivity protein structure simulation sperm whale whale Animal Biophysic Crystallography X-Ray Ligand Light Models Molecular Statistical Molecular Conformation Oxygen Photolysi Protein Binding Protein Conformation Secondary |
spellingShingle |
carbon monoxide deoxymyoglobin glutamine heme histidine iron mutant protein myoglobin pyrrole derivative solvent tyrosine unclassified drug water YQR deoxymyoglobin article dissociation hydrogen bond molecular dynamic mutation nonhuman photodissociation photoreactivity protein structure simulation sperm whale whale Animal Biophysic Crystallography X-Ray Ligand Light Models Molecular Statistical Molecular Conformation Oxygen Photolysi Protein Binding Protein Conformation Secondary Bossa, C. Daidone, I. Anselmi, M. Vallone, B. Brunori, M. Nola, AD AMADEI, ANDREA Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
topic_facet |
carbon monoxide deoxymyoglobin glutamine heme histidine iron mutant protein myoglobin pyrrole derivative solvent tyrosine unclassified drug water YQR deoxymyoglobin article dissociation hydrogen bond molecular dynamic mutation nonhuman photodissociation photoreactivity protein structure simulation sperm whale whale Animal Biophysic Crystallography X-Ray Ligand Light Models Molecular Statistical Molecular Conformation Oxygen Photolysi Protein Binding Protein Conformation Secondary |
description |
The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and the presence of the photolyzed CO in the proximity of the passage; here we show that in wild-type deoxy myoglobin, opening is almost random. In wild-type deoxy myoglobin, the passage between the distal pocket and the solvent is strictly correlated to the presence/absence of a water molecule that simultaneously interacts with the distal histidine side chain and the heme iron; conversely, in the photodissociated myoglobin, the connection with the bulk solvent is always open when CO is in the vicinity of the A pyrrole ring. In YQR deoxy myoglobin, the mutated Gln(E7)64 is stably H-bonded with the mutated Tyr(B10)29. The essential dynamics analysis unveils a different behavior for the three systems. The motion amplitude is progressively restricted in going from wild-type to YQR deoxy myoglobin and to wild-type myoglobin photoproduct. In all cases, the principal motions involve mainly the same regions, but their directions are different. Analysis of the dynamics of the preexisting cavities indicates large fluctuations and frequent connections with the solvent, in agreement with the earlier hypothesis that some of the ligand may escape from the protein through these pathways. |
author2 |
Bossa, C Amadei, A Daidone, I Anselmi, M Vallone, B Brunori, M Nola, A |
format |
Article in Journal/Newspaper |
author |
Bossa, C. Daidone, I. Anselmi, M. Vallone, B. Brunori, M. Nola, AD AMADEI, ANDREA |
author_facet |
Bossa, C. Daidone, I. Anselmi, M. Vallone, B. Brunori, M. Nola, AD AMADEI, ANDREA |
author_sort |
Bossa, C. |
title |
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
title_short |
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
title_full |
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
title_fullStr |
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
title_full_unstemmed |
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities |
title_sort |
molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped co on the structure and dynamics of cavities |
publisher |
Biophysical Society |
publishDate |
2005 |
url |
http://hdl.handle.net/2108/35255 https://doi.org/10.1529/biophysj.104.055020 |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/15849248 info:eu-repo/semantics/altIdentifier/wos/WOS:000230114500049 volume:89 issue:1 firstpage:465 lastpage:474 journal:BIOPHYSICAL JOURNAL http://hdl.handle.net/2108/35255 doi:10.1529/biophysj.104.055020 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-23244457434 |
op_doi |
https://doi.org/10.1529/biophysj.104.055020 |
container_title |
Biophysical Journal |
container_volume |
89 |
container_issue |
1 |
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465 |
op_container_end_page |
474 |
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1792054979208413184 |