Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin
We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon...
Published in: | Biophysical Journal |
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2004
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Online Access: | http://hdl.handle.net/11573/362116 https://doi.org/10.1529/biophysj.103.037432 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000222035200045&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-2942655520&partnerID=65&md5=c043a3f3583930b14086ac0ea4bfefda |
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ftunivromairis:oai:iris.uniroma1.it:11573/362116 2024-04-14T08:20:07+00:00 Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin C. BOSSA D. ROCCATANO A. AMADEI ANSELMI, MASSIMILIANO VALLONE, Beatrice BRUNORI, Maurizio DI NOLA, Alfredo C., Bossa Anselmi, Massimiliano D., Roccatano A., Amadei Vallone, Beatrice Brunori, Maurizio DI NOLA, Alfredo 2004 http://hdl.handle.net/11573/362116 https://doi.org/10.1529/biophysj.103.037432 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000222035200045&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-2942655520&partnerID=65&md5=c043a3f3583930b14086ac0ea4bfefda eng eng info:eu-repo/semantics/altIdentifier/pmid/15189882 info:eu-repo/semantics/altIdentifier/wos/WOS:000222035200045 volume:86 firstpage:3855 lastpage:3862 numberofpages:8 journal:BIOPHYSICAL JOURNAL http://hdl.handle.net/11573/362116 doi:10.1529/biophysj.103.037432 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-2942655520 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000222035200045&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-2942655520&partnerID=65&md5=c043a3f3583930b14086ac0ea4bfefda MYOGLOBIN MOLECULAR DYNAMICS SIMULATIONS info:eu-repo/semantics/article 2004 ftunivromairis https://doi.org/10.1529/biophysj.103.037432 2024-03-21T19:30:04Z We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins. Article in Journal/Newspaper Sperm whale Sapienza Università di Roma: CINECA IRIS Biophysical Journal 86 6 3855 3862 |
institution |
Open Polar |
collection |
Sapienza Università di Roma: CINECA IRIS |
op_collection_id |
ftunivromairis |
language |
English |
topic |
MYOGLOBIN MOLECULAR DYNAMICS SIMULATIONS |
spellingShingle |
MYOGLOBIN MOLECULAR DYNAMICS SIMULATIONS C. BOSSA D. ROCCATANO A. AMADEI ANSELMI, MASSIMILIANO VALLONE, Beatrice BRUNORI, Maurizio DI NOLA, Alfredo Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
topic_facet |
MYOGLOBIN MOLECULAR DYNAMICS SIMULATIONS |
description |
We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins. |
author2 |
C., Bossa Anselmi, Massimiliano D., Roccatano A., Amadei Vallone, Beatrice Brunori, Maurizio DI NOLA, Alfredo |
format |
Article in Journal/Newspaper |
author |
C. BOSSA D. ROCCATANO A. AMADEI ANSELMI, MASSIMILIANO VALLONE, Beatrice BRUNORI, Maurizio DI NOLA, Alfredo |
author_facet |
C. BOSSA D. ROCCATANO A. AMADEI ANSELMI, MASSIMILIANO VALLONE, Beatrice BRUNORI, Maurizio DI NOLA, Alfredo |
author_sort |
C. BOSSA |
title |
Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
title_short |
Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
title_full |
Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
title_fullStr |
Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
title_full_unstemmed |
Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin |
title_sort |
extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin |
publishDate |
2004 |
url |
http://hdl.handle.net/11573/362116 https://doi.org/10.1529/biophysj.103.037432 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000222035200045&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-2942655520&partnerID=65&md5=c043a3f3583930b14086ac0ea4bfefda |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/15189882 info:eu-repo/semantics/altIdentifier/wos/WOS:000222035200045 volume:86 firstpage:3855 lastpage:3862 numberofpages:8 journal:BIOPHYSICAL JOURNAL http://hdl.handle.net/11573/362116 doi:10.1529/biophysj.103.037432 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-2942655520 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000222035200045&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-2942655520&partnerID=65&md5=c043a3f3583930b14086ac0ea4bfefda |
op_doi |
https://doi.org/10.1529/biophysj.103.037432 |
container_title |
Biophysical Journal |
container_volume |
86 |
container_issue |
6 |
container_start_page |
3855 |
op_container_end_page |
3862 |
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1796298317236273152 |