The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin
We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-Angstrom resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to p...
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NATL ACAD SCIENCES
2000
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Online Access: | http://hdl.handle.net/11573/249459 https://doi.org/10.1073/pnas.040459697 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000085633200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-0034091637&partnerID=65&md5=2c0f463be11abf3b3987c2ce9eba5f2c |
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ftunivromairis:oai:iris.uniroma1.it:11573/249459 2024-04-21T08:12:21+00:00 The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin BRUNORI, Maurizio VALLONE, Beatrice CUTRUZZOLA', Francesca TRAVAGLINI ALLOCATELLI, Carlo J. Berendzen K. Chu R. M. Sweet I. Schlichting Brunori, Maurizio Vallone, Beatrice Cutruzzola', Francesca TRAVAGLINI ALLOCATELLI, Carlo J., Berendzen K., Chu R. M., Sweet I., Schlichting 2000 STAMPA http://hdl.handle.net/11573/249459 https://doi.org/10.1073/pnas.040459697 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000085633200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-0034091637&partnerID=65&md5=2c0f463be11abf3b3987c2ce9eba5f2c eng eng NATL ACAD SCIENCES info:eu-repo/semantics/altIdentifier/pmid/10681426 info:eu-repo/semantics/altIdentifier/wos/WOS:000085633200020 volume:97 issue:5 firstpage:2058 lastpage:2063 numberofpages:6 journal:PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA http://hdl.handle.net/11573/249459 doi:10.1073/pnas.040459697 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-0034091637 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000085633200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-0034091637&partnerID=65&md5=2c0f463be11abf3b3987c2ce9eba5f2c cryo-crystallography function heme protein ligand binding ligand-binding molecular-dynamic picosecond sperm whale myoglobin info:eu-repo/semantics/article 2000 ftunivromairis https://doi.org/10.1073/pnas.040459697 2024-03-28T01:58:09Z We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-Angstrom resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 Angstrom from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F,, Jr., Kuntz, I. D. & Petsko, G. A, (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat Struct. Biol, 1, 701-705] and room temperature [Srajer et al, (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein. Article in Journal/Newspaper Sperm whale Sapienza Università di Roma: CINECA IRIS Proceedings of the National Academy of Sciences 97 5 2058 2063 |
institution |
Open Polar |
collection |
Sapienza Università di Roma: CINECA IRIS |
op_collection_id |
ftunivromairis |
language |
English |
topic |
cryo-crystallography function heme protein ligand binding ligand-binding molecular-dynamic picosecond sperm whale myoglobin |
spellingShingle |
cryo-crystallography function heme protein ligand binding ligand-binding molecular-dynamic picosecond sperm whale myoglobin BRUNORI, Maurizio VALLONE, Beatrice CUTRUZZOLA', Francesca TRAVAGLINI ALLOCATELLI, Carlo J. Berendzen K. Chu R. M. Sweet I. Schlichting The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
topic_facet |
cryo-crystallography function heme protein ligand binding ligand-binding molecular-dynamic picosecond sperm whale myoglobin |
description |
We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-Angstrom resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 Angstrom from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F,, Jr., Kuntz, I. D. & Petsko, G. A, (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat Struct. Biol, 1, 701-705] and room temperature [Srajer et al, (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein. |
author2 |
Brunori, Maurizio Vallone, Beatrice Cutruzzola', Francesca TRAVAGLINI ALLOCATELLI, Carlo J., Berendzen K., Chu R. M., Sweet I., Schlichting |
format |
Article in Journal/Newspaper |
author |
BRUNORI, Maurizio VALLONE, Beatrice CUTRUZZOLA', Francesca TRAVAGLINI ALLOCATELLI, Carlo J. Berendzen K. Chu R. M. Sweet I. Schlichting |
author_facet |
BRUNORI, Maurizio VALLONE, Beatrice CUTRUZZOLA', Francesca TRAVAGLINI ALLOCATELLI, Carlo J. Berendzen K. Chu R. M. Sweet I. Schlichting |
author_sort |
BRUNORI, Maurizio |
title |
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
title_short |
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
title_full |
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
title_fullStr |
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
title_full_unstemmed |
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin |
title_sort |
role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin |
publisher |
NATL ACAD SCIENCES |
publishDate |
2000 |
url |
http://hdl.handle.net/11573/249459 https://doi.org/10.1073/pnas.040459697 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000085633200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-0034091637&partnerID=65&md5=2c0f463be11abf3b3987c2ce9eba5f2c |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/10681426 info:eu-repo/semantics/altIdentifier/wos/WOS:000085633200020 volume:97 issue:5 firstpage:2058 lastpage:2063 numberofpages:6 journal:PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA http://hdl.handle.net/11573/249459 doi:10.1073/pnas.040459697 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-0034091637 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000085633200020&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-0034091637&partnerID=65&md5=2c0f463be11abf3b3987c2ce9eba5f2c |
op_doi |
https://doi.org/10.1073/pnas.040459697 |
container_title |
Proceedings of the National Academy of Sciences |
container_volume |
97 |
container_issue |
5 |
container_start_page |
2058 |
op_container_end_page |
2063 |
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1796932370975162368 |