Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their wea...
Published in: | The Journal of Physical Chemistry B |
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Online Access: | http://hdl.handle.net/11381/2851794 https://doi.org/10.1021/acs.jpcb.8b07682 http://pubs.acs.org/journal/jpcbfk |
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ftunivparmairis:oai:air.unipr.it:11381/2851794 2024-04-21T07:49:12+00:00 Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. 2018 http://hdl.handle.net/11381/2851794 https://doi.org/10.1021/acs.jpcb.8b07682 http://pubs.acs.org/journal/jpcbfk eng eng info:eu-repo/semantics/altIdentifier/wos/WOS:000453488100068 volume:122 firstpage:11649 lastpage:11661 numberofpages:13 journal:JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL http://hdl.handle.net/11381/2851794 doi:10.1021/acs.jpcb.8b07682 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85054676790 http://pubs.acs.org/journal/jpcbfk Physical and Theoretical Chemistry Surfaces Coatings and Film Materials Chemistry2506 Metals and Alloys info:eu-repo/semantics/article 2018 ftunivparmairis https://doi.org/10.1021/acs.jpcb.8b07682 2024-03-28T01:22:27Z Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation. Article in Journal/Newspaper Antarc* Antarctic Archivio della ricerca dell'Università di Parma (CINECA IRIS) The Journal of Physical Chemistry B 122 49 11649 11661 |
institution |
Open Polar |
collection |
Archivio della ricerca dell'Università di Parma (CINECA IRIS) |
op_collection_id |
ftunivparmairis |
language |
English |
topic |
Physical and Theoretical Chemistry Surfaces Coatings and Film Materials Chemistry2506 Metals and Alloys |
spellingShingle |
Physical and Theoretical Chemistry Surfaces Coatings and Film Materials Chemistry2506 Metals and Alloys Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
topic_facet |
Physical and Theoretical Chemistry Surfaces Coatings and Film Materials Chemistry2506 Metals and Alloys |
description |
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation. |
author2 |
Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. |
format |
Article in Journal/Newspaper |
author |
Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. |
author_facet |
Boubeta, F. M. Boechi, L. Estrin, D Patrizi, B Di Donato, M. Iagatti, A. Giordano, D. Verde, C. Bruno, S. Abbruzzetti, S. Viappiani, C. |
author_sort |
Boubeta, F. M. |
title |
Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
title_short |
Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
title_full |
Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
title_fullStr |
Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
title_full_unstemmed |
Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
title_sort |
cold-adaptation signatures in the ligand rebinding kinetics to the truncated hemoglobin of the antarctic bacterium pseudoalteromonas haloplanktis tac125 |
publishDate |
2018 |
url |
http://hdl.handle.net/11381/2851794 https://doi.org/10.1021/acs.jpcb.8b07682 http://pubs.acs.org/journal/jpcbfk |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
info:eu-repo/semantics/altIdentifier/wos/WOS:000453488100068 volume:122 firstpage:11649 lastpage:11661 numberofpages:13 journal:JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL http://hdl.handle.net/11381/2851794 doi:10.1021/acs.jpcb.8b07682 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85054676790 http://pubs.acs.org/journal/jpcbfk |
op_doi |
https://doi.org/10.1021/acs.jpcb.8b07682 |
container_title |
The Journal of Physical Chemistry B |
container_volume |
122 |
container_issue |
49 |
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11649 |
op_container_end_page |
11661 |
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