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 |
---|---|
Main Authors: | , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
American Chemical Society
|
Subjects: | |
Online Access: | http://hdl.handle.net/11336/89445 |
id |
ftconicet:oai:ri.conicet.gov.ar:11336/89445 |
---|---|
record_format |
openpolar |
spelling |
ftconicet:oai:ri.conicet.gov.ar:11336/89445 2023-10-09T21:47:15+02:00 Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 Boubeta, Fernando Martín Boechi, Leonardo Estrin, Dario Ariel Patrizi, Barbara Di Donato, Mariangela Iagatti, Alessandro Giordano, Daniela Verde, Cinzia Bruno, Stefano Abbruzzetti, Stefania Viappiani, Cristiano application/pdf http://hdl.handle.net/11336/89445 eng eng American Chemical Society info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jpcb.8b07682 info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jpcb.8b07682 http://hdl.handle.net/11336/89445 Boubeta, Fernando Martín; Boechi, Leonardo; Estrin, Dario Ariel; Patrizi, Barbara; Di Donato, Mariangela; et al.; Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125; American Chemical Society; Journal of Physical Chemistry B; 122; 49; 12-2018; 11649-11661 1520-6106 CONICET Digital CONICET info:eu-repo/semantics/restrictedAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ COLD ADAPTATION LIGAND REBINDING KINETICS P. HALOPLANKTIS MOLECULAR DYNAMICS https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion ftconicet https://doi.org/10.1021/acs.jpcb.8b07682 2023-09-24T20:26:54Z 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. Fil: Boubeta, Fernando Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Boechi, Leonardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Cálculo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Estrin, Dario Ariel. Consejo Nacional de ... Article in Journal/Newspaper Antarc* Antarctic CONICET Digital (Consejo Nacional de Investigaciones Científicas y Técnicas) Antarctic The Antarctic Argentina The Journal of Physical Chemistry B 122 49 11649 11661 |
institution |
Open Polar |
collection |
CONICET Digital (Consejo Nacional de Investigaciones Científicas y Técnicas) |
op_collection_id |
ftconicet |
language |
English |
topic |
COLD ADAPTATION LIGAND REBINDING KINETICS P. HALOPLANKTIS MOLECULAR DYNAMICS https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 |
spellingShingle |
COLD ADAPTATION LIGAND REBINDING KINETICS P. HALOPLANKTIS MOLECULAR DYNAMICS https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 Boubeta, Fernando Martín Boechi, Leonardo Estrin, Dario Ariel Patrizi, Barbara Di Donato, Mariangela Iagatti, Alessandro Giordano, Daniela Verde, Cinzia Bruno, Stefano Abbruzzetti, Stefania Viappiani, Cristiano Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125 |
topic_facet |
COLD ADAPTATION LIGAND REBINDING KINETICS P. HALOPLANKTIS MOLECULAR DYNAMICS https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 |
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. Fil: Boubeta, Fernando Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Boechi, Leonardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Cálculo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Estrin, Dario Ariel. Consejo Nacional de ... |
format |
Article in Journal/Newspaper |
author |
Boubeta, Fernando Martín Boechi, Leonardo Estrin, Dario Ariel Patrizi, Barbara Di Donato, Mariangela Iagatti, Alessandro Giordano, Daniela Verde, Cinzia Bruno, Stefano Abbruzzetti, Stefania Viappiani, Cristiano |
author_facet |
Boubeta, Fernando Martín Boechi, Leonardo Estrin, Dario Ariel Patrizi, Barbara Di Donato, Mariangela Iagatti, Alessandro Giordano, Daniela Verde, Cinzia Bruno, Stefano Abbruzzetti, Stefania Viappiani, Cristiano |
author_sort |
Boubeta, Fernando Martín |
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 |
publisher |
American Chemical Society |
url |
http://hdl.handle.net/11336/89445 |
geographic |
Antarctic The Antarctic Argentina |
geographic_facet |
Antarctic The Antarctic Argentina |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jpcb.8b07682 info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jpcb.8b07682 http://hdl.handle.net/11336/89445 Boubeta, Fernando Martín; Boechi, Leonardo; Estrin, Dario Ariel; Patrizi, Barbara; Di Donato, Mariangela; et al.; Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125; American Chemical Society; Journal of Physical Chemistry B; 122; 49; 12-2018; 11649-11661 1520-6106 CONICET Digital CONICET |
op_rights |
info:eu-repo/semantics/restrictedAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
op_doi |
https://doi.org/10.1021/acs.jpcb.8b07682 |
container_title |
The Journal of Physical Chemistry B |
container_volume |
122 |
container_issue |
49 |
container_start_page |
11649 |
op_container_end_page |
11661 |
_version_ |
1779310244116037632 |