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...

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Autores principales:	Boubeta, F.M., Boechi, L., Estrin, D., Patrizi, B., Di Donato, M., Iagatti, A., Giordano, D., Verde, C., Bruno, S., Abbruzzetti, S., Viappiani, C.
Formato:	JOUR
Materias:	Bacteria Hemoglobin Kinetics Ligands Molecular dynamics Molecules Reaction rates Antarctic bacteria Bound water molecules Geminate rebinding Ligand rebinding Molecular dynamics simulations Pseudoalteromonas haloplanktis Thermobifida fusca Truncated hemoglobins Proteins
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11649_Boubeta
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_15206106_v122_n49_p11649_Boubeta
record_format	dspace
spelling	todo:paper_15206106_v122_n49_p11649_Boubeta2023-10-03T16:20:33Z 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. Bacteria Hemoglobin Kinetics Ligands Molecular dynamics Molecules Reaction rates Antarctic bacteria Bound water molecules Geminate rebinding Ligand rebinding Molecular dynamics simulations Pseudoalteromonas haloplanktis Thermobifida fusca Truncated hemoglobins Proteins 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. © 2018 American Chemical Society. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11649_Boubeta
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Bacteria Hemoglobin Kinetics Ligands Molecular dynamics Molecules Reaction rates Antarctic bacteria Bound water molecules Geminate rebinding Ligand rebinding Molecular dynamics simulations Pseudoalteromonas haloplanktis Thermobifida fusca Truncated hemoglobins Proteins
spellingShingle	Bacteria Hemoglobin Kinetics Ligands Molecular dynamics Molecules Reaction rates Antarctic bacteria Bound water molecules Geminate rebinding Ligand rebinding Molecular dynamics simulations Pseudoalteromonas haloplanktis Thermobifida fusca Truncated hemoglobins Proteins 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	Bacteria Hemoglobin Kinetics Ligands Molecular dynamics Molecules Reaction rates Antarctic bacteria Bound water molecules Geminate rebinding Ligand rebinding Molecular dynamics simulations Pseudoalteromonas haloplanktis Thermobifida fusca Truncated hemoglobins Proteins
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. © 2018 American Chemical Society.
format	JOUR
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
url	http://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11649_Boubeta
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Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125

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