Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125

Abstract Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold‐adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low tem...

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Bibliographic Details
Published in:Protein Science
Main Authors: de Armiño, Diego Javier Alonso, Di Lella, Santiago, Montepietra, Daniele, Delcanale, Pietro, Bruno, Stefano, Giordano, Daniela, Verde, Cinzia, Estrin, Dario A., Viappiani, Cristiano, Abbruzzetti, Stefania
Other Authors: Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Fondazione Cassa di Risparmio di Piacenza e Vigevano
Format: Article in Journal/Newspaper
Language:English
Published: Wiley 2024
Subjects:
Antarc*
Antarctic
Online Access:http://dx.doi.org/10.1002/pro.5064
https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.5064
Description
Summary:Abstract Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold‐adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 ( Ph TAC125) genome is one of the few examples of coexistence of multiple hemoglobin genes encoding, among others, two constitutively transcribed 2/2 hemoglobins (2/2Hbs), also named truncated Hbs (TrHbs), belonging to the Group II (or O), annotated as PSHAa0030 and PSHAa2217 . In this work, we describe the ligand binding kinetics and their interrelationship with the dynamical properties of globin Ph ‐2/2HbO‐2217 by combining experimental and computational approaches and implementing a new computational method to retrieve information from molecular dynamic trajectories. We show that our approach allows us to identify docking sites within the protein matrix that are potentially able to transiently accommodate ligands and migration pathways connecting them. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy barrier, while inner cavities play only a minor role in modulating rebinding kinetics.

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