Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125

• Main Authors: 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: Journal/Newspaper
• Language: unknown
• Subjects: 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; Antarc*; Antarctic
• Online Access: https://hdl.handle.net/20.500.12110/paper_15206106_v122_n49_p11649_Boubeta

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.