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

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

PROTEIN SCIENCE

JOHN WILEY & SONS INC

Lugar: New York; Año: 2024 vol. 33

0961-8368

Due to the low temperature, the Antarctic marine environment is challengingfor protein functioning. Cold-adapted organisms have evolved proteinsendowed with higher flexibility and lower stability in comparison to their ther-mophilic homologs, resulting in enhanced reaction rates at low temperatures.The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125)genome is one of the few examples of coexistence of multiple hemoglobingenes 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 ligandbinding kinetics and their interrelationship with the dynamical properties ofglobin Ph-2/2HbO-2217 by combining experimental and computationalapproaches and implementing a new computational method to retrieve infor-mation from molecular dynamic trajectories. We show that our approachallows us to identify docking sites within the protein matrix that are potentiallyable to transiently accommodate ligands and migration pathways connectingthem. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy bar-rier, while inner cavities play only a minor role in modulating rebindingkinetics.