Free-energy profile for CO binding to separated chains of human and Trematomus newnesi hemoglobin: insights from molecular dynamics simulations and perturbed matrix method.
The free-energy profile and the classical kinetics of the heme carbomonoxide binding-unbinding reaction have been derived by means of a theoretical method for the separated chains of human (HbA) and Trematomus newnesi major component (HbTn) hemoglobin. The results reveal that the alpha- and beta-chains of HbA have similar values of kinetic constants for the dissociation of the Fe-CO state, in agreement with experimental data. Comparisons of the present findings with the data obtained for the alpha- and beta-chains of HbTn and with theoretical and experimental results previously collected on myoglobin provide a detailed picture of this important biochemical reaction in globins. The sequence and structural differences among the globins are not reflected in meaningful variations in the rate of CO dissociation. These data support the conclusion that the differences observed for the reaction with CO of globins, if any, involve the rate of ligand migration to the solvent, rather than the Fe-CO complex formation/rupture. Furthermore, our results agree with the recent discovery that globin family proteins exhibit common dynamics, thus confirming the observation that the dynamic properties of proteins are strongly related to their overall architecture.
Merlino
Antonello
A
Dipartimento di Chimica, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy. antonello.merlino@unina.it
Vergara
Alessandro
A
Sica
Filomena
F
Aschi
Massimiliano
M
Amadei
Andrea
A
Di Nola
Alfredo
A
Mazzarella
Lelio
L
D000818:Animals; D002248:Carbon Monoxide / Q000737:chemistry*; D006454:Hemoglobins / Q000737:chemistry*; D006801:Humans; D007501:Iron / Q000737:chemistry; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010473:Perciformes / Q000378:metabolism*; D011485:Protein Binding; D013816:Thermodynamics
D006454:Hemoglobins; D002248:Carbon Monoxide; D007501:Iron