Molecular dynamics analysis of a second phosphate site in the hemoglobins of the seabird, south polar skua. Is there a site-site migratory mechanism along the central cavity?

Hemoglobin function is modulated by several non-heme ligands; among these e ffectors, organic phosphates generally bind to heterotropic sites with a on e-to-one stoichiometry. The phosphate binding site of human hemoglobin is l ocated at the interface between the two beta chains. An additional binding site for polyanions has been studied at the molecular level (Tamburrini, M. , A. Riccio, M. Romano, B. Giardina, and G. di Prisco. 2000. Eur. J. Bioche m. 267:6089-6098) in the hemoglobins of the south polar skua (Catharacta ma ccormicki). It is formed by a cluster of six positive charges of both alpha chains (Val-1, Lys-99, Arg-141); the two Lys-99 alpha have an essential ro le in the site structure. The present investigation, carried out on skua de oxyhemoglobins by using a molecular dynamics approach, confirms the structu ral feasibility of the additional site, possibly having the role of an entr y-leaving site, and leads to the proposal of a novel migration pathway for phosphate along the central cavity of hemoglobin from one binding site to t he other, occurring according to the hypothesis of a site-site migratory me chanism, which may assign a functional role to the central cavity. The role of Lys-99 alpha was further confirmed by molecular dynamics experiments on the mutant Lys-99 alpha --> Ala in which, at the end of the simulation, th e phosphate was external to the additional site.