Theoretical and Experimental Investigatrion of Small Ligand Migration in Truncated Hemoglobin of Thermobifida Fusca

BUSTAMANTE, JUAN PABLO; ABBRUZZETTI, STEFANIA; VIAPPIANI, CRISTIANO; ESTRIN, DARÍO

Conferencia; X-Meeting - 7th International Conference of the Brazilian Association for Bioinformatics and Computational Biology and 3rd International Conference of the IberoAmerican Society for Bioinformatics; 2011

Truncated hemoglobins (trHb) are a subfamily that belongs to the globins family of heme proteins. They are widely distributed among bacteria, unicellular eukaryotes and plants and although they can be phylogenetically classified in three distinct groups, named N, O and P, all structures determined so far show the same typical structural fold consisting of a two-over-two small and compact helical structure, with the heme group totally buried inside it. One of the most interesting features revealed by the structures is the presence of a tunnels system that connects solvent with the heme active site, where small ligands bind to the iron. Different computational methods have been developed to study these processes which can be roughly divided in two strategies: those costly methods in which the ligand is treated explicitly during the simulations where the free energy landscape of the process is computed; and those faster methods that use prior computed Molecular Dynamics simulation without the ligand, and incorporate it afterwards, called implicit ligand sampling (ILS) methods. ILS free energy calculations of ligand migration process in Thermobifida fusca trHb (Tf-trHbO) were performed and we elucidate just one tunnel associated with a cavities system through small ligands can enter and bind to the iron heme group. Based on experimental flash photolysis results, a kinetic model was proposed assuming the presence in the protein of two docking sites, one located close to the iron, and other further away. However, this model was not able to reproduce completely well the experimental data. This prompted us to perform classical Molecular Dynamics (MD) simulations to explore the protein cavity system. We found an additional conformation, due to a torsion of TyrCD1. Taking into account this additional conformation, we have been able to explain nicely the experimental results.