Quantitative estimation of kinetic rates in heme proteins from molecular dynamics simulations

MAURO BRINGAS; AXEL BIDON-CHANAL; DARIO A. ESTRIN; F. JAVIER LUQUE; LUCIANA CAPECE

Rio de Janeiro

Congreso; V Latin American Protein Society Meeting; 2016

Kineticdifferences between processes in proteins have been studied bycomparing activation free energies along a reaction coordinate, andthe use of Eyring equation. The choice of a coordinate and theconvergence of the free energy calculations are issues that difficultand limit the applicability of these biased methodologies.Migrationof ligands in proteins, among other processes, can be interpreted interms of memoryless Markovian phenomena, which can be described as aseries of independent sites that conform the nodes of a network. Thecharacterisation of these «jumps» between sites enables us tonumerically simulatethepopulation of each site as a function of time. Fitting an appropriatekinetic model to the population of the site of interest, a globalrate can be obtained and it can be compared to experimental data.Other powerful feature of this scheme is the possibility of analysingmigration of ligands through the possible pathways independently, byconsidering the sites of interest in the transition matrixconstruction.Ourcase of study is the truncated hemoglobin-N (trHbN) of mycobacteriumtuberculosis,a NO-detoxifying enzyme by oxidation to nitrate, which requires boththe migration of dioxygen and nitric oxide through the proteintowards the heme group. In this protein, two channels have beendescribed: the long and the short channel.Initially, O2must reach the sixth coordination position of the Fe(II)-heme complexso that the reaction can take place. Usingas starting point the work by Burmerger et al, we are currentlystudying oxygen migration through non-ligated trHbNand NO migration through oxy-trHbN.It is known thatoxygen binding can promote conformational changes and, therefore, thevariation of the characteristics of existent pathways. Preliminaryresults for oxy-trHbNNO uptake show good agreement with experimental data, validatingthe use of this methodology for its application in truncatedhemoglobins.p { margin-bottom: 0.1in; line-height: 120%; }