Quantitative estimation of kinetic rates of ligand binding to heme proteins from molecular dynamics simulations

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

Simposio; 2nd protein biophysics at the end of the world; 2017

Free energy estimations have been used as tools toobtain kinetic information from different processes, using Eyring´sequation. Those calculations may have convergence issues and arestrongly dependent on the reaction coordinate choice.Ligand migration through channels in proteins canbe interpreted as a sequence of «jumps»of the ligand between discrete sites, which form a global?memoryless? process. The numerical simulation of each sitepopulation and the fitting of the siteof interest allows us to estimate a global rate, that can directlycompared to experimental data.Based on previous studies byBlumberger et al (PCCP,vol. 13, p. 7708, 2011),we intend to study O2 and NO migration in truncated hemoglobin-N(trHbN) of mycobacteriumtuberculosis (aNO-detoxifying enzyme that converts NO to nitrate). First,O2must reach the sixth coordination position of the Fe(II)-heme complexso that the NO can befinally oxidized. Inthis protein, two channels toreach the active site havebeen described: the long channel and the short one.It is our aim toestimate uptake andrelease rate constants ofO2 and NOand determine if the conformation of side chains located inside thechannels influence the global rate constant for those processes. Itis of particular interest to analyze the effect of PheE15, which isproposed to act as a «gate»controlling ligandmigration through the long channel.We will present resultsfor oxy-trHbN NO uptake, whichshow good agreementwith experimental data,and will discuss perspectives regarding this kind of methodologies.