Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N

Abstract

In heme proteins, the efficient transport of ligands such as NO or O2 to the binding site is achieved via ligand migration networks. A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins. For this, Xe migration in truncated hemoglobin N (trHbN) of Mycobacterium Tuberculosis was studied using molecular dynamics simulations. Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol). Depending on the pocket from where Xe enters a particular transition, the conformation of the side chains lining the transition region differs which highlights the coupling between ligand and protein degrees of freedom. Furthermore, comparison of transition probabilities shows that Xe migration in trHbN is a non-Markovian process. Memory effects arise due to protein rearrangements and coupled dynamics as Xe moves through it.

Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations

“…As stated before, this lag time indicates that the count matrix construction will be performed comparing every frame of the MD trajectory with the frame corresponding to 40 ps after. This lag time is in the same order of magnitude with the characteristic timescale of intra site relaxation presented in Diamantis et al, [45] which is of 10 to 20 ps for the migration of Xe in Tr-HbN.…”

“…Thus, in the context of the simulations performed here in order to obtain the transition matrix and the associated rate constants, the sampling of the PheE15 conformations in a totally unbiased scheme would be poor and highly dependent on the initial conformation. It is important to remark, however, that the role of PheE15 sidechain has also been studied and described by Diamantis et al., where certain Markovian characteristic loss was observed in Xe migration when performing MD simulations without restraining this aminoacid conformation. Thus, although the computational strategy adopted here presents the limitation of being unable to evaluate directly the effect of the PheE15 conformational change on ligand migration, it allows estimating the kinetic rates for the two conformational states.…”

Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase

“…With the limited sampling presented in this work, although the location and physiological function of the major ligand docking sites can be predicted reliably, their equilibrium populations and accurate kinetics of the ligand migration require extensive sampling as well as in-depth analysis of the dynamical coupling of the motions of the enzyme and ligand. 73 While the comparison of the product ratios between the experiment 16 and the present simulations is not quantitatively accurate, the trends observed in the experiment are clearly reproduced by the present simulations. For example, the predominance of 8R product in wt-lox observed in the experiment is also seen in the simulations, although the simulations appear to overestimate the 12-products considerably, whereas the experimental results found 98% of the product as 8R.…”

“…It is noteworthy that the accurate determination of the equilibrium population of different pockets is a challenging task and requires a very large number of simulations for an extensive sampling of every possible ligand migration pathway. With the limited sampling presented in this work, although the location and physiological function of the major ligand docking sites can be predicted reliably, their equilibrium populations and accurate kinetics of the ligand migration require extensive sampling as well as in-depth analysis of the dynamical coupling of the motions of the enzyme and ligand …”