Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins

Abstract

The ubiquitous heme proteins perform a wide variety of tasks that rely on the subtle regulation of their affinity for small ligands like O2, CO, and NO. Ligand affinity is characterized by kinetic association and dissociation rate constants, that partially depend on ligand migration between the solvent and active site, mediated by the presence of internal cavities or tunnels. 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, and 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. To compare both approaches performance and to provide a combined protocol to study ligand migration in heme proteins, we performed ILS and multiple steered molecular dynamics (MSMD) free energy calculations of the ligand migration process in three representative and well theoretically and experimentally studied cases that cover a wide range of complex situations presenting a challenging benchmark for the aim of the present work. Our results show that ILS provides a good description of the tunnel topology and a reasonable approximation to the free energy landscape, while MSMD provides more accurate and detailed free energy profile description of each tunnel. Based on these results, a combined strategy is presented for the study of internal ligand migration in heme proteins.

The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin

“…The methodology relies on the fact that small ligands interact weakly with the protein matrix and therefore the interaction can be computed for protein structures that were obtained without the presence of the ligand in previous MD simulations. By performing the MD simulation of the protein without the ligand and treating its presence as a weak perturbation added afterwards, sampling of the ligand can be performed on the whole protein matrix simultaneously, from just one sufficiently long plain MD simulation [45]. In the present work ILS free energy profile is computed for the Oxy_HMP and Deoxy_HMP MD simulations, using 5000 snapshots and grid spacing of 0.5 Å.…”

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

“…This method has been thoroughly tested in heme proteins [70]. ILS calculations were performed in a rectangular grid (0.5 A resolution) that includes the whole simulation box (i.e.…”

“…Calculations were performed on 5000 frames taken from the last 180 ns of simulation time. The values for grid size, resolution and frame numbers have been thoroughly tested in a previous study [70]. the framework of the SCAR programme 'Antarctic Thresholds -Ecosystem Resilience and Adaptation' (AnT-ERA).…”

Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories

“…Using such work samplings in any of the currently available NEW theorems, inevitably results in systematic errors introduced into the calculated PMFs. Relations (8) and (9) can give safe limits for the value of k to be used in a given system, thereby avoiding the pathology just described. In any case, using peak-values (rather than averages) of the external work distributions in (2) results both in reduction of the bias, and considerable increase in the accuracy of the calculated PMFs.…”

“…For the HHC-36 peptide with a mass of 1.48 ku, and for simulations at T = 310 K, when a precision of 0.1Å is sought, (8) gives an upper limit of 24.7 kcal mol·Å limit of 61.6 kcal mol·Å 2 . As these limits give no common range, a value of 50 kcal mol·Å 2 has been chosen and used to meet both overdamping and precision requirements as closely as possible.…”