Molecular-Dynamics Simulation of Dioxygen Egress from 12/15-LipoxygenaseArachidonic Acid Complex

On the Permeation by Dioxygen of Urate Oxidase from Aspergillus flavus in Complex with Xanthine Anion: Dioxygen Pathways and a Portrait of the Enzyme Cavities from Molecular Dynamics Simulations in Water Solution

This work describes molecular dynamics (MD) simulations in aqueous media for the complex of the homotetrameric urate oxidase (UOX) from Aspergillus flavus with xanthine anion (5) in the presence of dioxygen (O2 ). After 196.6 ns of trajectory from unrestrained MD, a O2 molecule was observed leaving the bulk solvent to penetrate the enzyme between two subunits, A/C. From here, the same O2 molecule was observed migrating, across subunit C, to the hydrophobic cavity that shares residue V227 with the active site. The latter was finally attained, after 378.3 ns of trajectory, with O2 at a bonding distance from 5. The reverse same O2 pathway, from 5 to the bulk solvent, was observed as preferred pathway under random acceleration MD (RAMD), where an external, randomly oriented force was acting on O2 . Both MD and RAMD simulations revealed several cavities populated by O2 during its migration from the bulk solvent to the active site or backwards. Paying attention to the last hydrophobic cavity that apparently serves as O2 reservoir for the active site, it was noticed that its volume undergoes ample fluctuations during the MD simulation, as expected from the thermal motion of a flexible protein, independently from the particular subunit and no matter whether the cavity is filled or not by O2 .

A mutation interfering with 5-lipoxygenase domain interaction leads to increased enzyme activity

5-Lipoxygenase (5-LOX) catalyzes two steps in conversion of arachidonic acid to proinflammatory leukotrienes. Lipoxygenases, including human 5-LOX, consist of an N-terminal C2-like β-sandwich and a catalytic domain. We expressed the 5-LOX domains separately, these were found to interact in the yeast two-hybrid system. The 5-LOX structure suggested association between Arg(101) in the β-sandwich and Asp(166) in the catalytic domain, due to electrostatic interaction as well as hydrogen bonds. Indeed, mutagenic replacements of these residues led to loss of two-hybrid interaction. Interestingly, when Arg(101) was mutated to Asp in intact 5-LOX, enzyme activity was increased. Thus, higher initial velocity of the reaction (vinit) and increased final amount of products were monitored for 5-LOX-R101D, at several different assay conditions. In the 5-LOX crystal structure, helix α2 and adjacent loops (including Asp(166)) of the 5-LOX catalytic domain has been proposed to form a flexible lid controlling access to the active site, and lid movement would be determined by bonding of lid residues to the C2-like β-sandwich. The more efficient catalysis following disruption of the R101-D166 ionic association supports the concept of such a flexible lid in human 5-LOX.

On the pathways of biologically relevant diatomic gases through proteins. Dioxygen and heme oxygenase from the perspective of molecular dynamics

This work deals with dioxygen (O2 ) binding sites and pathways through inducible human heme oxygenase (HO-1). The experimentally known distal binding site 1, and sites 2-3 above it, could be reproduced by means of non-deterministic random-acceleration molecular-dynamics (RAMD) simulations. In addition, RAMD revealed the proximal binding site 5, a deeply-seated binding site 4, which lies behind heme, as well as a few gates communicating with the external medium. In getting from site 1 to the main gate, which lies on the protein front opposed to site 4, O2 follows chiefly the shortest direct pathway. Less frequently, O2 visits intermediate sites 2, 4, or 5 along longer pathways. A similarity between HO-1, myoglobin, and cytoglobin in using, for diatomic gas delivery, the direct shortest pathway from the heme center to the surrounding medium, is emphasized. Otherwise, comparing other proteins and diatomic gases, each system reveals its peculiarities as to sites, gates, and pathways. Thus, relating these properties to the physiological functions of the proteins remains in general a challenge for future studies.

Ligand release mechanisms and channels in histone deacetylases

Exploring the molecular channels of class I histone deacetylases (HDACs) with buried active sites are important to understand their structures and functionalities. In this work, we perform hybrid classical molecular dynamics and random acceleration molecular dynamics simulations to explore the B3N [i.e., (4-(dimethylamino)N-[7(hydroxyamino)-7-oxoheptyle] benzamide)] exit channels in the x-ray crystal structures of HDAC3 and HDAC8 enzymes. Our simulations identify B3N release through four different channels in HDAC3 (denoted as A1, A2, B1, and B2) and HDAC8 (referred as A1, B1, B2, and B3) enzymes, among which egression through channel A1 is more predominant in both the enzymes. This mechanism is similar to ligand release in HDAC1 and HDAC2 described in our previous study and can be the fingerprint ligand release mechanisms in class I HDACs. Ligand release events through B channels, on the other hand, are different among HDAC3 and HDAC8, highlighting the significances of substituted residues in controlling the access to these channels This study reveals a novel aromatic gating mechanism elicited by TYR154-TRP141-TYR111 that controls the B3N access to all the B channels in HDAC8. The TRP141 in HDAC8 is substituted by LEU133 in HDAC3, which do not hinder the access to B channels in HDAC3. However, two hydrogen bonded barricades formed as ARG28-GLY297-GLY295-GLY131 and TRP129-ARG28-ALA130-LEU29-TRP129 obstruct the B3N from exploring the B channels in HDAC3. The structural and dynamical characterizations of molecular channels and ligand unbinding mechanisms reported in this study provide novel structural insights and atomic level perspectives on HDAC3 and HDAC8 enzymes, thereby potentially aiding in the design of more specific HDAC inhibitors.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes.