Behavior of H-FABP-fatty acid complex in a protein crystal simulation

TL;DR

This study investigates the dynamic behavior of H-FABP-fatty acid complexes in crystal simulations, demonstrating how restraints and co-solutes like ethanol influence protein stability and motion predictions.

Contribution

It introduces a detailed methodology for simulating H-FABP crystals with crystallographic restraints and analyzes the effects of ethanol on protein stability and dynamics.

Findings

Restrainted MD simulations yield more accurate B-factors.

Unrestrained systems show higher microscopic heterogeneity.

Ethanol influences protein stability and fatty acid exchange.

Abstract

Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B-factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B-factors. Our results suggest that restrained MD simulations based in experimental B-factors produce lower simulated B-factors than simulations without restraints, leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.