The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model.

Yue Guo,Minghui Yang,Mojie Duan

doi:10.3390/ijms20143476

Abstract

As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. The uncovering of binding-relevant intermediate states and interactions would greatly increase our knowledge of the binding process. In this work, all-atom molecular dynamics (MD) simulations were performed to characterize the structural properties of nativelike intermediate states. Based on multiple 6 μs MD simulations and Markov state model (MSM) analysis, several “open” intermediate states were observed. The transition rates between these states and the native closed state are in good agreement with the experimental measurements, which indicates that these intermediate states are binding relevant. As a common property in the open states, the partially unfolded α2 helix generates a larger portal and provides the driving force to facilitate ligand binding. On the other side, there are two kinds of open states for the ligand-binding HFABP: one has the partially unfolded α2 helix, and the other has the looser β-barrel with disjointing βD-βE strands. Our results provide atomic-level descriptions of the binding-relevant intermediate states and could improve our understanding of the binding mechanism.

Highlights

Intracellular lipid binding proteins are critical to the transportation of lipid ligands between tissues and within cells [1,2,3]
As a member of the Intracellular lipid binding proteins (iLBPs) super-family, heart-type fatty acid binding protein (HFABP) is abundant in the heart and other tissues like skeletal muscle and brain, and it mainly serves as the transporter of fatty acids from the cell membrane to the mitochondria [4]
Atomic molecular dynamics (MD) simulations covering a total of 60 μs were performed on ligand-free HFABP and ligand-bound HFABP to characterize the “invisible” intermediates near the native structures

Summary

Introduction

Intracellular lipid binding proteins (iLBPs) are critical to the transportation of lipid ligands between tissues and within cells [1,2,3]. We analyzed the distribution of Q for the conformations sampled in our simulations For both the apo- and holo-FABP systems, the Q values are distributed in the range of 0.85 to 0.95 (Figure S2), which indicates that the sampling in our simulation is close to the native state, Int. J. Upon the binding of fatty acid, the Qi values for the residues on the C-terminal α2 helix increase by about 0.2, demonstrating a population shift of the conformational space toward the folded state induced by ligand binding. Except for the terminal residues, most of the residues with large conformational entropies are located in the ligand entrance portal for both apo- and holo-HFABP. The conformational entropies of the residues on the α2 helix of holo-HFABP are smaller than those on apo-HFABP, which further demonstrates the structure stabilization ability of ligand binding. It is unlikely to form an entrance to enable ligand binding or unbinding in the timescale of our simulation

Intermediate States of Apo-FABP

Ligand Binding Model

Materials and Methods

Apparent Free Energy Barrier

Mean First Passage Time

Conclusions