Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell

Pavel E Volynsky,Dmitry E Nolde,Rex A Palmer,Galina S Zakharova,Alexander G Tonevitsky,Roman G Efremov

doi:10.1038/s41598-018-36310-6

Abstract

How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain in a complex environment – comprising urea and chloroform/methanol (CHCl3/MeOH) mixture. Being well-packed in aqueous solution, viscumin A undergoes global structural rearrangements in both organic media. In urea, the protein is “swelling” and gradually loses its long-distance contacts, thus resembling the “molten globule” state. In CHCl3/MeOH, viscumin A is in effect turned “inside out”. This is accompanied with strengthening of the secondary structure and surface exposure of hydrophobic epitopes originally buried inside the globule. Resulting solvent-adapted models were further subjected to Monte Carlo simulations with an implicit hydrophobic slab membrane. In contrast to only a few point surface contacts in water and two short regions with weak protein-lipid interactions in urea, MD-derived structures in CHCl3/MeOH reveal multiple determinants of membrane interaction. Consequently it is now possible to propose a specific pathway for the structural adaptation of viscumin A with respect to the cell membrane – a probable first step of its translocation into cytoplasmic targets.

Highlights

The functioning of many proteins that possess a well-defined and densely packed spatial structure in water is often associated with their trafficking into and out of the cell via crossing the lipid membrane
Protein-membrane interactions have been extensively studied in computational experiments[6,7], such works either considered just initial stages of protein adsorption on membrane or protein insertion and translocation were accelerated using for example steered dynamics[8], special restraints[9] or simplified models including for example coarse-grained ones[6]
The principal aims of this molecular dynamics (MD) study were the following: (i) To find a putative pathway for MLI A chain (MLA) structural reorganization resembling that occurring near the membrane interface; (ii) To compare such a “membrane-induced” path with the denaturation of MLA usually observed in organic solvents or with respect to elevated temperature and to test specificity of the former transition

Summary

Introduction

The functioning of many proteins that possess a well-defined and densely packed spatial structure in water is often associated with their trafficking into and out of the cell via crossing the lipid membrane. Protein-membrane interactions have been extensively studied in computational experiments[6,7], such works either considered just initial stages of protein adsorption on membrane or protein insertion and translocation were accelerated using for example steered dynamics[8], special restraints[9] or simplified models including for example coarse-grained ones[6] This is because the global protein structural reorganization in the presence of explicit lipid bilayer and water is a slow process whose atomistic description on proper time scales is too computationally demanding and cannot be reached within a realistic timescale. Based on the totality of the computational results, we propose (at least in a first approximation) a molecular mechanism of the membrane-induced reorganization and translocation of a water-soluble ordered protein

Methods

Results

Conclusion