Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

Léo Degrève,Antonio Caliri,Carlos A Fuzo

doi:10.1007/s10822-012-9616-4

Abstract

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

Highlights

The basic general strategy of the molecular simulation to the dengue virus (DENV) problem, as adopted here, is to focus on a specific protein that acts outside the cell, or on a protein that plays a key role in the process of membrane fusion, trying to find potential sites whose corresponding activity can be inhibited by ligands, which have yet to be identified
We employed the Root Mean Square Deviation (RMSD) of Ca atoms in order to examine the configurational evolution of the monomeric E protein in solution at acid pH
The lowest RMSD level with respect to the crystallographic structure is found in the IS0 system; it increases until the IS150 and decreases back in IS225

Summary

Introduction

The basic general strategy of the molecular simulation to the DENV problem, as adopted here, is to focus on a specific protein that acts outside the cell, or on a protein that plays a key role in the process of membrane fusion, trying to find potential sites whose corresponding activity can be inhibited by ligands, which have yet to be identified. To implement such purposes, knowledge regarding the three-dimensional structure of the protein at the atomic level is imperative, and the E protein ectodomain is the only one that meets all such requirements

Methods

Results

Final comments and conclusions