Conformational Flexibility of the Protein–Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament

Abstract

The Ebola virus (EBOV) is a virulent pathogen that causes severe hemorrhagic fever with a high fatality rate in humans. The EBOV transformer protein VP40 plays crucial roles in viral assembly and budding at the plasma membrane of infected cells. One of VP40's roles is to form the long, flexible, pleomorphic filamentous structural matrix for the virus. Each filament contains three unique interfaces: monomer NTD-NTD to form a dimer, dimer-to-dimer NTD-NTD oligomerization to form a hexamer, and end-to-end hexamer CTD-CTD to build the filament. However, the atomic-level details of conformational flexibility of the VP40 filament is still elusive. In this study, we have performed explicit-solvent, all-atom molecular dynamic simulations to explore the conformational flexibility of the three different interface structures of the filament. Using dynamic network analysis and other calculational methods, we find that the CTD-CTD hexamer interface with weak inter-domain amino acid communities is the most flexible, and the NTD-NTD Oligomer interface with strong inter-domain communities is the least flexible. Our study suggests that the high flexibility of the CTD-CTD interface may be essential for the supple bending of the Ebola filovirus, and such flexibility may present a target for molecular interventions to disrupt the Ebola virus functioning.

A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation

“…eVP40 oligomerization is a hallmark of its ability to form pre-VLP structures that emanate from the plasma membrane [12,14,15,18]. Proper oligomerization of eVP40 from the dimer to a hexamer [12,15] and larger oligomers [12,14,[18][19][20] has been proposed to be a key step in proper egress and virion formation, as mutations that reduce oligomerization or alter hydrophobic contacts that facilitate proper CTD oligomer contacts reduce budding [15][16][17]. To monitor the effects of W191A and W191F on VP40 oligomeric state, we employed number and brightness (N&B) analysis, which has been used to study the apparent oligomerization state of GFP tagged proteins [31][32][33], including previous work on VP40 [12,14,[18][19][20].…”

“…Molecular dynamics (MD) simulations have been used to investigate VP40 structural dynamics [16,17], VP40-lipid interactions [36,37], and to better understand cellular and experimental observations of VP40 structure/function relationships [13,38,39]. To determine how Trp 191 may influence VP40 flexibility and interactions adjacent to Trp 191 , we performed MD simulations for WT VP40 and W191A.…”

“…eVP40 is a dimer that contains an N-terminal domain (NTD) involved in dimerization and a C-terminal domain (CTD) that regulates membrane binding. Additionally, both the NTD and CTD participate in interdomain interactions for eVP40 hexamers [15][16][17] and larger oligomers [18][19][20][21] that form at the membrane interface. An eVP40 octameric ring structure has also been identified that is mediated by a different NTD oligomerization interface [15,21].…”

“…eVP40 octamers also play a role distinct from assembly and budding as the octamers have not been detected at the plasma membrane or in viral particles. A number of studies have implicated different regions or amino acids of eVP40 to play critical roles in processes such as membrane binding [13,15,19,20], oligomerization [15,17] and protein-protein interactions [22][23][24]. While a number of key interactions between VP40 and host molecules have been found, much less is known regarding the structural dynamics that regulate eVP40 oligomeric states and elements of the eVP40 structure critical to protein stability or conformational change.…”

Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

“…Ebola virus VP40 comprises an N-terminal domain (NTD; residues 1-194) and a C-terminal domain (CTD;. The NTD and the CTD adjoin in monomeric or dimeric VP40; this is also true for CTDs that dimerize with each other at structurally important flexible interfaces in the virion matrix (Dessen et al, 2000;Bornholdt et al, 2013;Pavadai et al, 2019). The NTD and the CTD are, however, not joined in the VP40 ring.…”