Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer

Filovirus infections cause hemorrhagic fever in humans and non-human primates that often results in high fatality rates. The Marburg virus is a lipid-enveloped virus from the Filoviridae family and is closely related to the Ebola virus. The viral matrix layer underneath the lipid envelope is formed by the matrix protein VP40 (VP40), which is also involved in other functions during the viral life-cycle. As in the Ebola virus VP40 (eVP40), the recently determined X-ray crystal structure of the Marburg virus VP40 (mVP40) features loops containing cationic residues that form a lipid binding basic patch. However, the mVP40 basic patch is significantly flatter with a more extended surface than in eVP40, suggesting the possibility of differences in the plasma membrane interactions and phospholipid specificity between the VP40 dimers. In this paper, we report on molecular dynamics simulations that investigate the roles of various residues and lipid types in PM association as well as the conformational changes of the mVP40 dimer facilitated by membrane association. We compared the structural changes of the mVP40 dimer with the mVP40 dimer in both lipid free and membrane associated conditions. Despite the significant structural differences in the crystal structure, the Marburg VP40 dimer is found to adopt a configuration very similar to the Ebola VP40 dimer after associating with the membrane. This conformational rearrangement upon lipid binding allows Marburg VP40 to localize and stabilize at the membrane surface in a manner similar to the Ebola VP40 dimer. Consideration of the structural information in its lipid-interacting condition may be important in targeting mVP40 for novel drugs to inhibit viral budding from the plasma membrane

Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments

Ebola virus infections cause hemorrhagic fever that often results in very high fatality rates. In addition to exploring vaccines, development of drugs is also essential for treating the disease and preventing the spread of the infection. The Ebola virus matrix protein VP40 exists in various conformational and oligomeric forms and is a potential pharmacological target for disrupting the virus life-cycle. Here we explored graphene-VP40 interactions using molecular dynamics simulations and graphene pelleting assays. We found that graphene sheets associate strongly with VP40 at various interfaces. We also found that the graphene is able to disrupt the C-terminal domain (CTD-CTD) interface of VP40 hexamers. This VP40 hexamer-hexamer interface is crucial in forming the Ebola viral matrix and disruption of this interface may provide a method to use graphene or similar nanoparticle based solutions as a disinfectant that can significantly reduce the spread of the disease and prevent an Ebola epidemic

The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation

The transcription antiterminator RfaH has been shown to undergo major structural rearrangements to perform multiple functions. Structural determination of the C-terminal domain (CTD) of RfaH showed that it can exist as either an α-helix bundle when interfacing with the N-terminal domain (NTD) or as a β-barrel conformation when it is not interfacing with the NTD. In this paper, we investigate the full RfaH with both CTD and NTD using a variety of all-atom molecular dynamics (MD) simulation techniques, including targeted molecular dynamics, steered molecular dynamics, and adaptive biasing force, and calculate potentials of mean force. We also use network analysis to determine communities of amino acids that are important in transferring information about structural changes. We find that the CTD–NTD interdomain interactions constitute the main barrier in the CTD α-helix to β-barrel structural conversion. Once the interfacial interactions are broken, the structural conversion of the CTD is relatively easy. We determined which amino acids play especially important roles in controlling the interdomain motions and also describe subtle structural changes that may be important in the functioning of RfaH

The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation

The transcription antiterminator RfaH has been shown to undergo major structural rearrangements to perform multiple functions. Structural determination of the C-terminal domain (CTD) of RfaH showed that it can exist as either an α-helix bundle when interfacing with the N-terminal domain (NTD) or as a β-barrel conformation when it is not interfacing with the NTD. In this paper, we investigate the full RfaH with both CTD and NTD using a variety of all-atom molecular dynamics (MD) simulation techniques, including targeted molecular dynamics, steered molecular dynamics, and adaptive biasing force, and calculate potentials of mean force. We also use network analysis to determine communities of amino acids that are important in transferring information about structural changes. We find that the CTD–NTD interdomain interactions constitute the main barrier in the CTD α-helix to β-barrel structural conversion. Once the interfacial interactions are broken, the structural conversion of the CTD is relatively easy. We determined which amino acids play especially important roles in controlling the interdomain motions and also describe subtle structural changes that may be important in the functioning of RfaH

Molecular Dynamics Investigations of the α‑Helix to β‑Barrel Conformational Transformation in the RfaH Transcription Factor

The C-terminal domain (CTD) of the transcription antiterminator RfaH folds to an α-helix bundle when it interacts with its N-terminal domain (NTD) but it undergoes an all-α to all-β conformational transformation when it does not interact with the NTD. The RfaH-CTD in the all-α topology is involved in regulating transcription whereas in the all-β topology it is involved in stimulating translation by recruiting a ribosome to an mRNA. Because the conformational transformation in RfaH-CTD gives it a different function, it is labeled as a transformer protein, a class that may eventually include many other functional proteins. The structure and function of RfaH is of interest for its own sake, as well as for the value it may serve as a model system for investigating structural transformations in general. We used replica exchange molecular dynamics simulations with implicit solvent to investigate the α-helix to β-structure transformation of RfaH-CTD, followed by structural relaxation with detailed all atom simulations for the best replica. The importance of interfacial interactions between the two domains of RfaH is highlighted by the compromised structural integrity of the helical form of the CTD in the absence NTD. Calculations of free-energy landscape and transfer entropy elucidate the details of the RfaH-CTD transformation process

Molecular basis for the recognition of 24-(S)-hydroxycholesterol by integrin αvβ3

Abstract A growing body of evidence suggests that oxysterols such as 25-hydroxycholesterol (25HC) are biologically active and involved in many physiological and pathological processes. Our previous study demonstrated that 25HC induces an innate immune response during viral infections by activating the integrin-focal adhesion kinase (FAK) pathway. 25HC produced the proinflammatory response by binding directly to integrins at a novel binding site (site II) and triggering the production of proinflammatory mediators such as tumor necrosis factor-α (TNF) and interleukin-6 (IL-6). 24-(S)-hydroxycholesterol (24HC), a structural isomer of 25HC, plays a critical role in cholesterol homeostasis in the human brain and is implicated in multiple inflammatory conditions, including Alzheimer’s disease. However, whether 24HC can induce a proinflammatory response like 25HC in non-neuronal cells has not been studied and remains unknown. The aim of this study was to examine whether 24HC produces such an immune response using in silico and in vitro experiments. Our results indicate that despite being a structural isomer of 25HC, 24HC binds at site II in a distinct binding mode, engages in varied residue interactions, and produces significant conformational changes in the specificity-determining loop (SDL). In addition, our surface plasmon resonance (SPR) study reveals that 24HC could directly bind to integrin αvβ3, with a binding affinity three-fold lower than 25HC. Furthermore, our in vitro studies with macrophages support the involvement of FAK and NFκB signaling pathways in triggering 24HC-mediated production of TNF. Thus, we have identified 24HC as another oxysterol that binds to integrin αvβ3 and promotes a proinflammatory response via the integrin-FAK-NFκB pathway