Structural Dynamics of Membrane Interacting Viral Proteins

Viruses do not possess complete cellular machinery but have the ability to reproduce by utilizing cellular machinery inside host cells. They are nanoscale machines that rapidly modify (evolve) their molecular components to cause disease and death. Therefore, emergence of deadly infectious viruses is a monumental health concern and understanding how viruses are able to enter, replicate, assemble and egress from the host cell is important to mitigate the threat. A fully active, infectious viral structure is known as a virion. A virion contains genetic material and is enclosed by a capsid. The capsid is a protein shell and some viruses also are coated by a lipid membrane. My research focuses on viral proteins that interact with lipid membranes in host cells. The lipid molecules can be part of the cellular membrane or part of lipid structures within a cell, such as the endoplasmic reticulum. In my research, I used molecular dynamics computational techniques to study the interactions of the filovirus matrix protein, also known as VP40, of Ebola and Marburg viruses with the lipid molecules in the human plasma membrane. VP40 proteins associate in the inner layer of the plasma membrane and oligomerize to form the matrix that gives the shape of the virion particle. My research focuses on the membrane association, membrane transportation of VP40, which represents the early stage of the virus’ assembly inside the cell. I have identified the amino acids playing important roles in both membrane association and conformational flexibility. I also investigated the Zika virus NS1 protein association on the outer layer of endoplasmic reticulum, which is where the Zika virus forms the virion. The aim of my research is to use molecular level understanding of the virus life-cycle to develop improved molecular interventions such as designing drug molecules that disrupt the functions of the VP40 and NS1 proteins, for prevention and cure of viral diseases

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

Biostimulantien als Blattapplikation wirken auf Spross- und Wurzelmasse sowie Wurzelaktivität in Ackerbohnen (Vicia Faba)

Topfversuch wurde die Wirkung von Biostimulanzien auf die Wurzel- und Sprossparameter der Ackerbohne untersucht. Komposttee und sterilisierter Komposttee erhöhten die Trockensubstanz der Wurzel- und Sprossmasse signifikant. Lithokraft® erhöhte das Gewicht der Rhizosheath und der Knöllchen

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers

Cysteine mutations in the ebolavirus matrix protein VP40 promote phosphatidylserine binding by increasing the flexibility of a lipid-binding loop

Ebolavirus (EBOV) is a negative-sense RNA virus that causes severe hemorrhagic fever in humans. The matrix protein VP40 facilitates viral budding by binding to lipids in the host cell plasma membrane and driving the formation of filamentous, pleomorphic virus particles. The C-terminal domain of VP40 contains two highly-conserved cysteine residues at positions 311 and 314, but their role in the viral life cycle is unknown. We therefore investigated the properties of VP40 mutants in which the conserved cysteine residues were replaced with alanine. The C311A mutation significantly increased the affinity of VP40 for membranes containing phosphatidylserine (PS), resulting in the assembly of longer virus-like particles (VLPs) compared to wild-type VP40. The C314A mutation also increased the affinity of VP40 for membranes containing PS, albeit to a lesser degree than C311A. The double mutant behaved in a similar manner to the individual mutants. Computer modeling revealed that both cysteine residues restrain a loop segment containing lysine residues that interact with the plasma membrane, but Cys311 has the dominant role. Accordingly, the C311A mutation increases the flexibility of this membrane-binding loop, changes the profile of hydrogen bonding within VP40 and therefore binds to PS with greater affinity. This is the first evidence that mutations in VP40 can increase its affinity for biological membranes and modify the length of Ebola VLPs. The Cys311 and Cys314 residues therefore play an important role in dynamic interactions at the plasma membrane by modulating the ability of VP40 to bind PS

The perfect storm: Disruptions to institutional delivery care arising from the COVID-19 pandemic in Nepal

Background The COVID-19 pandemic has led to system-wide disruption of health services globally. We assessed the effect of the pandemic on the disruption of institutional delivery care in Nepal. Methods We conducted a prospective cohort study among 52356 women in nine hospitals to assess the disruption of institutional delivery care during the pandemic (comparing March to August in 2019 with the same months in 2020). We also conducted a nested follow up cohort study with 2022 women during the pandemic to assess their provision and experience of respectful care. We used linear regression models to assess the association between provision and experience of care with volume of hospital births and women’s residence in a COVID-19 hotspot area. Results The mean institutional births during the pandemic across the nine hospitals was 24563, an average decrease of 11.6% (P<0.0001) in comparison to the same time-period in 2019. The institutional birth in high-medium volume hospitals declined on average by 20.8% (P<0.0001) during the pandemic, whereas in low-volume hospital institutional birth increased on average by 7.9% (P=0.001). Maternity services halted for a mean of 4.3 days during the pandemic and there was a redeployment staff to COVID-19 dedicated care. Respectful provision of care was better in hospitals with low-volume birth (β=0.446, P<0.0001) in comparison to high-medium-volume hospitals. There was a positive association between women’s residence in a COVID-19 hotspot area and respectful experience of care (β=0.076, P=0.001). Conclusions The COVID-19 pandemic has had differential effects on maternity services with changes varying by the volume of births per hospital with smaller volume facilities doing better. More research is needed to investigate the effects of the pandemic on where women give birth and their provision and experience of respectful maternity care to inform a “building-back-better” approach in post-pandemic period

Experiences and Lessons from a Multicountry NIDIAG Study on Persistent Digestive Disorders in the Tropics.

<p>Experiences and Lessons from a Multicountry NIDIAG Study on Persistent Digestive Disorders in the Tropics</p