scholarly journals HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions

2018 ◽  
Author(s):  
L.R. Hollingsworth ◽  
J.A. Lemkul ◽  
D.R. Bevan ◽  
A.M. Brown
Keyword(s):  
Host Cell ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Transmembrane Domain ◽  
Chloride Ions ◽  
Viral Envelope ◽  
Membrane Properties ◽  
Viral Fusion ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations

AbstractThe gp41 transmembrane domain (TMD) of the envelope glycoprotein (Env) of the human immunodeficiency virus (HIV) modulates the conformation of the viral envelope spike, the only druggable target on the surface of the virion. Understanding of TMD dynamics is needed to better probe and target Env with small molecule and antibody therapies. However, little is known about TMD dynamics due to difficulties in describing native membrane properties. Here, we performed atomistic molecular dynamics simulations of a trimeric, prefusion TMD in a model, asymmetric viral membrane that mimics the native viral envelope. We found that water and chloride ions permeated the membrane and interacted with the highly conserved arginine bundle, (R696)3, at the center of the membrane and influenced TMD stability by creating a network of hydrogen bonds and electrostatic interactions. We propose that this (R696)3- water - anion network plays an important role in viral fusion with the host cell by modulating protein conformational changes within the membrane. Additionally, R683 and R707 at the exofacial and cytofacial membrane-water interfaces, respectively, are anchored in the lipid headgroup region and serve as a junction point for stabilization of the termini. The membrane thins as a result of the tilting of the TMD trimer, with nearby lipids increasing in volume, leading to an entropic driving force for TMD conformational change. These results provide additional detail and perspective on the influence of certain lipid types on TMD dynamics and rationale for targeting key residues of the TMD for therapeutic design. These insights into the molecular details of TMD membrane anchoring will build towards a greater understanding of dynamics that lead to viral fusion with the host cell.

scholarly journals Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

2020 ◽  
Author(s):  
Anna Pabis ◽  
Robert J. Rawle ◽  
Peter M. Kasson
Keyword(s):  
Viral Entry ◽  
Transmembrane Domain ◽  
Critical Role ◽  
Cellular Membrane ◽  
Membrane Curvature ◽  
Viral Envelope ◽  
Enveloped Viruses ◽  
Influenza Hemagglutinin ◽  
Hemagglutinin Protein ◽  
Dynamics Simulations

AbstractEnveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We have used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring prior to stalk formation and one after, are consistent with experimental measurements we report of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate prior mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N-terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also utilize sequential processes of acyl tail exposure followed by membrane curvature and distal leaflet engagement.

scholarly journals Viral Membrane Fusion and the Transmembrane Domain

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 693 ◽  
Author(s):  
Chelsea T. Barrett ◽  
Rebecca Ellis Dutch
Keyword(s):  
Membrane Fusion ◽  
Host Cell ◽  
Fusion Proteins ◽  
Transmembrane Domain ◽  
Critical Role ◽  
Viral Fusion ◽  
Transmembrane Region ◽  
Host Cell Membrane ◽  
The Past ◽  
Viral Fusion Proteins

Initiation of host cell infection by an enveloped virus requires a viral-to-host cell membrane fusion event. This event is mediated by at least one viral transmembrane glycoprotein, termed the fusion protein, which is a key therapeutic target. Viral fusion proteins have been studied for decades, and numerous critical insights into their function have been elucidated. However, the transmembrane region remains one of the most poorly understood facets of these proteins. In the past ten years, the field has made significant advances in understanding the role of the membrane-spanning region of viral fusion proteins. We summarize developments made in the past decade that have contributed to the understanding of the transmembrane region of viral fusion proteins, highlighting not only their critical role in the membrane fusion process, but further demonstrating their involvement in several aspects of the viral lifecycle.

Molecular Basis Explanation of Imatinib Resistance of Bcr-Abl Due to T315I and P-Loop Mutations from Molecular Dynamics Simulations.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2917-2917
Author(s):  
Tai-Sung Lee ◽  
Steven Potts ◽  
Hagop Kantarjian ◽  
Jorge Cortes ◽  
Francis Giles ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Large Scale ◽  
Resistance Mechanism ◽  
Md Simulations ◽  
Resistance Mechanisms ◽  
Static Structure ◽  
Imatinib Resistance ◽  
Dynamics Simulations

Abstract Molecular dynamics (MD) simulations on the complex of imatinib with the wild-type, T315I, and other 10 P-loop mutants of the tyrosine kinase Bcr-Abl have been performed to study the imatinib resistance mechanism at the atomic level. MD simulations show that large scale computational simulations could offer insight information that a static structure or simple homology modeling methods cannot provide for studying the Bcr-Abl imatinib resistance problem, especially in the case of conformational changes due to remote mutations. By utilizing the Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA) techniques and analyzing the interactions between imatinib and individual residues, imatinib resistance mechanisms not previously thought have been revealed. Non-directly contacted P-loop mutations either unfavorably change the direct electrostatic interactions with imatinib, or cause the conformational changes influencing the contact energies between imatinib and other non-P-loop residues. We demonstrate that imatinib resistance of T315I mainly comes from the breakdown of the interactions between imatinib and E286 and M290, contradictory to previously suggested that the missing hydrogen bonding is the main contribution. We also demonstrate that except for the mutations of the direct contact residues, such as L248 and Y253, the unfavorable electrostatic interaction between P-loop and imatinib is the main reason for resistance for the P-loop mutations. Furthermore, in Y255H, protonation of the histidin is essential for rendering this mutation resistant to Gleevec. Our results demonstrate that MD is a powerful way to verify and predict clinical response or resistance to imatinib and other potential drugs.

scholarly journals Development of a Novel High-Throughput Surrogate Assay to Measure HIV Envelope/CCR5/CD4-Mediated Viral/Cell Fusion Using BacMam Baculovirus Technology

2003 ◽  
Vol 8 (4) ◽  
pp. 463-470 ◽  
Author(s):  
Stephen Jenkinson ◽  
David C. Mc Coy ◽  
Sandy A. Kerner ◽  
Robert G. Ferris ◽  
Wendell K. Lawrence ◽  
...  
Keyword(s):  
Host Cell ◽  
Cell Fusion ◽  
High Throughput ◽  
Viral Envelope ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Viral Fusion ◽  
Fusion Event ◽  
Surrogate Assay ◽  
Cell Cell

The initial event by which M-tropic HIV strains gain access to cells is via interaction of the viral envelope protein gp120 with the host cell CCR5 coreceptor and CD4. Inhibition of this event reduces viral fusion and entry into cells in vitro. The authors have employed BacMam baculovirus-mediated gene transduction to develop a cell/cell fusion assay that mimics the HIV viral/cell fusion process and allows high-throughput quantification of this fusion event. The assay design uses human osteosarcoma (HOS) cells stably transfected with cDNAs expressing CCR5, CD4, and long terminal repeat (LTR)-luciferase as the recipient host cell. An HEK-293 cell line transduced with BacMam viral constructs to express the viral proteins gp120, gp41, tat, and rev represents the virus. Interaction of gp120 with CCR5/CD4 results in the fusion of the 2 cells and transfer of tat to the HOS cell cytosol; tat, in turn, binds to the LTR region on the luciferase reporter and activates transcription, resulting in an increase in cellular luciferase activity. In conclusion, the cell/cell fusion assay developed has been demonstrated to be a robust and reproducible high-throughput surrogate assay that can be used to assess the effects of compounds on gp120/CCR5/CD4-mediated viral fusion into host cells.

scholarly journals Hidden electrostatic basis of dynamic allostery in a PDZ domain

2017 ◽  
Vol 114 (29) ◽  
pp. E5825-E5834 ◽  
Author(s):  
Amit Kumawat ◽  
Suman Chakrabarty
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Pdz Domain ◽  
Allosteric Modulation ◽  
Side Chain ◽  
Salt Bridges ◽  
Population Shift ◽  
Domain Protein ◽  
Dynamics Simulations

Allosteric effect implies ligand binding at one site leading to structural and/or dynamical changes at a distant site. PDZ domains are classic examples of dynamic allostery without conformational changes, where distal side-chain dynamics is modulated on ligand binding and the origin has been attributed to entropic effects. In this work, we unearth the energetic basis of the observed dynamic allostery in a PDZ3 domain protein using molecular dynamics simulations. We demonstrate that electrostatic interaction provides a highly sensitive yardstick to probe the allosteric modulation in contrast to the traditionally used structure-based parameters. There is a significant population shift in the hydrogen-bonded network and salt bridges involving side chains on ligand binding. The ligand creates a local energetic perturbation that propagates in the form of dominolike changes in interresidue interaction pattern. There are significant changes in the nature of specific interactions (nonpolar/polar) between interresidue contacts and accompanied side-chain reorientations that drive the major redistribution of energy. Interestingly, this internal redistribution and rewiring of side-chain interactions led to large cancellations resulting in small change in the overall enthalpy of the protein, thus making it difficult to detect experimentally. In contrast to the prevailing focus on the entropic or dynamic effects, we show that the internal redistribution and population shift in specific electrostatic interactions drive the allosteric modulation in the PDZ3 domain protein.

scholarly journals Mechanism of dehydration in a non-porous variable hydrate

2014 ◽  
Vol 70 (a1) ◽  
pp. C1000-C1000
Author(s):  
Laszlo Fabian
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Chloride Ions ◽  
Smooth Transition ◽  
Water Molecules ◽  
Present Contribution ◽  
Gated Channel ◽  
Mechanism Of Dehydration ◽  
Paroxetine Hydrochloride ◽  
Dynamics Simulations

Paroxetine hydrochloride form II (PHCl-II) is a variable hydrate with a peculiar behaviour [1]. It changes its water content in response to changes in relative humidity with remarkable speed and in a completely reversible fashion. This is commonly observed for channel hydrates, but no continuous channels exist in the PHCl-II structure [2]. Powder diffraction results showed that loss of water produces an isostructural anhydrate, suggesting a simple, non-destructive mechanism of dehydration. The aim of the present contribution is to explain this unusual behaviour at a molecular level by using molecular dynamics simulations. Models of both the hydrated and anhydrous state could be created from the experimental hydrate structure by simple energy minimisation, which is in accordance with the experimentally observed smooth transition. A partially dehydrated supercell model was used to study the mechanism which allows water molecules to cross the steric barrier between adjacent solvent cavities. Since such transitions are rare on the simulation timescale (µs to ms), a steered molecular dynamics approach was applied. The results show that the passage of water molecules is facilitated by conformational changes, in which a ring system acts as a gate between cavities. When passing through the 'gate', water molecules are relayed between two chloride ions: as one Cl...HOH hydrogen bond is broken, another HOH...Cl one is formed. The progress of water molecules along the gated channel is not continuous, they spend a significant amount of time in each cavity between consecutive passages.

scholarly journals Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels

2020 ◽  
Author(s):  
Mahesh Kondapuram ◽  
Benedikt Frieg ◽  
Sezin Yüksel ◽  
Tina Schwabe ◽  
Christian Sattler ◽  
...  
Keyword(s):  
Patch Clamp ◽  
Conformational Changes ◽  
Cyclic Nucleotide ◽  
Transmembrane Domain ◽  
Helical Structure ◽  
Md Simulations ◽  
Patch Clamp Technique ◽  
Channel Pore ◽  
Dynamics Simulations ◽  
Combined Mutagenesis

ABSTRACTHyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics simulations to show that residue K464 of the C-linker is essential for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that both cAMP and K464E induce a rotation of the intracellular domain relative to the channel pore, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. The adopted poses are in excellent agreement with structural results.

scholarly journals Influenza A H1 and H3 Transmembrane Domains Interact Differently with Each Other and with Surrounding Membrane Lipids

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1461
Author(s):  
Szymon Kubiszewski-Jakubiak ◽  
Remigiusz Worch
Keyword(s):  
Host Cell ◽  
Influenza A ◽  
Transmembrane Domain ◽  
Membrane Lipids ◽  
Transmembrane Protein ◽  
Accessible Surface Area ◽  
Amino Acid Sequences ◽  
Viral Envelope ◽  
Phylogenetic Groups ◽  
Host Cell Membrane

Hemagglutinin (HA) is a class I viral membrane fusion protein, which is the most abundant transmembrane protein on the surface of influenza A virus (IAV) particles. HA plays a crucial role in the recognition of the host cell, fusion of the viral envelope and the host cell membrane, and is the major antigen in the immune response during the infection. Mature HA organizes in homotrimers consisting of a sequentially highly variable globular head and a relatively conserved stalk region. Every HA monomer comprises a hydrophilic ectodomain, a pre-transmembrane domain (pre-TMD), a hydrophobic transmembrane domain (TMD), and a cytoplasmic tail (CT). In recent years the effect of the pre-TMD and TMD on the structure and function of HA has drawn some attention. Using bioinformatic tools we analyzed all available full-length amino acid sequences of HA from 16 subtypes across various host species. We calculated several physico-chemical parameters of HA pre-TMDs and TMDs including accessible surface area (ASA), average hydrophobicity (Hav), and the hydrophobic moment (µH). Our data suggests that distinct differences in these parameters between the two major phylogenetic groups, represented by H1 and H3 subtypes, could have profound effects on protein–lipid interactions, trimer formation, and the overall HA ectodomain orientation and antigen exposure.

Histidine protonation and the activation of viral fusion proteins

2008 ◽  
Vol 36 (1) ◽  
pp. 43-45 ◽  
Author(s):  
Daniela S. Mueller ◽  
Thorsten Kampmann ◽  
Ragothaman Yennamalli ◽  
Paul R. Young ◽  
Bostjan Kobe ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Envelope Protein ◽  
Fusion Proteins ◽  
Side Chain ◽  
Viral Fusion ◽  
Histidine Residues ◽  
Local Environments ◽  
Viral Fusion Proteins ◽  
Dynamics Simulations

Many viral fusion proteins only become activated under mildly acidic condition (pH 4.5–6.5) close to the pKa of histidine side-chain protonation. Analysis of the sequences and structures of influenza HA (haemagglutinin) and flaviviral envelope glycoproteins has led to the identification of a number of histidine residues that are not only fully conserved themselves but have local environments that are also highly conserved [Kampmann, Mueller, Mark, Young and Kobe (2006) Structure 14, 1481–1487]. Here, we summarize studies aimed at determining the role, if any, that protonation of these potential switch histidine residues plays in the low-pH-dependent conformational changes associated with fusion activation of a flaviviral envelope protein. Specifically, we report on MD (Molecular Dynamics) simulations of the DEN2 (dengue virus type 2) envelope protein ectodomain sE (soluble E) performed under varied pH conditions designed to test the histidine switch hypothesis of Kampmann et al. (2006).

scholarly journals Transmembrane Domains of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
pp. e00047-18 ◽  
Author(s):  
Stacy R. Webb ◽  
Stacy E. Smith ◽  
Michael G. Fried ◽  
Rebecca Ellis Dutch
Keyword(s):  
Fusion Protein ◽  
Conformational Changes ◽  
Fusion Proteins ◽  
Ebola Virus ◽  
Transmembrane Domain ◽  
Transmembrane Domains ◽  
Viral Fusion ◽  
Viral Fusion Proteins ◽  
The Stability ◽  
The Right

ABSTRACT Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details of the role of the TMD in these fusion events remain unclear. Previously, we demonstrated that isolated paramyxovirus fusion protein TMDs associate in a monomer-trimer equilibrium, using sedimentation equilibrium analytical ultracentrifugation. Using a similar approach, the work presented here indicates that trimeric interactions also occur between the fusion protein TMDs of Ebola virus, influenza virus, severe acute respiratory syndrome coronavirus (SARS CoV), and rabies virus. Our results suggest that TM-TM interactions are important in the fusion protein function of diverse viral families. IMPORTANCE Many important human pathogens are enveloped viruses that utilize membrane-bound glycoproteins to mediate viral entry. Factors that contribute to the stability of these glycoproteins have been identified in the ectodomain of several viral fusion proteins, including residues within the soluble ectodomain. Although it is often thought to simply act as an anchor, the transmembrane domain of viral fusion proteins has been implicated in protein stability and function as well. Here, using a biophysical approach, we demonstrated that the fusion protein transmembrane domains of several deadly pathogens—Ebola virus, influenza virus, SARS CoV, and rabies virus—self-associate. This observation across various viral families suggests that transmembrane domain interactions may be broadly relevant and serve as a new target for therapeutic development.

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