Biology subjects

Voth, G. A.

Publications and source records attributed to Voth, G. A..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Cracked actin filaments as mechanosensitive receptors

Actin filament networks are exposed to mechanical stimuli, but the effect of strain on actin filament structure has not been well-established in molecular detail. This is a critical gap in understanding because the activity of a variety of actin-binding proteins have recently been determined to be altered by actin filament strain. We therefore used all-atom molecular dynamics simulations to apply tensile strains to actin filaments and find that changes in actin subunit organization are minimal in mechanically strained, but intact, actin filaments. However, a conformational change disrupts the critical D-loop to W-loop connection between longitudinal neighboring subunits, which leads to a metastable cracked conformation of the actin filament, whereby one protofilament is broken prior to filament severing. We propose that the metastable crack presents a force-activated binding site for actin regulatory factors that specifically associate with strained actin filaments. Through protein-protein docking simulations, we find that 43 evolutionarily-diverse members of the dual zinc finger containing LIM domain family, which localize to mechanically strained actin filaments, recognize two binding sites exposed at the cracked interface. Furthermore, through its interactions with the crack, LIM domains increase the length of time damaged filaments remain stable. Our findings propose a new molecular model for mechanosensitive binding to actin filaments. SIGNIFICANCE STATEMENTCells continually experience mechanical strain, which has been observed to alter the interactions between actin filaments and mechanosensitive actin-binding proteins in recent experimental studies. However, the structural basis of this mechanosensitivity is not well understood. We used molecular dynamics and protein-protein docking simulations to investigate how tension alters the actin filament binding surface and interactions with associated proteins. We identified a novel metastable cracked conformation of the actin filament, whereby one protofilament breaks before the other, presenting a unique strain-induced binding surface. Mechanosensitive LIM domain actin-binding proteins can then preferentially bind the cracked interface, and this association stabilizes damaged actin filaments.

biophysics↗

bioRxiv2023

Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules

Microtubules (MTs) are large cytoskeletal polymers, composed of {beta}-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within {beta}-tubulin. Hydrolysis is favored in the MT lattice compared to free heterodimer with an experimentally observed rate increase of 500 to 700 fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated -tubulin residues, :E254 and :D251, as catalytic residues completing the {beta}-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP-state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive QM/MM simulations with transition-tempered metadynamics free energy sampling of compacted and expanded inter-dimer complexes, as well as free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. :E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice disruption of a key salt bridge interaction renders :E254 less effective. The simulations reveal a barrier decrease of 3.8 {+/-} 0.5 kcal/mol for the compacted lattice compared to free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 {+/-} 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip. Significance StatementMicrotubules (MTs) are large and dynamic components of the eukaryotic cytoskeleton with the ability to stochastically convert from a polymerizing to a depolymerizing state and vice-versa. Depolymerization is coupled to the hydrolysis of guanosine-5-triphosphate (GTP), which is orders of magnitude faster in the MT lattice than in free tubulin heterodimers. Our results computationally ascertain the catalytic residue contacts in the MT lattice that accelerate GTP hydrolysis compared to the free heterodimer as well as confirm that a compacted MT lattice is necessary for hydrolysis while a more expanded lattice is unable to form the necessary contacts and thereby hydrolyze GTP.

biochemistry↗

bioRxiv2022

The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7

Cells remodel glycerophospholipid acyl chains via the Lands cycle to adjust membrane properties. Membrane-bound O-acyltransferase (MBOAT) 7 acylates lyso-phosphatidylinositol (lyso-PI) with arachidonyl-CoA. MBOAT7 mutations cause brain developmental disorders, and reduced expression is linked to fatty liver disease. Further, increased MBOAT7 expression is linked to hepatocellular and renal cancers. The mechanistic basis of MBOAT7 catalysis and substrate selectivity are unknown. Here, we report the structure and a model for the catalytic mechanism of human MBOAT7. Arachidonyl-CoA and lyso-PI access the catalytic center through a twisted tunnel from the cytosol and lumenal sides, respectively. N-Terminal residues on the ER lumenal side determine phospholipid headgroup selectivity: swapping them between MBOATs 1, 5, and 7 converts enzyme specificity for different lyso-phospholipids. Finally, the MBOAT7 structure and virtual screening enabled identification of small-molecule inhibitors that may serve as lead compounds for pharmacologic development.

biochemistry↗

bioRxiv2022

Organization of Upstream ESCRT Machinery at the HIV-1 Budding Site

In the late stages of the HIV-1 life cycle, membrane localization and self-assembly of the Gag polyproteins induce membrane deformation and budding. However, release of the immature virion requires direct interaction between Gag lattice and upstream ESCRT machinery at the budding site, followed by assembly of the downstream ESCRT-III factors, culminating in membrane scission. In this work, using "bottom-up" coarse-grained (CG) molecular dynamics (MD) simulations we investigated the interactions between Gag and different upstream ESCRT components to delineate the molecular organization of proteins at the membrane neck of the HIV-1 budding site. We developed CG models of upstream ESCRT proteins and HIV-1 structural protein Gag based on experimental structural data and extensive all-atom MD simulations. We find that ESCRT-I proteins bound to the immature Gag lattice can recruit multiple copies of ESCRT-II coating the membrane neck. ESCRT-I can effectively oligomerize to higher-order complexes both in absence of ESCRT-II and when multiple copies of ESCRT-II are localized at the bud neck. The ESCRT-I/II supercomplexes observed in our simulations exhibit predominantly extended conformations. Importantly, the ESCRT-I/II supercomplex modulates the membrane mechanical properties at the budding site by decreasing the overall Gaussian curvature of membrane neck. Our findings serve to elucidate a network of interactions between the upstream ESCRT machinery, immature Gag lattice, and membrane bud neck that regulate the protein assemblies and enable bud neck constriction.

biophysics↗

bioRxiv2022

Structure of SARS-CoV-2 M protein in lipid nanodiscs

SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 [A] resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.

biophysics↗

bioRxiv2022

Critical Mechanistic Role of Inositol Hexakisphosphate (IP6) in HIV-1 Viral Capsid Assembly

The maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice encasing the condensed RNA genome is critical for viral infectivity. During HIV-1 maturation, CA can self-assemble into a wide range of capsid morphologies made of ~175-250 hexamers and 12 pentamers. Most recently, the cellular polyanion inositol hexakisphosphate (IP6) has been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the precise kinetic interplay of events during IP6 and CA co-assembly is unclear. In this work, we use Coarse-grained Molecular Dynamics (CGMD) simulations to elucidate the underlying molecular mechanism of capsid formation, including the crucial role played by IP6. We show that IP6, in relatively small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior towards kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids. TeaserComputer simulations reveal that IP6 promotes fullerene-like capsid formation by stabilizing high curvature regions of the capsid.

biophysics↗

bioRxiv2022

Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies

During the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically-trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.

biophysics↗

bioRxiv2022

Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins

Summary paragraphSelective proton transport through proteins is essential for forming and utilizing proton gradients in cells. Protons are conducted along hydrogen-bonded "wires" of water molecules and polar sidechains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways inferred from static protein structures. We hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess proton itself in the water wire. To test this hypothesis, we used molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform mechanisms of biological proton conduction and principles for engineering proton-conductive materials.

biophysics↗

bioRxiv2022

Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions

Filopodia are actin-rich membrane protrusions essential for cell morphogenesis, motility, and cancer invasion. How cells control filopodia initiation on the plasma membrane remains elusive. We performed experiments in cellulo, in vitro and in silico to unravel the mechanism of filopodia initiation driven by the membrane curvature sensor IRSp53. We showed that full-length IRSp53 self-assembles into clusters on membranes depending on PIP2. Using well-controlled in vitro reconstitution systems, we demonstrated that IRSp53 clusters recruit the actin polymerase VASP to assemble actin filaments locally on membranes, leading to the generation of actin-filled membrane protrusions reminiscent of filopodia. By pulling membrane nanotubes from live cells, we observed that IRSp53 can only be enriched and trigger actin assembly in nanotubes at highly dynamic membrane regions. Our work supports a regulation mechanism of IRSp53 in its attributes of curvature sensation and partner recruitment to ensure a precise spatial-temporal control of filopodia initiation.

biophysics↗

bioRxiv2021

Ion Transport, Selectivity, and Electronic Polarization in Fluoride Channels

Fluoride channels (Fluc) export toxic F- from the cytoplasm. Crystallography and mutagenesis have identified several conserved residues crucial for fluoride transport, but the permeation mechanism at the molecular level has remained elusive. Herein we have applied constant-pH molecular dynamics and free energy sampling methods to investigate fluoride permeation through a Fluc protein from Escherichia coli. We find that fluoride is facile to permeate in its charged form, i.e., F-, by traversing through a non-bonded network. The extraordinary F- selectivity is gained by the hydrogen-bonding capability of the central binding site and the Coulombic filter at the channel entrance. The F- permeation rate calculated using an electronically polarizable force field is significantly more accurate compared to the experimental value than that calculated using a more standard additive force field, suggesting an essential role for electronic polarization in the F- - Fluc interactions. O_TEXTBOXSIGNIFICANCE A comprehensive atomistic-level computational study is presented of the mechanism of fluoride permeation through fluoride channels. The mechanism of fluoride permeation of the F- anion is established and the microscopic determinants of F- selectivity revealed. The essential nature of electronic polarization during F- permeation is also demonstrated through the computational modeling. C_TEXTBOX

biophysics↗

bioRxiv2021

Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane

Lipid droplets (LDs) are organelles formed in the endoplasmic reticulum (ER) to store triacylglycerol (TG) and sterol esters. The ER protein seipin is key for LD biogenesis. Seipin forms a cage-like structure, with each seipin monomer containing a conserved hydrophobic helix (HH) and two transmembrane (TM) segments. How the different parts of seipin function in TG nucleation and LD budding is poorly understood. Here, we utilized molecular dynamics simulations of human seipin, along with cell-based experiments, to study seipins functions in protein-lipid interactions, lipid diffusion, and LD maturation. All-atom (AA) simulations indicate that most seipin TM segment residues located in the phospholipid (PL) tail region of the bilayer attract TG. We also find seipin TM segments control lipid diffusion and permeation into the protein complex. Simulating larger, growing LDs with coarse-grained (CG) models, we find that the seipin TM segments form a constricted neck structure to facilitate conversion of a flat oil lens into a budding LD. Using cell experiments and simulations, we also show that conserved, positively charged residues at the end of seipins TM segments affect LD maturation. We propose a model in which seipin TM segments critically function in TG nucleation and LD growth.

biophysics↗

bioRxiv2021

Key Factors Governing Initial Stages of Lipid Droplet Formation

Lipid droplets (LDs) are neutral lipid storage organelles surrounded by a phospholipid (PL) monolayer. LD biogenesis from the endoplasmic reticulum (ER) is driven by phase separation of neutral lipids, overcoming surface tension and membrane deformation. However, the core biophysics of the initial steps of LD formation remain relatively poorly understood. Here, we use a tunable, phenomenological coarse-grained (CG) model to study triacylglycerol (TG) nucleation in a bilayer membrane. We show that PL rigidity has a strong influence on TG lensing and membrane remodeling: When membrane rigidity increases, TG clusters remain more planar with high anisotropy but a minor degree of phase nucleation. This finding is confirmed by free energy sampling simulations that calculate the potential of mean force (PMF) as a function of the degree of nucleation and anisotropy. We also show that asymmetric tension, controlled by the number of PLs on each membrane leaflet, determines the budding direction. A TG lens buds in the direction of the monolayer containing excess PLs to allow for better PL coverage of TG, consistent with reported experiments. Finally, two governing mechanisms of the LD growth, Ostwald ripening and merging, are observed. Taken together, this study characterizes the interplay between two thermodynamic quantities during the initial LD phases, the TG bulk free energy and membrane remodeling energy.

biophysics↗

bioRxiv2021

Strain and crack propagation of HIV-1 capsids during uncoating

Viral replication in HIV-1 relies on a fullerene-shaped capsid to transport genetic material deep into the nucleus of an infected cell. Capsid stability is linked to the presence of cofactors, including inositol hexakisphosphate (IP6) that bind to pores found in the capsid. Using extensive all-atom molecular dynamics simulations of HIV-1 cores imaged from cryo-electron tomography (cryo-ET) in intact virions, which contain IP6 and a ribonucleoprotein complex, we find markedly striated patterns of strain on capsid lattices. The presence of these cofactors also increases rigidity of the capsid. Conformational analysis of capsid (CA) proteins show CA accommodates strain by locally flexing away from structures resolved using x-ray crystallography and cryo-electron microscopy. Then, cryo-ET of HIV-1 cores undergoing endogenous reverse transcription demonstrate that lattice strain increases in the capsid prior to mechanical failure and that the capsid ruptures by crack propagation along regions of high strain. These results uncover HIV-1 capsid properties involved in their critical disassembly process. Significance statementThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.

biophysics↗

bioRxiv2021

Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter

Proton coupled peptide transporters (POTs) are crucial for the uptake of di- and tri-peptides as well as drug and pro-drug molecules in prokaryotes and eukaryotic cells. We illustrate from multiscale modeling how transmembrane proton flux couples within a POT protein to drive essential steps of the full functional cycle: 1) protonation of a glutamate on transmembrane helix (TM) 7 opens the extracellular gate, allowing ligand entry; 2) inward proton flow induces the cytosolic release of ligand by varying the protonation state of a second conserved glutamate on TM10; 3) proton movement between TM7 and TM10 is thermodynamically driven and kinetically permissible via water proton shuttling without the participation of ligand. Our results, for the first time, give direct computational confirmation for the alternating access model of POTs, and point to a quantitative multiscale kinetic picture of the functioning protein mechanism. SIGNIFICANCEProton-coupled peptide transporters (POTs) utilize transmembrane proton gradient to deliver small peptides and peptide-like drug molecules into cells. Despite extensive biochemical and structural studies, major question regarding protonation-induced shift from inward-facing state to outward-facing state remains obscure. Here, we report direct evidence through multiscale simulations that the extracellular salt bridge controls the outward-open conformational transition of POTs, and how proton influx through POTs couples ligand transport. The computational modeling also suggests a multiscale kinetic mechanism of POTs.

biophysics↗

bioRxiv2021

Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior

The influenza A M2 channel, a prototype for the viroporin class of viral channels, is an acid-activated viroporin that conducts protons across the viral membrane, a critical step in the viral life cycle. As the protons enter from the viral exterior, four central His37 residues control the channel activation by binding subsequent protons, which opens the Trp41 gate and allows proton flux to the viral interior. Asp44 is essential for maintaining the Trp41 gate in a closed state at high pH, which results in asymmetric conduction. The prevalent D44N mutant disrupts this gate and opens the C-terminal end of the channel, resulting in overall increased conduction in the physiologically relevant pH range and a loss of this asymmetric conduction. Here, we use extensive Multiscale Reactive Molecular Dynamics (MS-RMD) and Quantum Mechanics/Molecular mechanics (QM/MM) simulations with an explicit, reactive excess proton to calculate the free energy of proton transport in the M2 mutant and to study the dynamic molecular-level behavior of D44N M2. We find that this mutation significantly lowers the barrier of His37 deprotonation in the activated state and shifts the barrier for entry up to the Val27 tetrad. These free energy changes are reflected in structural shifts. Additionally, we show that the increased hydration around the His37 tetrad diminishes the effect of the His37 charge on the channels water structure, facilitating proton transport and enabling activation from the viral interior. Altogether, this work provides key insight into the fundamental characteristics of PT in WT M2 and how the D44N mutation alters this PT mechanism, and it expands our understanding of the role of emergent mutations in viroporins.

biophysics↗

bioRxiv2021

A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces

Water assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge - and thus to define a new quantitative paradigm for facile proton transport in confined spaces - a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl-/H+ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and - by the simple measure of the mere existence of a water structure - the proton transport would have been predicted to be facile via that oversimplified measure. In this new paradigm, however, the simple presence of water is not sufficient for inferring proton translocation since an excess proton itself is able to drive hydration and, additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport. Significance StatementAs first proposed more than 200 years ago by Grotthuss, proton transport is enabled by a chemical bond-breaking and bond-making proton hopping mechanism through water networks or "wires", often contained within confined systems such as protein channels or nanotubes. Herein, concepts from graph theory are utilized in order to define a new continuously differentiable collective variable (CV) for water wire connectivity and facile proton transport. As such, the water connectivity can be explicitly quantified via free energy sampling, to both qualitatively and quantitatively describe the thermodynamics and kinetics of water-facilitated proton transport via Grotthuss hopping - something that has been lacking since the first conceptual identification of this key chemical process in Nature.

biophysics↗

bioRxiv2021

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

biophysics↗

bioRxiv2021

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central tomaturation inhibition

The assembly and maturation of human immunodeficiency virus type-1 (HIV-1) requires proteolytic cleavage of the Gag polyprotein. The rate-limiting step resides at the junction between the capsid protein CA and spacer peptide 1, which assembles as a six-helix bundle (6HB). bevirimat (BVM), the first-in-class maturation inhibitor drug, targets the 6HB and impedes proteolytic cleavage, yet the molecular mechanisms of its activity, and relatedly, the escape mechanisms of mutant viruses, remain unclear. Here, we employed extensive molecular dynamics (MD) simulations and free energy calculations to quantitatively investigate molecular structure-activity relationships, comparing wild-type and mutant viruses in the presence and absence of BVM and inositol hexakisphosphate (IP6), an assembly cofactor. Our analysis shows that the efficacy of BVM is directly correlated with preservation of six-fold symmetry in the 6HB, which exists as an ensemble of structural states. We identified two primary escape mechanisms, and both lead to loss of symmetry, thereby facilitating helix uncoiling to aid access of protease. Our findings also highlight specific interactions that can be targeted for improved inhibitor activity and support the use of MD simulations for future inhibitor design.

biophysics↗