Physical Chemistry Chemical Physics

There has been a surge in antibiotic resistance in recent years, making traditional antibiotics less effective against key pathogens. RNA has recently emerged as a potential target for antibiotics due to its involvement in crucial microbial functions. It is possible to expand the range of therapeutic targets by using RNA-based therapies, but it remains necessary to improve the molecular-level understanding of interactions between RNA and known and potential binders. The SAM-I riboswitch, which controls the transcriptional termination of gene expression involved in sulfur metabolism in most bacteria, is an excellent ligand target. Thus, understanding its behavior with and without ligand complexes would be very helpful for drug design applications. In this manuscript, we studied the interactions between the SAM-I riboswitch and its natural ligand, SAM, which controls riboswitch function, and compared those interactions to its interactions with the very similar small molecular SAH, which does not control riboswitch function, and to its interactions with a potential binder JS4, identified via virtual screening. From our simulations, we gain a deeper understanding of small molecule interactions with the SAM-I riboswitch. The results reveal how differently the small molecules (SAM, SAH and JS4) bind to and potentially induce conformational changes in the riboswitch. Our findings offer valuable insight into the molecular mechanisms underlying riboswitch RNA-ligand interactions for the design of more effective RNA-targeting therapeutics.

The conformational dynamics of a model cationic protein in water and in the presence of anionic sodium dodecyl sulphate (SDS) and cationic cetyltrimethylamonium bromide (CTAB) surfactants at different concentrations were investigated using all-atom molecular dynamics simulations. Free-energy landscapes constructed along principal components reveal a compact, well-defined native basin at 25 {degrees}C in water, whereas elevated temperature (100 {degrees}C) induces a broadening of the conformational space and the emergence of multiple metastable states. The presence of surfactants further modulates this behavior in a concentration-dependent manner. Cluster population analysis shows that SDS promotes a highly heterogeneous ensemble characterized by reduced dominance of the native-like cluster, while CTAB partially protects the protein from thermal denaturation at higher concentrations. Radial distribution functions demonstrate strong accumulation of SDS headgroups around the protein and pronounced insertion of SDS alkyl tails into hydrophobic protein regions, indicating direct hydrophobic destabilization and micelle-assisted unfolding. In contrast, CTAB exhibits weaker headgroup association owing to electrostatic repulsion and reduced tail-hydrophobic contacts, suggesting a less disruptive interaction mechanism. At high concentration, CTAB aggregates provide a structured hydrophobic environment that stabilizes the folded state and suppresses denaturation. Together, these results provide a molecular-level picture of how surfactant chemistry and concentration govern the conformational stability of a cationic protein, highlighting the dominant role of hydrophobic interactions in surfactant-induced denaturation at high temperature. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/717321v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@f68004org.highwire.dtl.DTLVardef@14e9a98org.highwire.dtl.DTLVardef@18771d3org.highwire.dtl.DTLVardef@141fc6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

Polyethylene terephthalate (PET) is a commonly used plastic worldwide and reducing its prevalence is crucial to improving environmental pollution. PETase that degrades PET plastic have received a lot of attention recently. This paper evaluates the ester hydrolysis process under both acidic and basic conditions, and shows that the local environment of the protein active site takes advantage of both. High pH in the protein buffer creates a better nucleophile to attack the ester through a proton shuttle channel in the protein, while local hydrogen bonds to the carbonyl of the ester stabilizes the intermediate/transition state of the hydrolysis reaction. With the understanding at the atomic level, we propose two engineering directions that can potentially improve the reactivity of the PETase: 1) increase the alkaline stability of the protein in general; 2) perturb the local hydrogen bond network to increase the partial charge on the PET carbonyl to be hydrolyzed. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/703441v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@151b69borg.highwire.dtl.DTLVardef@1abb95dorg.highwire.dtl.DTLVardef@116a225org.highwire.dtl.DTLVardef@ef2bb1_HPS_FORMAT_FIGEXP M_FIG C_FIG

Lebers Hereditary Optic Neuropathy (LHON) is a rare genetic condition and severe neurological disorder characterized by dysfunctional mitochondria under extreme oxidative stress, resulting in retinal ganglion cell death and subsequent rapid bilateral loss of central vision. The m.14484T>C mutation in the ND6 subunit of mitochondrial complex I is known for inducing LHON, and is a prevalent LHON-associated mutation, yet its mechanism of impairment at the molecular level is currently unresolved. In this study, we explore the biophysical underpinnings of this mutation and its role in LHON through disruption of human complex I function. We consider, using atomistic simulations, the differential thermodynamics and kinetics of coenzyme Q10 binding between the mutant and wild-type forms, altered dynamics of the complex upon mutation, and key interactions between coenzyme Q10 and complex I binding sites. The hydrogen bond network present near and within the coenzyme Q10 binding domain, along with proper hydration of E-channel residues that couple redox chemistry to proton pumping, is found to be critical for complex I stability and quinone binding, which the ND6-centered mutation disrupts.

This study presents a comprehensive analysis of the dynamic properties and allosteric regulation mechanisms of Class A G protein-coupled receptors (GPCRs) by integrating molecular dynamics (MD) simulations with nuclear magnetic resonance (NMR) relaxation measurements. Utilizing generalized order parameters derived from NMR data and MD trajectories, we quantitatively assess conformational entropy changes that occur during receptor activation and ligand binding events. This approach enables a detailed characterization of protein flexibility at multiple timescales, revealing how dynamic fluctuations contribute to allosteric signal transmission within the receptor. Our results demonstrate that conformational entropy plays a pivotal role in modulating the functional states of Class A GPCRs, influencing the equilibrium between inactive and active conformations. By elucidating the interplay between structural dynamics and allostery, this work advances the molecular-level understanding of GPCR function and highlights the importance of entropy-driven effects in receptor signaling. The integrative methodology and findings provide a valuable framework for future investigations aimed at targeting receptor dynamics in drug discovery and rational design of allosteric modulators.

Retinal is a chromophore covalently bound to various photoreceptors. Its photo-induced isomerization triggers a series of structural changes named photocycle, leading to diverse biological functions. Despite tremendous advances in structural biology and artificial intelligence-driven structure prediction, it remains challenging to analyze all photocyclic intermediates. Here, we present an optimized computational approach to calculate RSBH+ isomerization and its induced structural changes based on a classical molecular mechanics approach using quantum mechanically improved retinal force field parameters. Isomerization is induced by an excited state restraint which is subsequently relaxed to allow the return to the electronic ground state. We applied this approach to the key protein of optogenetics, Channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Besides the reformation of the alltrans/CN-anti ground state, we observed the production of a mixture of two isomeric states 13-cis/CN- anti and 13-cis/CN-syn. These findings agree with the previously found branched photocycle model based on experimental data. Our calculations show an asymmetric potential energy landscape of the excited state leading to a corresponding isomerization state distribution. Unlike earlier publications, our procedure describes the retinal photoisomerization on the natural timescale of 500 fs. As our newly derived retinal force field parameter set precisely relies on quantum biological knowledge, it assists to improve the refinement of experimental structure biological data. Our readily customizable strategy provides mechanistic insights at high spatio-temporal resolution, which permits accurate structural predictions of early photocycle intermediates. These insights will stimulate the rational design of optogenetic tools thus providing improved diagnostic and therapeutic approaches for neuronal and other diseases. HighlightsO_LIuniversal method to study molecular mechanism of optogenetic tools C_LIO_LIretinal photo-isomerization calculation in real time C_LIO_LIprediction of branched photo cycle agrees with experimental IR spectroscopic results C_LIO_LIdetected asymmetric excited state potential energy landscape C_LIO_LIassists to improve structural model refinement of retinal proteins C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=116 HEIGHT=200 SRC="FIGDIR/small/707937v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@71f7fdorg.highwire.dtl.DTLVardef@503482org.highwire.dtl.DTLVardef@1a77120org.highwire.dtl.DTLVardef@1f410a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Protein condensates that form via phase separation typically become more viscous over time and can harden in a process referred to as "molecular aging". Several mechanisms have been identified for this phenomenon. Of these, the ones involving enhanced {beta}-sheet or -strand interactions are of pathological relevance since they have been associated with neurodegeneration. Although there is much understanding of biopolymer phase behavior, an inclusive thermodynamic framework that unifies phase separation and {beta}-sheet-based aging is lacking. We present a time-dependent, multi-component extension of associating polymer theory that describes phase separation and aging of an intrinsically disordered protein (IDP) capable of associating through local, reversible folding. The model shows how the Second Law of Thermodynamics applies throughout, whether phase separation precedes and encourages aging or, vice versa, whether the increase in "stickiness" during aging drives phase separation. Our calculations show how the time-dependence of the average valency of associating sites determines the aging kinetics and the development of viscoelastic properties of a biocondensate. The agreement between our calculations and the change in dynamics of condensates of perfect repeat analogues of nucleoporin-98 not only validates the theory but also identifies these Nup98 variants as model systems for studying aging.

Nuclear Pore Complexes (NPCs) are large protein complexes in eukaryotic cells that span the double-membrane of the nucleus and regulate bi-directional transport between nucleus and cytoplasm. T h e NPC core is lined by intrinsically disordered protein chains called nucleoporins (Nups) which form a selective barrier where large macromolecules (cargoes) need to bind to nuclear transport receptors (NTRs) such as Karyopherins (Kaps) to cross. Previous experimental results have suggested that not only Nups but Kaps, too, are important in the transport process of other NTRs/NTR-cargo complexes. In this work, we assess the role of Kaps in the transport of other NTRs (specifically, NTF2s) through the NPC, a process referred to as the "Kap-centric transport model". Here, using coarse-grained MD simulation we show that Kaps are able to direct NTF2s into the Nup meshwork, which leads to their increased flow. Our results also suggest that NTRs follow specific lanes inside the pore to maximize efficient transport.

Protein translation is a highly regulated process influenced by multiple factors at the initiation, elongation, and termination stages. One notable regulatory element of the ribosome is the CAR interaction surface, a three-residue motif in the structure of the ribosome composed of C1274 and A1427 of S. cerevisiae 18S rRNA (corresponding to C1054 and A1196 in E. coli 16S rRNA) and R146 of ribosomal protein Rps3. CAR is highly conserved and positioned adjacent to the amino-acyl (A site) decoding center. It establishes hydrogen bonds with the +1 codon next in line to enter the ribosome A site, acting as an extension of the tRNA anticodon and forming base-stacking interactions with nucleotide 34 of the tRNA. However, despite CARs enzymatically strategic positioning within the ribosome, its functional relationship with the A site remains poorly characterized. Using molecular dynamics (MD) simulations, we examined the interplay between the A site and CAR site, revealing sequence-dependent modulation of H-bonding and {pi}-stacking interactions within and between the two sites. These findings highlight the interplay between the A site and CAR site, suggesting a structural and functional connection between these two regions of the ribosome that may contribute to mRNA sequence-specific tuning of translation elongation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/714784v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1d783d3org.highwire.dtl.DTLVardef@f9cd8org.highwire.dtl.DTLVardef@102667corg.highwire.dtl.DTLVardef@967c56_HPS_FORMAT_FIGEXP M_FIG C_FIG

O_LIThe N-terminal signal sequences of plant cytochrome P450 enzymes are recognized as critical determinants for subcellular localization and functional diversification, yet their evolutionary drivers and mechanisms remain largely unresolved. C_LIO_LIIn this study, the evolutionary trajectories of these signals were systematically decoded through the integration of the protein language model ESM-2 with phylogenetic and selection analyses. A conserved functional fingerprint was identified. This region may serve as the essential endoplasmic reticulum targeting signal and be evolutionarily decoupled from adjacent surfaces under positive selection during lineage-specific expansions. C_LIO_LIA functional-adaptive decoupling model is proposed to explain this pattern, wherein a conserved functional core is maintained while surrounding interfaces diversify. This evolutionary architecture is interpreted as the outcome of a two-step cycle: an initial phase of positive selection driving functional innovation, followed by pervasive neutral evolution that facilitates structural exploration and potentiates future adaptations. C_LIO_LIThis work demonstrates how interpretable machine learning can be integrated with evolutionary theory to reconcile neutralist and selectionist perspectives on protein evolution. A novel framework is thus provided for understanding the layered evolution of protein modules, where structural constraint, adaptive innovation, and neutral drift operate on distinct tiers to generate functional diversity. C_LI

Intercalation of small molecules between DNA base pairs affects DNA conformation, disrupting essential cellular processes including replication, transcription, and repair. We investigated conformational changes in 18-mer DNA upon intercalation of doxorubicin, SYBR Gold and YOYO-1 using extensive MD simulations. Two main patterns for the intercalation were identified: RISE-type intercalation occurs between adjacent base pairs and extends the DNA helix with decreased twist angles, while OPEN-type intercalation proceeds through base-pair opening without significant DNA extension. Kinetic analysis revealed that association rates for intercalation followed the order: first YO-moiety (mono-intercalation) > SYBR Gold > doxorubicin > YOYO-1 (bis-intercalation). Free energy landscape showed that forces at DNA termini reached up to 117 pN during stretching. Notably, base pairs adjacent to intercalators were protected from strand separation, accompanied by additional helical unwinding. MM-PBSA/GBSA analysis revealed that the driving force for intercalation is the stacking energy, and the binding affinity was highest for minor groove binding. Persistence length decreased with single molecule binding but recovered with two molecules due to their electrostatic repulsion. Mechanical properties of intercalated DNA showed position-dependence, demonstrating that multiple intercalation modes coexist in solution. The heterogeneous nature of intercalation explains why experimental measurements reflect ensemble averages rather than single binding configurations.

Proton pumping by respiratory Complex I is one essential element for generating the proton motive force that drives ATP synthesis in mitochondria. Although it is understood that electrons from NADH reduce ubiquinone at the peripheral arm and that four protons are transferred in the membrane domain, the mechanism by which this redox reaction initiates proton translocation remains unclear. A lateral pathway linking the quinone binding site to the membrane domain via ND1, ND3, and ND4L subunits has been proposed as the initial path of an excess proton. However, in experimental structures this region lacks a continuous water network between D66ND3 and E34ND4L, resulting in a hydration bottleneck that may regulate proton transfer. Using multiscale reactive molecular dynamics (MS-RMD) and a water wire connectivity metric, we directly simulate proton transport through this region as coupled the the hydration by water molecules. Our results reveal that proton transfer is thermodynamically feasible when transient hydration aligns with the presence of an excess proton, revealing the strong coupling between hydration and proton (PT) in this region of Complex I. These findings support a model where proton injection enhances local hydration, dynamically opening the pathway for proton transfer and regulating the onset of proton pumping in Complex I.

We have conducted all atom molecular dynamics simulations of POPC and DPPC lipid bilayers using AMBER Lipid21 force field with eight different water models, including SPC/E, TIP3P, TIP3P-FB, TIP4P-FB, TIP4P-Ew, TIP4P/2005, TIP4P-D, and OPC, to identify the most compatible one without any modification. A number of parameters have been computed in order to understand the structure of the lipid bilayer: Area per lipid, Isothermal compressibility modulus, average Volume per lipid, electron density profile, bilayer thickness, X-ray and neutron scattering form factors, deuterium order parameter, and radial distribution function. The estimated Area per lipid, Isothermal compressibility factor, volume per lipid and bilayer thickness are highly consistent with experimental results for the SPC/E water model, indicating its suitability with the AMBER Lipid21 force field, insted of any modification. The bilayer electron density profiles of both the lipid bilayers demonstrate a little augmentation of water penetration with respect to the membrane surface for TIP4P-D water model. However, the experimental X-ray and neutron scattering form factors are aligning well with the simulated results for all studied water models, and TIP4P-D shows better for X-ray data. The deuterium order parameter for lipid acyl chains value less than 0.25 for all observed water models, depicting their disorderness for both the lipid bilayers. The lateral diffusion and reorientation autocorrelation function of the lipid molecules in both the bilayers are computed to reveal their dynamics across all water models. In comparison to other water models, the simulated trajectories predict better structure and reasonably fair dynamic properties for the SPC/E water model. The TIP4P-Ew water model reproduces the lateral diffusion co-efficient in close agreement with experiment. Reorientational dynamics for both the lipids in the bilayers for eight different water models are observed; the presence of slow and slowest time components corresponds to the lipid axial motion (wobble motion) and Twist/Splay motions. So, in view of the overall performance of the different water models with the AMBER Lipid21 all atom force field in reproducing membrane physical properties, the SPC/E water model appears to be an optimal choice.

Coral, as a bioreactor, has to continuously interact with surrounding environment to maintain a healthy state. A multi-physics reaction engineering model has been developed to capture this interaction. The coral interior is modeled as interconnected reaction units respectively for photosynthesis, respiration, and calcification, whose reaction kinetics are influenced by environmental fluctuations. Coupling between coral and environment is realized by bi-directional mass transfer at the coral-seawater interface, with consideration of the unique flow fields induced by ciliary beating. By resorting to this comprehensive model, we discover that ciliary beating demonstrates distinctively different diurnal and nocturnal functions. During daytime, beating can help reduce photosynthetic oxygen accumulation to prevent hyperoxia-induced mortality, while enhancing carbon dioxide uptake efficiency to promote nutrient production. At night, however, beating promotes oxygen acquisition for adequate respiration, while expelling carbon dioxide to inhibit symbiotic destruction under acidic stress. The model further enables mechanistic analysis of the detrimental impact of climate change on coral health, where the influences from two key factors (i.e., temperature and CO2 level) can be decoupled. Its interesting to find out that the elevated temperature plays a dominant role during daytime, while at night the coral is dominantly influenced by rising CO2 level.

Single molecule methods have become prevalent tools in elucidating molecular processes across various life science fields over the past three decades, driving breakthroughs in understanding their underlying molecular mechanisms. In our study, we employed two single-molecule methods, Forster Resonance Energy Transfer (smFRET) and high-resolution optical tweezers, to investigate the transcription of Mycobacterium tuberculosis RNA polymerase (MtbRNAP) from initiation through to termination. We aim to provide a set of comprehensive biophysical tools to deepen our current understanding of MtbRNAP and its transcription factors. These experimental assays represent an important step towards unraveling the molecular dynamics and interactions that support transcription in Mycobacterium tuberculosis.

The Na+-pumping NADH-quinone oxidoreductase (Na+-NQR) is a respiratory chain enzyme found in pathogenic bacteria, including Vibrio cholerae, and is essential for energy metabolism by generating a transmembrane Na+ gradient that drives ATP synthesis and flagellar motility. Because the molecular structure of Na+-NQR is unrelated to the corresponding mitochondrial H-pumping NADH-quinone oxidoreductase (respiratory complex I), it is a promising antibiotic target. Although it has been shown that Na+ pumping is mediated by an alternating-access conformational change in the NqrD/E subunits, coupled to redox switching of a cofactor, the thermodynamics and kinetics of the conformational transition, including the free-energy profile and the rate-limiting steps, remain unclear. Here, we construct redox-state-dependent Markov state models (MSMs) from extensive molecular dynamics (MD) trajectories in the oxidized and reduced states to quantify the conformational free-energy landscapes and primary transition pathway. To accelerate conformational sampling, MD simulations are initiated from diverse NqrD/E conformations generated by AlphaFold. Our analysis clarifies how the NqrD/E conformation is regulated by the redox state and by Na+ binding to achieve Na+ translocation. This study provides a quantitative framework for understanding ion-pumping mechanisms of redox-driven membrane proteins.

Granulocyte macrophage-colony stimulating factor (GM-CSF) is a cytokine that plays a role in immune modulation. Its expression is associated with a multitude of different effects ranging from harmful, as in diseases such as rheumatoid arthritis and multiple sclerosis, to beneficial, as in the case of mitigation of diabetes type I and neutropenia. However, there is a large gap in knowledge explaining how GM-CSF toggles its structure for such physiological and pathological interactions. Our work describes an ongoing attempt to address this gap by focusing on a clustered histidine triad within -helices near the N-terminus, which prior studies have suggested play a role in binding ligands at an acidic pH. While GM-CSF is known to be highly flexible at a more acidic pH, several properties of its histidine triad remain unclear at the physiological pH at which GM-CSF would encounter its binding partners. We describe an effort to characterize the role of the GM-CSF histidines under physiological pH, specifically to determine if these histidines are key to GM-CSF structural integrity, and whether individual histidine residues modulate binding as they do at a lower pH. Our findings reveal that, while the histidine residues have an impact on GM-CSF structure, flexibility, and stability, they alone do not modulate the affinity for ligands at neutral pH. These data provide an initial explanation for the pleiotropic functions and interactions of GM-CSF within a biophysical context. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/700583v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@a6fffcorg.highwire.dtl.DTLVardef@1f00c30org.highwire.dtl.DTLVardef@b04c50org.highwire.dtl.DTLVardef@6224d9_HPS_FORMAT_FIGEXP M_FIG C_FIG

Douglass Cooperativity and Ciullis Cooperativity in induced-proximity systems, remains controversial with paradoxes such as path-dependent metrics and apparent universal negative Cooperativity. We noticed that in "partial-embedded" model, a substantial portion of giant ligand remains exposed outside and does not engage with the host proteins force field. It incurs an entropic cost due to the restriction of translational/rotational degrees of freedom. This large, mass-dependent unfavorable ligand entropy penalty normally shifts binding affinity to 104[~]108-fold. ITC thermodynamic cycles analysis confirmed the dramatic entropy loss among reaction pair. This reconciles the conflicting Cooperativity definitions, yielding true path-independent positive PPI Cooperativity from observed entropy loss subtracting ligand entropy penalty. ITC data showed rigid linkers appear superior to flexible linkers with respect to both oral bioavailability and safety profile in PROTAC design. "ligand entropy barrier wall/Cooperativity ladder" pair is not only impact induced-proximity systems but also constitute the physical basis for all biosystems.

Reactive oxygen species generated during inflammation can oxidize viral envelope lipids, with outcomes ranging from modulated infectivity to viral inactivation. For SARS-CoV-2, the molecular mechanisms by which membrane lipid oxidation influences spike protein anchoring remain poorly understood. We use all-atom molecular dynamics (MD) simulations to quantify how graded oxidation of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) affects the anchoring of the SARS-CoV-2 spike transmembrane (TM) region in an endoplasmic-reticulum-Golgi intermediate compartment (ERGIC)-like multicomponent membrane. Viral envelopes containing 0, 25, 50, 75, and 100% oxidized POPC (PoxnoPC) corresponding to 0 - 55% oxidation of all PO-type phospholipids were simulated with the spike TM helix and cytoplasmic tail embedded in a POPC/POPE/POPI/POPS/cholesterol mixture. Steered MD and umbrella sampling were used to calculate the potential of mean force (PMF) for extracting the TM+CT region along the membrane normal. Partial oxidation (25 - 75% POPC) produced reductions in the detachment barrier that were not statistically distinguishable from the native system within the sampling uncertainty, whereas full POPC oxidation lowered the anchoring free energy by about 23% (from 606 {+/-} 39 to 464 {+/-} 38 kJ mol-1), indicating that oxidation of roughly half of the glycerophospholipids can measurably weaken spike-membrane coupling. Despite this reduction, the remaining barrier (about 180kBT ) is still large, suggesting that oxidation alone may be insufficient for spontaneous spike detachment and likely acts synergistically with mechanical forces during fusion or immune engagement. Analysis of acyl-chain order parameters, area per lipid, membrane thickness, number-density profiles, and lateral lipid clustering reveals that POPC peroxidation decreases lipid order, thins and softens the bilayer, and disrupts cholesterol-stabilized clusters that refer to large cooperative lipid assemblies (>10 lipids) identified via RDF-based clustering. These oxidation-induced changes reduce hydrophobic matching around the TM helix and facilitate its extraction from the viral envelope. Our results provide a mechanistic link between lipid peroxidation, membrane nanostructure, and spike anchoring, supporting lipid oxidation for example during cold atmospheric plasma or ozone treatment as a physically grounded contributing antiviral mechanism against SARS-CoV-2.

Targeted protein degradation is an emerging approach that utilizes cellular degradation pathways to inhibit a target protein. Small molecules such as molecular glues or PROTACs can be used to mediate the formation of a ternary complex with an E3 ligase and the target protein, which can dramatically enhance the degradation process. This approach is promising for cancer therapy, where degradation of oncogenic proteins can lead to cancer cell toxicity. To design new molecular glues, it is important to develop methods that predict how well a given molecule stabilizes a protein-protein interaction. However, conventional molecular dynamics simulations face challenges in capturing the long-timescale binding and unbinding events that would be used to evaluate this stabilization. In this study, we developed a strategy that allows us to evaluate the stability of protein-protein interactions in the presence of a glue molecule using weighted ensemble simulations in combination with weakened protein-protein interactions. Using this strategy, we generated unbinding trajectories of the DCAF15-RBM39 system with small molecules E7820, Indisulam, and several other Indisulam analogs. We were able to observe distinctly different behaviors between systems with different glues, which was in agreement with their reported EC50 values. We believe this approach could aid drug discovery efforts by expanding the set of druggable targets and improving the success rate of molecular glue development.