Physical Chemistry Chemical Physics

The molten globule (MG) state is an intermediate in the unfolding pathway of proteins, typically triggered by denaturing agents such as urea, extreme pH, high pressure, or heat. The microscopic details of such states are far from understood. Here we study the MG states in protein Hen Egg-White Lysozyme (PDB ID: 1AKI) using microscopic constant pH molecular dynamics (CpHMD) simulations and experiments across a wide pH range. We observe that the titratable residues act as key drivers of conformational fluctuations, promoting the emergence of MG states at extreme pH. These states display partial unfolding, and small global structural changes (< 7% deviation). Hydration around the fluctuating acidic residues shows reduced water density and weakened hydrogen bonding at low pH. At high pH, hydration around acidic residues increases relative to pH = 7, whereas hydration around basic residues decreases. The translational and rotational dynamics of hydration water also exhibit pronounced pH dependence: the translational diffusion coefficient (Dtrans) increases linearly with decrease in pH in acidic medium and increases linearly with increasing pH in the basic regime. The rotational diffusion (Drot) shows similar dependencies on pH except a break at pH {approx} 4 corresponding to acidic residue pKa values. Our results may be useful to identify ligand binding of lysozyme in extreme pH conditions.

In mammalian cells, lipid monolayers support the integrity of lipid droplets (LDs), organelles that function as storage for neutral lipids. Liver-targeting illnesses such as liver cancer interrupt normal LD metabolism and prompt changes in the chemical content of these organelles, which can have effects on structural and organizational behavior of the lipids. In LDs, liver cancer induces concentric crystalline phases of cholesteryl esters (CEs) and triglycerides near the NL-monolayer interface, which become more pronounced as CE concentration increases. Yet, there is little known about how this phenomenon may link to persistence of undigested LDs in liver cancer patients. To shed light on this, all-atom molecular dynamics simulations were used to model LD micropipette aspiration experiments and gain insight into the effect of CE concentration on partitioning, structural, and mechanical properties of LDs. We successfully model micropipette aspiration by application of constant surface tension laterally, which stretches lipid bilayers and monolayers as the magnitude increased. The results show increased phospholipid packing due to insertion of CE fatty tails into the monolayer. Increasing CE concentration induces a non-linear change in surface packing defects on the LDs, notable rigidification, and stiffness. Taken together, these insights improve our understanding of the physical properties at the LD monolayer-core interface during liver cancer progression.

Intrinsic tryptophan fluorescence is widely used as a sensitive reporter of protein conformational dynamics, yet the molecular origin of its temperature-dependent modulation remains unclear. Here we investigate the conformational dynamics of Trp134 in bovine serum albumin (BSA) using molecular dynamics (MD) simulations, free-energy calculations based on umbrella sampling and WHAM, quantum mechanical (QM) calculations, and QM/MM approaches. MD simulations show that the global structure of BSA remains stable while temperature induces a gradual population shift from the Ia+ to the Ia- rotamer. The corresponding free-energy landscapes reveal that this shift arises from subtle changes in basin stability and transition barriers along the rotameric coordinate. In contrast, standalone QM calculations on isolated tryptophan predict different energetic trends, highlighting the sensitivity of rotamer stability to electronic-structure treatments and environmental effects. QM/MM calculations partially reconcile these differences by incorporating the protein environment. Together, these results suggest that temperature reshapes the rotamer free-energy landscape of Trp134, leading to population shifts that modulate intrinsic tryptophan fluorescence in proteins.

The repair of photo-induced DNA lesions through nucleotide excision repair machinery is still the source of important questions. It has been observed that the repair rate of the different cyclobutane pyrimidine dimers, i.e. the photoproducts induced by dimerization of two {pi}-stacked pyrimidines (T<>T, T<>C, C<>T, C<>C), depends on the nucleobases involved in the lesion. TT derivatives (T<>T) are removed more slowly than those containing cytosine, especially in 5. Using all-atom molecular dynamics simulations and free-energy calculations, we demonstrate that the variation of the repair rate observed in human skin and in cultured cutaneous cell is associated to the recognition of the four lesions by the DDB2 protein moiety, and more specifically by the differential structural deformation induced on the complementary strand. Indeed, while C<>C and C<>T induce a larger deviation on the groove parameters, T<>T and T<>C, instead, affect DNA structure to a lesser extent. less affected. These effects then hamper differentially the downstream recruitment of the repair complexes. The observed DNA deformation correlates with the experimental repair rate and provides a structural rationale for the different repair rates of CPD by nucleotide excision repair machinery. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/724087v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@cf6b6dorg.highwire.dtl.DTLVardef@195e35forg.highwire.dtl.DTLVardef@1829296org.highwire.dtl.DTLVardef@165baba_HPS_FORMAT_FIGEXP M_FIG C_FIG

DNA topology is a key regulator of chromatin structure and transcription, yet its direct role in transcription factor recognition remains unclear. Here, we investigate how distinct DNA topological states modulate binding of the Saccharomyces cerevisiae bZIP transcription factor GCN4 using topologically defined plasmids. By combining, complementary biochemical approaches, including Bio-Layer Interferometry applied here for the first time to topology-dependent protein-DNA interactions, we show that DNA supercoiling directly reshapes GCN4-DNA recognition. Positively supercoiled DNA forms more stable and persistent complexes, whereas negatively supercoiled DNA retains greater conformational heterogeneity. To interpret these effects, we performed multiscale molecular simulations. Coarse-grained simulations of plasmids recapitulate the global topology-dependent trends observed experimentally, while matched minicircle models reproduce the same behaviour at the local scale. In strong agreement with experimental data, simulations reveal that DNA topology modulates the conformational ensemble of the GCN4 basic region. Overall, positively supercoiled DNA promotes a more ordered binding mode and localized protein distribution, whereas negatively supercoiled DNA supports increased structural plasticity. These findings identify DNA topology as an active determinant of transcription factor recognition and provide a multiscale framework linking global DNA mechanics to local protein-DNA interactions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/722604v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@18f8ba9org.highwire.dtl.DTLVardef@11a395dorg.highwire.dtl.DTLVardef@ac093borg.highwire.dtl.DTLVardef@923212_HPS_FORMAT_FIGEXP M_FIG C_FIG

Invertebrate vision relies on bistable visual pigments flipping upon photon absorption between rhodopsin and metarhodopsin states. In living butterflies, the UV-VIS absorption spectra of rhodopsin and metarhodopsin, respectively with 11-cis and all-trans isomers of 3-hydroxy-retinal (A3) chromophore, can be conveniently recorded from the eyeshine, the light reflected from the compound eye after passing twice through the light-guiding rhabdoms. * Here, a microscope coupled with a broadband LED source and a microspectrometer was used to record photorelaxations reported in eyeshine reflection spectra. Fitting temporal exponential relaxations to log-reflectance arrays yielded transient and baseline spectra that are analogous to absorbance difference and sum, respectively. Both types of spectra were subjected to singular value decomposition and to fitting of templated visual pigment absorption spectra. * The compound eye of the high brown fritillary Fabriciana adippe was exposed to a series of second-long broadband light pulses, causing photorelaxations with time constants between 40 and 120 ms that led to 80% metarhodopsin in equilibrium. The transient and baseline spectra were fitted with pigment templates, estimating the alpha peak wavelength 547-552 nm for rhodopsin and 496-501 nm for metarhodopsin. The metarhodopsin to rhodopsin alpha peak absorbance ratio 1.25-1.35 is consistent with the isosbestic wavelength at 530 nm. The second isosbestic wavelength indicates that rhodopsin beta (UV) peak absorbs more strongly than metarhodopsin below 405 nm. * Baseline spectra, which were not explicitly analysed in previous studies, enable concatenation of exposures, monitor long-term changes of pigment, and enhance the estimation of beta peak parameters. * The method can be directly used in many butterflies and could be adapted to other insects, particularly fruitflies, facilitating studies of the relation between the visual pigment spectra and the opsin sequences. Spectroscopic results can be complemented with physiologically measured photoreceptor spectral sensitivity datasets and analysed with the same global fitting procedure.

Genomic organization within the nucleus is crucial for gene regulation and cell health, as disruptions in this organization are linked to genetic disorders and cancers. Recent studies suggest that molecular-scale organization of chromatin near the nuclear periphery (lamina-associated domains, LADs) affects gene regulation, providing transciptional supression, but the biophysical mechanisms of supression behind remain unclear. LADs are large heterochromatic regions near the nuclear lamina, where transcriptional factors and RNA polymerase are scarce, implying a nonspecific filtering property. Here, we investigate the steric filtering capabilities of LADs by performing coarse-grained polymer simulations. Our results show that LAD thickness can be affected by the interaction between chromatin and nuclear periphery as well as chromatin self-compaction. Regardless, the LAD layer acts as a size-selective steric partitioning environment for protein particles limiting their access to nuclear periphery. Notably, increasing bulk protein levels enhances protein access linearly. These results align with experimental observations and suggest that LADs could control the presence of transcription machinery on the periphery of the nucleus, providing a polymer-physical mechanism for gene regulation in nuclei.

The binding of fluorescent dyes to nucleic acids and their fluorogenic properties are indispensable tools for nucleic acid detection, quantification, and imaging, yet the molecular structures of several widely used commercial dyes have remained unknown. Here, we de novo determined the molecular structures of RiboGreen and OliGreen and confirmed the previously proposed structure of PicoGreen using high-field NMR spectroscopy. All three dyes were identified as unsymmetric cyanine dyes, where a benzoxazole/benzothiazole moiety is linked to a 4-quinoline by a monomethine bridge. Complete 1H and 13C resonance assignments enabled us to expand the existing chemical shift reference set for this important class of dyes. Photophysical characterization with standardized single- and double-stranded DNA and RNA targets indicated that all dyes performed similarly upon binding despite being marketed towards different nucleic acid types. NMR spectroscopy and long-timescale molecular dynamics simulations showed that RiboGreen interacts with double-stranded DNA predominantly by two binding modes, electrostatic interactions with the phosphodiester backbone and {pi}-{pi} stacking with the ultimate and penultimate base pairs of the DNA molecule. These results establish the molecular structures of three widely used commercial dyes and provide a structural and mechanistic framework for understanding the fluorogenic properties of this class of dyes. HighlightsO_LIDetermination of the molecular structures of nucleic acid dyes RiboGreen, OliGreen, and PicoGreen C_LIO_LINMR spectroscopic characterization of all three dyes. C_LIO_LINMR and MD data indicate binding to be dominated by electrostatic and {pi}-{pi} stacking interactions C_LI

Building on a complex between a tubulin protofilament (PF) and a fragment of the Tau protein containing residues 169 to 367, we investigate the dynamics of the disordered elements of the system, namely the tubulin C-terminal tails (CTTs) and the Tau protein, using classical all-atom molecular dynamics simulations. Our results show that CTTs adopt a hook-like dynamic pattern on the bare PF while remaining highly mobile. The binding of Tau on the PF surface alters the dynamics of the I-CTTs in a sequence-dependent manner. While the repeat domains of Tau are mostly maintained on the PF by weak and strong binding patches with the tubulin cores, the Proline-Rich Region (PRR) relies on the wrapping phenomenon of I-CTTs to fuzzily stabilize its interaction with the PF. Our study thus provides a deep dive into the dynamic interplay between the Tau protein and the CTTs of microtubules, the latter being characterized extensively using a variety of disorder-adapted metrics. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/721901v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@b3f985org.highwire.dtl.DTLVardef@1c2bf70org.highwire.dtl.DTLVardef@a66b95org.highwire.dtl.DTLVardef@1e138e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

HrpZ2, a harpin protein produced by Pseudomonas syringae, a gram-negative plant pathogenic bacterium, elicits hypersensitive response and pathogen defense in non-host plants. Harpins from various bacterial sources elicit varying responses in different non-host plants, due to its structural variations, their precise mechanisms of action are not yet completely understood. As per previous reports, harpins from diverse bacterial sources interact with distinctive members of integral membrane proteins, known as aquaporins. For example, harpin (Hpa1Xoo) interacts with OsPIP1;3 in rice, whereas, in Arabidopsis the harpins Hpa1 and HrpZ interacts with AtPIP1;4 and AtPIP1;3 respectively. Here, we conducted the first genome-wide computational screening of protein-protein interactions between HrpZ2 and all 47 members of tomato aquaporins. Molecular docking identified nine interactors across five subfamilies of aquaporins, with HrpZ2 N-terminal residues mediating these interactions. We validated these via molecular dynamics (MD) simulations, principal component analysis, and free energy landscape analysis, assessing the stability (RMSD, RMSF, radius of gyration), dynamics, and affinity (MM-GMSA). PIP complexes, especially PIP2;1 (-460.46 kcal/mol) and PIP1;7 (-303.82 kcal/mol), exhibited superior stability, compactness, and defined energy minima, confirming PIPs as primary sensors of harpins. Non-PIP aquaporins like TIP1;1 and NIP4;1 showed moderate stability, outperforming weaker interactors (SIP2;1, XIP1;5, XIP1;3). These findings provide robust evidence that HrpZ2 preferentially targets PIPs in tomato, while engaging TIPs and NIPs as auxiliary partners. This multifaceted interaction profile of harpins suggests complex plant-pathogen recognition, modulating aquaporin-mediated cellular responses like growth and stress management in plants.

Proteins in solution adsorb to the corona of nanoparticles such as single-walled carbon nanotubes (SWCNTs), but these interactions are difficult to predict and analyze due to ambiguities in the structure of the latter. In this work, we employ ss(GT)15-DNA wrapped SWCNTs, a commonly used fluorescent sensor construct, to examine protein adsorption by quantifying binding dissociation constants and characterizing the corresponding photophysical effects. A library of 20 proteins are used to evaluate adsorption-induced changes in photoluminescence (PL) intensity ({Delta}I/I0) and emission wavelength upon solution phase binding. We find that 15 proteins produce monotonic dose-response behavior well described using a single-site Langmuir model. Alternatively, five proteins exhibited more complex, non-monotonic behavior consistent with a two-step binding model representing protein-protein interactions coupled to adsorption. The study reveals that metalloproteins, which comprised 12 of the 20 proteins in the library, induced greater PL quenching compared with metal-free proteins for this system, with maximum binding-associated quenching ({Delta}I/I0) of 94% for metalloproteins versus 20% for metal-free proteins. For metalloproteins, we introduce a proximity-based quenching framework in which protein size provides a coarse proxy for cofactor-SWCNT separation, offering a mechanistic interpretation of the observed quenching variation across proteins. Together, these results establish the use of metal coordination sites, such as those in metalloproteins, to assist the transduction of certain nanoparticle fluorescent sensors, helping with sensor probe design and interpretation in biological environments.

When three cyanobacterial proteins--KaiA, KaiB, and KaiC--are incubated with ATP in vitro, the phosphorylation level of KaiC exhibits stable circadian oscillations. Biochemical and structural analyses have shown that KaiCs ATPase activity is crucial for these oscillations, leading to the hypothesis that ATP-consuming dynamics function as a molecular clock, determining the oscillation period of individual molecules. Moreover, these molecular clocks synchronize with one another, resulting in collective oscillations at the ensemble level. In this study, we develop a theoretical model to test this molecular clockwork hypothesis. Our model clarifies the relationship between the oscillation period and ATPase activity, explaining the significant changes in the period induced by amino-acid substitutions near the CI-CII domain boundary of the KaiC hexamer. Furthermore, the model addresses the physical basis for temperature compensation concerning both the oscillation period and ATPase activity. Thus, the molecular clockwork perspective provides a framework for understanding the atomic design behind collective oscillations.

Artemisinin is an effective antimalarial drug sourced from Artemisia annua, but its low and variable yields require enhancement either semi-synthetically or in-planta to meet the global demand for treatment. Though essential enzymes have been identified in the artemisinin biosynthetic pathway, including an essential Cytochrome P450 monooxygenase (CYP71AV1), there are still many unknowns. Cytochrome P450 reductase 1 (herein, AaCPR1), has been experimentally confirmed as an electron transfer partner for CYP71AV1 in its three step oxygenation of key artemisinin precursors. However, the recent discovery of a highly related CPR, herein AaCPR2, introduces the possibility that another, potentially more catalytically favourable interaction, could exist for CYP71AV1. Therefore, enzyme kinetics and differential scanning fluorimetry (DSF) were used in the characterisation of both AaCPR1 and AaCPR2 to determine the existence and source of their catalytic differences. Tested enzyme activity under cytochrome c and NADPH concentrations revealed that AaCPR1 had lower Km and higher kcat/Km values, while AaCPR2 had higher Vmax and kcat values. This suggests that AaCPR1 is more effective at reducing cytochrome c when substrate conditions are limiting, whereas AaCPR2 is more effective than AaCPR1 at reducing cytochrome c when substrate conditions are saturating. This implies a functional partitioning of the two enzymes on the basis of substrate availability. The DSF results provided deeper insight into the different protein-ligand interactions between the two enzymes. AaCPR2 reached lower maximum melting temperatures across all tested conditions, whereas AaCPR1 had higher maximum melting temperatures. Thus, AaCPR1 exhibits higher thermal stability and has a higher temperature threshold than AaCPR2. This contributes to the notion that the AaCPRs are functionally divergent also on the basis of temperature. The cumulative differences in melting behaviour between the two enzymes led to the hypothesis that AaCPR1 and AaCPR2 exhibit different domain motions that may lead to preferential catalysis for one redox partner over another. This was further supported by the prediction of a highly variable loop region between the two enzymes at the connecting domain just after the flexible hinge. If such loops are highly mobile, as predicted, then the residue differences therein could provide a bio-structural basis for the kinetic and thermal/biophysical differences observed between AaCPR1 and AaCPR2. These data support that AaCPR1 and AaCPR2 possess fundamental biophysical differences despite their high degree of relatedness. Ultimately, these differences suggest differential metabolic functions of the two enzyme in artemisinin biosynthesis and/or other important secondary metabolic processes.

The isolation of cellulose nanofibrils (CNFs), a promising precursor for sustainable and high-performance materials, has relied on chemically intensive, energy-demanding processes. As these processes were originally designed for the isolation of CNFs from wood, we herein show that the intrinsic ultrastructure of non-structural plant cells provides unique opportunities, namely direct access to loosely organized cellulose nanonetworks. We demonstrate that this loose nanofibrillar tissue can be transformed into CNFs with sizes down to elementary nanofibrils ([~]4 nm) at high yields (reaching [~]32%) under exceptionally mild hydrothermal conditions. Three distinct plants were evaluated and the physicochemical properties of the obtained nanonetworks and corresponding CNFs were thoroughly studied, including the hydrodynamics of the resulting gels. Films prepared from the obtained CNFs showed similar performance to those obtained from conventionally isolated wood-based CNFs. Overall, this study demonstrates that CNFs can be obtained through low-intensity, hazard-free, processes from widely available biomass. Thus, this approach offers a unique shift in the range of opportunities to produce CNFs facilitating the integration of their use into the food supply chain, biomedical applications, and other regulatory-constrained applications.

Rhizosphere oxidation is a key adaptive mechanism in reductive soil environments, in which oxygen released from roots alters rhizosphere redox conditions and regulates biogeochemical processes. Rice plants possess an internal oxygen transport system, and radial oxygen loss (ROL) from roots is closely associated with root development. However, the spatial patterns of ROL in soil and their relationships with root traits remain poorly characterized. In this study, we developed a multimodal imaging system that integrates planar oxygen optodes with X-ray computed tomography to simultaneously visualize rhizosphere oxidation and root development in rice. Daily time-course tracking of individual crown roots revealed dynamic changes in the spatial distribution and magnitude of rhizosphere oxygen in relation to root elongation and aging. Root thickness was positively correlated with dissolved oxygen levels near root tips. Genotypic comparisons further identified a cultivar with reduced rhizosphere oxidation despite possessing thicker roots among the tested genotypes, thereby indicating the involvement of additional physiological processes. Overall, these findings demonstrate that rhizosphere oxidation is regulated by root growth stage and thickness and dynamically modulated during root development.

Mycobacterium tuberculosis fatty acid synthase I (Mtb FAS-I) is a multifunctional hexameric complex essential for fatty acid (FA) synthesis. The need of a hexameric structure for activity of the complex in Mtb remains elusive. Here, we model a conformation of the functionally active complex with acyl carrier protein (ACP) at ketoacyl synthase (KS). Our model reveals a crucial cross-dome dependence in the mechanism of FA synthesis at the condensation step. Using molecular dynamics simulation, we identify key ACP and KS residues that mantain persistent interactions. ACPs phosphopantetheine (PPT) arm adopts several conformations while accessing KSs catalytic pocket, including two distinct conformations that correlate with volumes of ACP and KS pockets. A PHE residue, reported as a gatekeeper of the KS pocket in other species, also shows open and closed orientations in our simulation. Our results provide crucial insights that are essential for a mechanistic undersanding of the Mtb FAS-I complex.

Agriphotovoltaics (APV) combines crop production with solar energy generation to address increasing demands for food and energy while reducing land-use competition. Unlike conventional opaque photovoltaic systems, semitransparent organic photovoltaics (OPVs) selectively absorb light, potentially improving efficiency but also altering both light quantity and spectral quality, key factors affecting plant growth. Here, we developed a rapid bioassay based on hypocotyl elongation to evaluate plant responses to OPV-filtered light using Arabidopsis thaliana and Cardamine hirsuta, two species with contrasting shade strategies. Screening a diverse set of OPV materials revealed that plant growth responses depend more on spectral composition than on total light intensity alone. Certain materials, such as PTB7-Th and D18, produced growth patterns similar to neutral shading, while others promoted elongation. Our analyses identified blue light wavelengths, linked to cryptochrome activity, as more critical than red light wavelengths, linked to phytochrome activity, for maintaining normal development. These findings provide a scalable framework to assess OPV-plant compatibility and demonstrate that optimizing spectral quality alongside light intensity is essential for designing efficient APV systems that sustain crop performance while generating renewable energy.

Significant cellular processes, including protein sorting, signal transduction, and pathogen entry, amongst others, are associated with membrane microdomains, also known as lipid rafts. Lipid rafts, due to their unique biophysical properties compared to their surrounding environment, which stem from their distinct lipid and protein profiles, have garnered interest in methods and techniques that tune their coexisting liquid-ordered/liquid-disordered state, aiming to disrupt or destabilize them. Since cholesterol stabilizes the membrane domain, cholesterol-depleting compounds like cyclodextrin can be used to destabilize and disrupt the membrane rafts. Overall, given the membrane rafts importance in biological processes, it is crucial to understand the biophysical factors that influence its stability. In this study, we present a new method for disrupting and dissolving lipid rafts in a model system of phase-separated supported lipid bilayer (SLB) patches composed of DOPC, DPPC, and cholesterol. Using fluorescence microscopy to monitor the liquid ordered (Lo) and liquid disordered (Ld) phases of the SLB patches, we observed that adding DOPC liposomes causes a transformation of the co-existing Ld and Lo phases into a single-phase bilayer. On the other hand, adding liposomes that match the lipid content of the phase-separated SLB patch increase the areas of the existing Ld and Lo phases. This work also offers a new method for redistributing raft-localized molecules, confirmed by tracking the redistribution of cholera toxin bound to GM1 after domain dissolution with DOPC liposomes. The work describes an alternative method for dynamically altering membrane composition and dissolving domains via liposome addition, rather than lipid depletion or exchange.

Wild-type T4 lysozyme (T4L) is used as a benchmark to evaluate conformational sampling across generative AI, AI-accelerated molecular simulation (AMS), and physics-based enhanced molecular dynamics (EMD). A four-state model: exposed/open, exposed/closed, buried/open, and buried/closed; is defined using physically meaningful collective variables. While generative AI methods (AF-cluster, MSA subsampling of AlphaFold2, ConforFold, AlphaFlow, ESMFlow, ConfRover, BioEmu) largely sample only the exposed/open state, AMS integrating generative ensembles with iterative molecular dynamics, recovering all states and reproducing equilibrium populations similar to EMD and experimental smFRET signatures.

HIV-1 buds from infected cells as immature virion particles with a scattered envelope glycoprotein (Env) distribution on their envelope. It then undergoes maturation, during which the viral protease cleaves the Gag polyprotein at multiple sites, leading to structural reorganization of the viral particle and lateral redistribution of Env proteins, ultimately rendering the virion infectious. However, the underlying mechanism of maturation-induced Env reorganization remains elusive. In this study, we combine microsecond-long all-atom (AA), bottom-up coarse-grained (CG) molecular dynamics simulations, and diffusion model-based backmapping to investigate the structural organization and key interactions of Env in viral membranes. AA simulations of fully glycosylated Env embedded in HIV-1 mimetic asymmetric bilayers were first performed to characterize its conformational dynamics and Env-lipid interactions. We then developed a bottom-up CG model of glycosylated Env from that AA data and simulated the mature HIV-1 virion envelope containing multiple Env proteins. The CG simulations predict that Env proteins form clusters through interactions mediated by the cytoplasmic tail domain (CTD) and adopt diverse tilted conformations within these clusters. These CG simulations were then backmapped to AA resolution and further AA simulations were carried out to identify, in detail, the specific interacting residues in the Env clusters. Additionally, analysis of epitope accessibility shows that broadly neutralizing antibodies (bnAbs) targeting the V1/V2 and V3 loops may efficiently interact with Env clusters on the mature virion surface. Together, these results provide a molecular mechanism for Env oligomerization during viral maturation and offer new insights into the accessibility of bnAb epitopes on Env clusters.