The Journal of Chemical Physics
● AIP Publishing
Preprints posted in the last 90 days, ranked by how well they match The Journal of Chemical Physics's content profile, based on 56 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit.
Sang, M.; Johnson, M. E.
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Binding reactions in effectively one-dimensional systems, such as proteins diffusing along DNA or other filaments, pose a fundamental coarse-graining challenge because stochastic trajectories are recurrent in one dimension and therefore do not admit a unique, separation-independent macroscopic association rate. As a result, continuum rate equations are not exact in 1D even for initially homogeneous systems. Here we develop a practical framework for mapping stochastic 1D reaction-diffusion dynamics onto effective kinetic models. Using mean-first-passage arguments and particle-based simulations, we define a density-dependent association rate and a corresponding single-rate approximation, and quantify when each provides an accurate description of the underlying stochastic dynamics. We implement 1D reaction-diffusion with excluded volume in the NERDSS software using a free-propagator reweighting algorithm and validate it against known pairwise and many-body limits. Our results show that ordinary rate equations with a single effective rate can accurately reproduce 1D reaction kinetics when the dimensionless parameter governing the ratio of intrinsic to diffusion-limited reactivity is small, with excellent agreement in the strongly rate-limited regime and increasing deviations as diffusion control strengthens. We further show that excluded volume in 1D can appreciably alter both kinetics and equilibrium populations, even at modest particle densities, by reducing accessible length and introducing blockade effects. Together, these results provide quantitative guidance for selecting between spatial simulations, density-dependent rate models, and single-rate continuum descriptions of reversible 1D binding reactions.
Krott, L. B.; Puccinelli, T.; Oliveira, W. d.; Gomes, M. E. N.; Lomba, E.; Piazza, F.; Bordin, J. R.
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Synapsin-1 is a multidomain neuronal protein containing extensive intrinsically disordered regions and is a key component of synaptic-vesicle condensates. Direct residue-level simulation of the collective organization of thousands of synapsin molecules remains computationally demanding. Here, we develop a coarse-grained description that connects residue-level CALVADOS 3 simulations to a one-particle-per-protein model. A potential of mean force between two synapsin molecules is obtained by umbrella sampling and represented by an isotropic effective interaction containing a short-range attractive region and a weak outer repulsive contribution. We compare two treatments of this interaction that differ only in the retention of the outer tail. Langevin dynamics simulations of effective proteins show aggregation upon cooling and compression in both models, but with markedly different collective organization. The shorter-ranged model progressively coarsens toward a single dense domain, whereas retaining the outer repulsive contribution favors the persistence of multiple mesoscale aggregates. The two models also display distinct relationships between aggregate size and particle mobility at low temperature. These results show that weak features of an effective protein-protein interaction can have pronounced consequences for collective synapsin organization at mesoscopic scales. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/745062v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@854288org.highwire.dtl.DTLVardef@d2fc52org.highwire.dtl.DTLVardef@1b37d5aorg.highwire.dtl.DTLVardef@eac583_HPS_FORMAT_FIGEXP M_FIG C_FIG
Jadhav, A.; Ghosh, P.
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Small molecules regulate biomolecular condensates in a biphasic manner, promoting liquid-liquid phase separation (LLPS) at low concentrations while suppressing it at higher concentrations. Despite increasing experimental evidence for such re-entrant behavior, a unified physical description remains lacking. Here, we identify a minimal thermodynamic mechanism for re-entrant LLPS by coupling Cahn-Hilliard dynamics to a concentration-dependent Flory interaction parameter containing competing LLPS-promoting and inhibitory contributions. The resulting model reproduces experimentally observed nonmonotonic condensate formation in Tau-tannic acid and TDP-43-bis-ANS systems, including the concentration-dependent emergence and dissolution of protein-rich domains. Spinodal analysis reveals finite concentration windows for phase instability and demonstrates that re-entrant mixing is encoded directly in the free-energy landscape. The framework further captures morphology transitions and diffusive coarsening within the phase-separated regime. These results establish a general mesoscale description of chemically regulated condensates and provide design principles for controlling phase separation through small-molecule modulators.
Nadeem, H.; Kleiman, D. E.; Shukla, D.
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Adaptive sampling accelerates the exploration of conformational space in molecular dynamics (MD) simulations by repeatedly analyzing the accumulated trajectories and seeding a new round of simulations from informative configurations. A growing collection of adaptive sampling policies has been proposed, each built around a particular notion of what makes a configuration informative, yet these methods are scattered across separate and often incompatible implementations, which complicates their systematic comparison and their combined use in meta adaptive sampling schemes. Here, we present AdaptivePy, a compact and extensible Python framework that implements nine seed-selection policies behind a single configuration-driven interface, spanning simple population-based baselines, several established machine-learning and geometry-based methods, and two ensemble or meta sampling policies introduced in this work. We show that the shared implementation reproduces the characteristic selection behavior of each policy on a series of analytic benchmark landscapes. We also introduce a new adaptive sampling scheme that employs TS-DAR, a deep learning framework originally designed to identify transition states, into an acquisition criterion that drives the discovery of an entire multi-basin landscape starting from a single basin. We further demonstrate that the common interface enables meta adaptive sampling policies, which aggregate the rankings of several policies into a single set of seeds. AdaptivePy thereby provides a unified testbed for the adoption, benchmarking, and continued development of adaptive sampling methods for biomolecular MD simulations.
Dhibar, S.; Jana, B.
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The process of drug unbinding is of immense importance in the field of biophysics and therapeutics. The behavior of these systems is greatly influenced by their thermodynamic and kinetic properties. Therefore, it is crucial to accurately estimate the ligand binding free energies and rate of ligand dissociation, yet these processes are often governed by rare event transitions that lie beyond the reach of standard brute-force molecular dynamics simulations. While enhanced sampling simulations offer a solution, their efficacy is strictly contingent upon the selection of appropriate collective variables (CVs) which is non-trivial for complex systems like protein-ligand complexes. In this study, we present a method to derive optimized CV from transition state region (TS) via an interpretable machine learning (ML) model, Elastic Net. By employing some physically intuitive order parameters, the derived optimized CV from the TS-region greatly accelerate ligand binding-unbinding transitions and achieves rapid free energy surface (FES) convergence across diverse systems including buried and solvent exposed active sites such as Trpsin-benzamidine complex, host-guest systems and sodium epoxidase etc. Intriguingly significant contribution of the ligand hydration is found in the optimized CV which depicts crucial role of solvent in driving ligand binding-unbinding transitions. The estimated binding free energies for different protein-ligand complexes match quite well with experiments, while maintaining a low computational cost. The derived optimized CV is also used to calculate the ligand residence times across different systems and calculated residence times are within the experimental range for all systems, again with very little computational costs. Moreover, we show that the optimized CV constructed from TS region via an interpretable ML model is transferable across diverse systems, offering a robust and scalable framework for drug discovery and investigation of complex biomolecular recognition.
Elgendy, A.; Zeipelt, A. P.; Schäfer, L. V.
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Molecular dynamics (MD) simulations of slow biomolecular processes, such as exploration of the conformational ensembles of intrinsically disordered proteins (IDPs), are computationally demanding. Although coarse-grained (CG) models can substantially speed up the simulations compared to all-atom MD, the sampling challenge can still be significant for large systems and long time scales. Here, we present light Martini water, a low-viscosity water model that accelerates sampling in MD simulations with the Martini CG force field. We systematically reduced the mass of the Martini water beads and verified stable, accurate integration of the equations of motion with 20 fs time steps, as typically used in Martini simulations. Light Martini water has a reduced mass of 20 amu (compared to 72 amu in the standard water model), yielding up to a 2.68-fold increase in the sampling rate of IDP chain reconfiguration in water and a 16 % increase in the lateral diffusion of lipids in a POPC bilayer. Equilibrium properties remained unaffected by the mass scaling, and the speedup was achieved without compromising simulation accuracy. The water model is trivial to implement, has no computational overhead, and should be universally applicable to Martini simulations.
Yang, Y.
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Gaussian accelerated molecular dynamics (GaMD) enhances conformational sampling by adding a smooth boost potential without requiring predefined collective variables, but an engine-integrated implementation has not been available in GROMACS. Here, we implement total-, dihedral-, and dual-boost GaMD in GROMACS 2025.4, including staged energy-statistics collection, GPU-based bias evaluation and force scaling, restart support, and outputs required for cumulant-based free-energy reweighting. The implementation was evaluated using four benchmark systems spanning conformational free energies, protein folding, and ligand recognition. For alanine dipeptide, a reweighted 100 ns GaMD trajectory recovered the major free-energy basins and rotational barriers in overall agreement with a 1000 ns conventional MD simulation. For chignolin and TC5b, all three independent trajectories for each system sampled native-like folded states from extended conformations within 300 ns and 1 s, respectively; the best TC5b structure had a minimum backbone RMSD of 0.03 nm from the experimental structure. In the benzene-T4 lysozyme system, two of five independent 500 ns trajectories captured both ligand binding and dissociation, yielding a bound pose with a minimum ligand RMSD of 0.06 nm from the crystal structure. Across all four systems, the boost-potential distributions were approximately Gaussian, and second-order cumulant reweighting resolved the expected conformational and binding free-energy basins. These results demonstrate that GROMACS-GaMD provides a practical, GPU-enabled, collective-variable-free enhanced-sampling framework for biomolecular free-energy calculations, protein folding, and ligand-binding studies.
Mitra, R.; Jana, B.
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Protein folding is the process by which a polypeptide chain organizes into its three-dimensional structure through a balance of stabilizing and destabilizing interactions encoded by the sequence. A central question in protein biophysics is how thermodynamic factors guide a polypeptide toward its native folded state despite the rugged energy landscape and the competing influence of nonnative interactions. In many biomolecular processes, cooperativity provides a mechanism by which multiple weak interactions act collectively to generate a robust response. In the context of protein folding, such cooperative effects may arise when the formation of one native contact enhances the stability or likelihood of nearby native contacts, thereby promoting collective organization toward the folded state. At the same time, folding is opposed by the much larger number of non-native interactions, whose heterogeneity can introduce frustration and destabilize folding even when the average native bias favors the folded phase. The interplay of these competing effects in determining foldability remains unclear in statistical-mechanical models. Here, we address this problem using a one-dimensional spin-glass model of protein folding with explicit shared-residue cooperative interactions encoded through wedge-based motifs. We show that modest cooperative bias can stabilize folding even where the noncooperative system remains unfolded, whereas non-native energetic fluctuation suppresses folding and shifts the transition to higher cooperative strengths. We further find that partial cooperative coverage is sufficient to lower the folding threshold. Therefore, the model provides a mean-field framework for incorporating cooperative interaction strength into the native one-dimensional model of protein folding and for describing how local cooperativity reshapes the folding transition.
Argun, B. R.; Stachowiak, J.; Ren, P.
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Recent experiments show that protein condensates sitting on opposite surfaces of a flat lipid membrane move together and prefer to overlap, even though they cannot touch each other. This points to an indirect, membrane-mediated interaction. Two mechanisms could be responsible: a curvature-induced interaction, which is energetic in origin, and a fluctuation-induced interaction, which is entropic. Here we study both with coarse-grained molecular dynamics simulations, using Cookes implicit-solvent lipid model together with a generic bead-spring polymer model for the condensate. We compute the potential of mean force between two condensates across the membrane. For condensates of the same size, full overlap is unfavorable, and the pair instead settles into a partially overlapping state that bends the membrane into an S-like shape. When the two condensates differ strongly in size, full overlap becomes favorable. We explain this with a simple geometric picture. The condensate wets the membrane as a thin film and imposes curvature only along its rim, while membrane tension flattens the membrane under its interior. The resulting ring of curvature can trap a smaller condensate on the opposite side. We also compare the bending undulations and the effective bending modulus of a bare membrane, a membrane with one condensate, and a membrane with condensates on both sides. A wetting condensate suppresses the undulation modes and stiffens the membrane, but whether this makes overlap entropically favorable remains inconclusive. Our results indicate that the coupling is driven mainly by curvature, and that it depends on the wetting mechanism and on the membrane tension.
Zhang, S.; Li, S.; Coronado-Ipina, M. A.; Comas-Garcia, M.; Gopinathan, A.; Schoot, P. v. d.; Zandi, R.
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Budding is a fundamental membrane-remodeling process central to many cellular functions and is exploited by numerous enveloped viruses to acquire their lipid envelopes. Despite extensive molecular characterization, the physical mechanisms that determine whether budding proceeds to completion or becomes stalled remain unclear. Here, we develop a theoretical model based on the Helfrich elastic formalism to investigate how membrane geometry and boundary conditions regulate the elastic energy of viral budding. We analyze two representative cases: budding from a flat membrane, characteristic of HIV-1 and alphaviruses, and budding from a vesicle, as observed for SARS-CoV-2 in the ER-Golgi intermediate compartment (ERGIC). Our results reveal distinct energetic pathways: vesicle-like geometries exhibit a stronger energetic bias toward closure, whereas flat membranes develop extended low-slope regions in the energy landscape that can hinder completion. Relaxing far-field boundary constraints reduces the energetic cost associated with membrane area conservation and renders the flat-membrane case energetically comparable to the vesicle case, providing a physical explanation for why viruses frequently bud adjacent to one another or within pre-curved membrane regions. Comparison with thin-section TEM images of alphavirus budding shows results consistent with the theoretical membrane profiles. Together, these findings establish how curvature coupling, boundary flexibility, and local membrane geometry cooperate to control the efficiency and completion of membrane budding.
ADUPA, V.; Polet, J. D.; Dekker, M.; Onck, P. R.
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Polyglutamine (polyQ) aggregation plays a central role in several neurodegenerative diseases, including Huntington's disease. DNAJB6b, a molecular chaperone involved in protein quality control, is known to efficiently suppress polyQ aggregation, but its anti-aggregation mechanism remains unclear. In this work we investigate the interaction between DNAJB6b and the polyQ region (Q48) of mutant Huntingtin Exon 1 (mHttEx1) using a custom-built coarse-grained molecular dynamics model. The model incorporates a two-bead-per-amino-acid representation with hydrogen bonding (termed 2BPA-HB), and is calibrated against all-atom molecular dynamics data in terms of geometry, hydrophobicity, and hydrogen bonding. The model reproduces the tertiary structure of DNAJB6b and its interactions with Q48, and reveals an inverse correlation between DNAJB6b concentration and Q48 aggregation propensity. Our simulations show that DNAJB6b co-condensates with polyQ molecules, thereby shielding the polyQ from forming the intermolecular hydrogen bonds necessary for amyloid formation. The 2BPA-HB CGMD model en- ables efficient exploration of DNAJB6b conformations, supporting future studies of chaperone-mediated aggregation suppression and therapeutic development.
Schachter, I.; Jungwirth, P.; Harries, D.
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Vesicle internalization proceeds through a series of multivesicular topologies essential for endocytic transport and cellular compartmentalization. The energetic landscapes of related transitions, including vesicle budding and pearling, are known to be governed by the coupling of spontaneous curvature, leaflet area asymmetry, and reduced volume. However, the physical principles driving the structural transformation of hemifused intermediates remain unresolved. Using a continuum elastic model, we identify a morphological phase transition in hemifused invaginating vesicles, from an initial lens-like geometry to an elongated "kettle" geometry. This transition is discontinuous as long as the invaginating vesicles reduced volume is below a critical threshold, but continuous otherwise. The kettle-like morphology is metastable across a broad range of leaflet area asymmetries, potentially enabling a hysteretic externalization pathway. Increasing either the spontaneous curvature of the shared outer leaflet or the size of the invaginating vesicle, alone or in tandem with the host vesicle, turns the kettle morphology into the global free energy minimum. Notably, simply scaling up the size of both vesicles does not eliminate the free energy barrier. This quantitative characterization provides a structural reference for identifying internalization intermediates witnessed in experimental imaging, and maps the morphological evolution of the internalization pathway across its physical parameter space.
Zhang, Y.; Sood, A.; Athreya, A.; Zhang, B.
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Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are often described using stickers-and-spacers models, in which specific sticker motifs form reversible crosslinks and spacer regions modulate phase behavior. Recent theory predicts that heterogeneous nonspecific spacer interactions can promote condensation but may also disrupt sticker-mediated organization. Here, we develop an off-lattice coarse-grained stickers-and-spacers polymer model for continuous molecular dynamics simulations and implement it in the GPU-accelerated OpenABC package. The model uses a directional sticker-sticker interaction to encode limited valency through interaction geometry, producing effectively one-to-one sticker binding without explicit bond assignment. Simulations of one-component systems show that sticker affinity and multivalency promote porous, network-like condensates, while nonspecific spacer interactions can also drive phase separation but produce more compact, spacer-dominated dense phases. When both interaction types are present, strong spacer heterogeneity reduces sticker conversion, suppresses sticker mobility, and disrupts the sticker-mediated network. In two-component systems, specific sticker interactions buffer client recruitment into host condensates, while nonspecific spacer interactions produce reservoir-dependent uptake. These results support a tradeoff in which spacer heterogeneity promotes condensation at the cost of condensate organization and compositional robustness, providing a physical rationale for the suppression of promiscuous spacer interactions in low-complexity IDP regions.
Chen, L.;Chen, Y.;Cheng, Z.;Guo, J.;He, M.;Li, H.;Li, X.;Li, Z.;Ma, J.;Ma, S.;Peng, C.;Qian, C.;Qu, Z.;Sun, X.;Tang, X.;Wang, Y.;Yu, B.;Zhai, Y.;Zhang, B.;Zhang, S.;Zhang, S.;Hu, Z.;Shan, Y.;Mei, Y.
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MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.
Chan, B.; Rubinstein, M.
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In the active loop extrusion model, the cohesin protein complex creates chromatin loops in eukaryotic cells. Extrusion maintains topologically associated domains (TADs), which are contiguous segments of chromatin that preferentially colocalize in space and are typically bounded by CTCF proteins that pause cohesin translocation. Here, we model active loop extrusion with hybrid molecular dynamics - Monte Carlo simulations in entangled flexible linear polymer melts. Intra-chain contact probabilities of polymers with active loop extrusion are enhanced compared to their equilibrium, passive counterparts. Extrusion causes the size of chain segments to be much smaller than in passive melts. While the overlap parameter in passive melts without extrusion monotonically increases with segment length, it is nonmonotonic in active melts and on the order of unity within the parameters of this study. Active loop extrusion suppresses contacts between TADs in favor of intra-TAD contacts. Reduction of overlaps between chain segments dilutes entanglements in active melts. Depending on parameters, active extrusion without TADs may induce more compact conformations than with TADs, due in part to fractal loopy globule-like dynamics. This work suggests that active loop extrusion reduces overlaps between TADs, contributing to effective gene regulation by cis-regulatory elements.
Herb, N.; Brajkovic, M.; DArrigo, G.; Kokh, D. B.; Wade, R. C.
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Interleukin-13 (IL-13) is an immunomodulatory cell signaling cytokine that has been implicated in neurodegenerative disease and chronic inflammation. IL-13 binds to its low and high affinity receptors, IL-13 receptor 1 (IL-13R1) and IL-13 receptor 2 (IL-13R2), respectively, with residence times that vary accordingly. As the binding kinetics of the cytokine-receptor complexes influence cellular responses, we employed the molecular dynamics (MD) simulation-based{tau} -random acceleration molecular dynamics method ({tau}RAMD) to compute relative residence times for wild-type (WT) IL-13 and 19 IL-13 mutants to the two receptors. Comparison with experimental kinetic data shows that the{tau} RAMD computations capture the trends in residence times. Analysis of simulated dissociation trajectories of the cytokine-receptor complexes reveals two distinct dissociation pathways of IL-13 from each of the receptors. This study thus pinpoints key determinants of the interaction of IL-13 with its receptors which could be targeted for therapeutic design. Statement of SignificanceCytokines are regulatory proteins that bind to cell surface receptors and thereby send signals to the cellular interior. Interleukin-13 (IL-13) is a cytokine that has a low and a high affinity receptor. It has important physiological roles, and its deregulation is involved in diseases such as atopic dermatitis and asthma. We employed a molecular dynamics simulation-based method to compute the effects of changes in the sequence of IL-13 on the lifetimes of complexes of IL-13 and its receptors. Comparison with experiments supports the validity of the computational approach and analysis of the simulations reveals two distinct ways in which IL-13 dissociates from each receptor. These results thus provide a map for targeting IL-13 - receptor interactions for the design of therapeutics.
Liu, Y.; Chen, M.; Lin, G.
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AO_SCPLOWBSTRACTC_SCPLOWMolecular dynamics (MD) provides a principled method for modeling equilibrium protein conformational energy landscapes, but its computational cost limits access to long timescales and larger protein systems. Recently, generative protein ensemble models and machine-learned coarse-grained force fields have emerged as complementary approaches for accelerating conformational sampling. However, they are typically developed separately despite modeling the same underlying equilibrium distribution. We introduce UniFlow, the first scalable generative model that unifies protein ensemble generation and machine-learned coarse-grained force fields for molecular dynamics simulation within a single framework. UniFlow employs an internal-coordinate normalizing flow that supports efficient i.i.d. sampling, exact likelihood evaluation, and differentiable energy and force computation. Across diverse protein systems, UniFlow generates ensembles that closely match reference MD simulations, generalizes to proteins beyond its training dataset, and samples substantially faster than diffusion-based ensemble-generation baselines. The same learned density further enables stable long-timescale molecular dynamics simulations. Together, UniFlow paves the way for a unified class of models that bridges generative ensemble modeling with physics-based molecular simulation. Codehttps://github.com/Harrydirk41/UniFlow.git
Vaiwala, R.; Christy, E.; Waskar, M.; Ayappa, K. G.
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We present a comparative study of the inner membrane of three Gram-positive bacterial strains, namely S. aureus, S. epidermidis and N. lacusekhoensis. A lipidomics study is used to obtain the lipid architecture and composition for S. epidermidis found in the skin microbiome and N. lacusekhoensis, an extremophile present in halophilic and alkophilic environments. Differences between the strains arise from both the lipid architecture and the cardiolipin content varying from 5% in S. aureus to 85% in N. lacusekhoensis. We develop coarse grained (CG) Martini-3 membrane models which reproduce structural properties such as membrane area, thickness, density distributions as well as ion-correlations with all-atom models. Inter-lipid correlations reveal a homogeneous distribution of lipids in the membranes despite the wide variation in lipid types and composition. Mechanical properties such as the area stretch modulus increased with cardiolipin content, however the bending modulus has a more complex dependence on membrane charge and lipid type. Using the CG models we evaluate the insertion free energies for four widely used antimicrobial molecules. Entry barriers for thymol and methylparaben arise from the charge density modulation at the membrane headgroups due to counterion condensation. The entry mechanisms of the antimicrobial peptide cecropin-melittin-15 (CM15) and the preservative molecule ethyl-lauroyl-arginate (ELAR) are found to be similar across all three strains. We also illustrate the manner in which the extremophilic strain, N. lacusekhoensis with its high cardiolipin content, modulates the partitioning kinetics of the antimicrobial molecule thymol with pH and salt. Our study reveals that membrane properties are largely conserved across the three model membranes. The molecular models and insights emerging from the present work should aid in the development of novel antimicrobials against Gram-positive strains.
Nidriche, A.; Ollivier, J.; Stewart, R.; Peters, J.
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Neutron scattering is a powerful technique to investigate atomic structures and molecular dynamics of proteins at the nano-scale. When it comes to dynamics, incoherent and coherent scattering respectively provide information on the single and collective dynamics of nuclei. In proteins, hydrogen has the highest incoherent cross-section, and it is common practice to overlook the contribution of coherent terms stemming from all nuclei. However, the fast collective dynamics of heavier nuclei could also be studied if coherent scattering and incoherent scattering were experimentally separated. The recent advent of polarized neutron spectroscopy with sufficient flux and energy resolution has made it possible, and opens new perspectives to investigate the relative importance of coherent scattering and the information it provides on biological samples. The present study reports on the use of polarized quasi-elastic neutron scattering (QENS) and the application of a minimalistic model adapted to both individual and collective dynamics. Using a perdeuterated green fluorescent protein as a model globular protein, the study provides an interpretation of the dynamical parameters obtained with QENS, and a comparative study of the Elastic Coherent and Incoherent Scattering Factor. Based on both experiments and calculations, we discuss the relative importance of distinct and self components of coherent scattering, which is often wrongly assumed to be representative of collective dynamics only. The results highlight the current impediments rendering complicated a straightforward analysis of fast collective dynamics in hydrated protein samples.
Vugmeyster, L.; Yadav, K.; Holmes, S. T.; Ostrovsky, D.
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Calcium oxalates are naturally occurring minerals, with the monohydrate form CaC2O4xH2O (COM) being the most stable. COM contains two crystallographically different water sites. We investigate the details of water internal dynamics in the high and low temperature phases of COM using 17O central transition solid-state NMR line shapes, as well as laboratory and rotating frame relaxation rates. The measurements were performed either under static or magic angle spinning conditions and in a wide temperature range from 343 to 180 K. The combination of all measurements allows for precise constraints on motional mechanisms, rate constants, and amplitudes of motions. The high temperature phase is dominated by large-angle fluctuations with an amplitude of about 100 degrees, identical in both sites. During the phase transition between 323 to 300 K, these large-angle jumps freeze out in one of the water sites, while remaining active in the other. In the low temperature phase from 280 to 180 K, small-angle fluctuations of 2-8 degrees in amplitude dominate the relaxation. Transverse relaxation rates also point to the existence of a very slow collective rocking motion down to about 220-200 K.