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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Unexpected Role of Cations in the Self-Assembly of Positively Charged Amphiphiles at Liquid/Liquid Interfaces

Conventional wisdom suggests that cations play a minimal role in the assembly of cationic amphiphiles. Here, we show that at liquid/liquid (L/L) interfaces, specific cation effects can modulate the assemblies of hydrophobic tails in an oil phase despite being attached to cationic headgroups in the aqueous phase. In this work, we used oligo-dimethylsiloxane (ODMS) methyl imidazolium amphiphiles to identify these specific interactions at hexadecane/aqueous interfaces. Small cations, such as Li + , bind to the O atoms in the ODMS tail and pin it to the interface, thereby imposing a kinked conformation-as evidenced by vibrational sum frequency generation spectroscopy and molecular dynamics simulations. While larger Cs + ions more readily partition to the interface, they do not form analogous complexes. Our data not only point to ways for controlling amphiphile structure at L/L interfaces but also suggest a means for the separation of Li + , or related applications, in soft-matter electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

The substrate for ribosomes actively engaged in protein synthesis is a ternary complex of elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA), and GTP. EF-Tu plays a critical role in mRNA decoding by increasing the rate and fidelity of aa-tRNA selection at each mRNA codon. Here, using three-color single-molecule fluorescence resonance energy transfer imaging and molecular dynamics simulations, we examine the timing and role of conformational events that mediate the release of aa-tRNA from EF-Tu and EF-Tu from the ribosome after GTP hydrolysis. Our investigations reveal that conformational changes in EF-Tu coordinate the rate-limiting passage of aa-tRNA through the accommodation corridor en route to the peptidyl transferase center of the large ribosomal subunit. Experiments using distinct inhibitors of the accommodation process further show that aa-tRNA must at least partially transit the accommodation corridor for EF-Tu∙GDP to release. aa-tRNAs failing to undergo peptide bond formation at the end of accommodation corridor passage after EF-Tu release can be reengaged by EF-Tu∙GTP from solution, coupled to GTP hydrolysis. These observations suggest that additional rounds of ternary complex formation can occur on the ribosome during proofreading, particularly when peptide bond formation is slow, which may serve to increase both the rate and fidelity of protein synthesis at the expense of GTP hydrolysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1 -2 kcal · mol -1 . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal · mol -1 and -6.3 to +3.8 kcal · mol -1 depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. In conclusion, the results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Fluorescent toxins as ion channel activity sensors.

Voltage gated ion channels (VGICs) shape the electrical character of cells by undergoing structural changes in response to membrane depolarization. High-resolution techniques have provided a wealth of data on individual VGIC structures, but the conformational changes of endogenous channels in live cell membranes have remained unexplored. Here, we describe methods for imaging structural changes of voltage-gated K + channels in living cells, using peptidyl toxins labeled with fluorophores that report specific protein conformations. These Endogenous Voltage-sensor Activity Probes (EVAPs) enable study of both VGIC allostery and function in the context of endogenous live-cell membranes under different physiological states. In this chapter, we describe methods for the synthesis, imaging, and analysis of dynamic EVAPs, which can report K + channel activity in complex tissue preparations via 2-photon excitation microscopy, and environment-sensitive EVAPs, which report voltage-dependent conformational changes at the VGIC-toxin interface. The methods here present the utility of current EVAPs and lay the groundwork for the development of other probes that act by similar mechanisms. EVAPs can be correlated with electrophysiology, offering insight into the molecular details of endogenous channel function and allostery in live cells. This enables investigation of conformational changes of channels in their native, functional states, putting structures and models into a context of live-cell membranes. The expansive array of state-dependent ligands and optical probes should enable probes more generally for investigating the molecular motions of endogenous proteins.

Stewart, Robert↗
DOE OSTI2023

Chain trajectories, domain shapes, and terminal boundaries in block copolymers

The packing geometry of macromolecules in complex mesophases is of key importance to self-organization in synthetic and biological soft materials. While approximate or heuristic models rely on often-untested assumptions about how flexible molecules “fit in” to distinct locations of complex assemblies, physical assemblies derive from ensembles of fluctuating conformations, obscuring the connection between mesophase geometry and the underlying arrangements. Here, we present an approach to extract and analyze features of molecular packing in diblock block copolymer (BCP) melts, a prototypical soft matter system, based on the statistical description of chain conformations in self-consistent field (SCF) theory. We show how average BCP chain trajectories in ordered morphologies can be analyzed from the SCF-derived orientational order parameter of chain segments. We use these extracted trajectories to analyze the features of local packing geometry, including chain bending and tilt, as well as the terminal boundaries that delineate distinct domains in ordered BCP morphologies. In conclusion, we illustrate this analysis by focusing on measurable features of packing frustration in 2D (columnar) and 3D (spherical and bicontinuous) morphologies, notably establishing an explicit link between chain conformations in complex morphologies and their medial geometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Shear-Induced Conformations of Salt-Free Polyelectrolytes in Semidilute Solutions

Here, we present coarse-grained molecular dynamics simulations of salt-free polyelectrolyte chains in semidilute solutions under simple shear flow, with full hydrodynamic interactions and explicit dipolar solvent. At equilibrium, chain orientation statistics follow a pseudo-Voigt distribution, and the structural correlation length and chain end-to-end vector autocorrelation function exhibit scaling behavior consistent with theoretical predictions for polyelectrolytes. Under shear, chains transition from coiled to stretched states and the end-to-end vector autocorrelation function reveals oscillatory dynamics at high Weissenberg numbers. Analysis of the gyration tensor and shear strain distributions identified three distinct chain populations with directional alignment along and against the shear gradient. Compared with their neutral polymer counterparts, polyelectrolytes exhibit stronger shear thinning and enhanced chain alignment under the same Weissenberg number, which is attributed to electrostatic interactions and shear-induced counterion release. These findings provide molecular insight into the distinct flow response of charged polymers and have implications for tailoring the rheological properties of polyelectrolyte-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations

Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.

adsorption↗
DOE OSTI2021

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Scaling Theory of Neutral Sequence-Specific Polyampholytes

The primary sequence of charged monomers in a polyampholyte has a profound effect on its conformational properties. In this work, theory and simulations are used to predict how the sequence influences the single-chain behavior of globally neutral polyampholytes (PAs) under salt-free conditions. We consider PAs with Markov statistics of charges, where charge “blockiness” is defined by the correlation λ along the chain. These PAs cover a wide spectrum of primary sequences ranging from alternating (λ = –1) to ideally random (λ = 0) to diblock (λ → 1). In a theta solvent, sufficiently long PAs of any primary sequence form globules, but their internal structure, as well as the position and sharpness of the coil–globule transition, crucially depends on λ. Further, using scaling arguments, we demonstrate that the excess charge of the globule correlation volume (blob) increases with increasing λ, thereby inducing stronger Coulomb attractions between neighboring blobs of opposite charge and leading to higher density PA globules. Scaling predictions are supported by the results of the random phase approximation (RPA) and coarse-grained molecular dynamics simulations. A generalization to good and poor solvents is presented that enables the construction of the resulting scaling diagram of PA conformations in terms of solvent quality and charge blockiness, thereby providing a comprehensive molecular understanding of the role of the PA primary sequence in the chain structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2021

Probing Clustering Dynamics between Silicon and PAA or LiPAA Slurries under Processing Conditions

This work explores the complex interplay between slurry aggregation, agglomeration, and conformation (i.e., shape) of poly(acrylic acid) (PAA)- and lithiated PAA-based silicon slurries as a function of the shear rate and the resulting slurry homogeneity. These values were measured by small-angle neutron scattering (SANS) and rheology-coupled ultra-SANS at conditions relevant to battery electrode casting. Different binder solution preparation methods, either a ball milling (BM) process or a planetary centrifugal mixing (PCM) process, dramatically modify the resulting polymer dynamics and organization around a silicon material. This is due to the different energy profiles of mixing where the more violent and higher energy PCM causes extensive breakdown and reformation of the binder, which is now likely in a branched conformation, while the lower energy BM results in simply lower-molecular weight linear polymers. In conclusion, the breakdown and reorganization of the polymer structure affect silicon slurry homogeneity, which affects subsequent electrode architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High-performance piezoelectric composites via β phase programming

Polymer-ceramic piezoelectric composites, combining high piezoelectricity and mechanical flexibility, have attracted increasing interest in both academia and industry. However, their piezoelectric activity is largely limited by intrinsically low crystallinity and weak spontaneous polarization. Here, we propose a Ti 3 C 2 T x MXene anchoring method to manipulate the intermolecular interactions within the all-trans conformation of a polymer matrix. Employing phase-field simulation and molecular dynamics calculations, we show that OH surface terminations on the Ti 3 C 2 T x nanosheets offer hydrogen bonding with the fluoropolymer matrix, leading to dipole alignment and enhanced net spontaneous polarization of the polymer-ceramic composites. We then translated this interfacial bonding strategy into electrospinning to boost the piezoelectric response of samarium doped Pb (Mg1/3Nb 2/3 )O 3 -PbTiO 3 /polyvinylidene fluoride composite nanofibers by 160% via Ti 3 C 2 T x nanosheets inclusion. With excellent piezoelectric and mechanical attributes, the as-electrospun piezoelectric nanofibers can be easily integrated into the conventional shoe insoles to form a foot sensor network for all-around gait patterns monitoring, walking habits identification and Metatarsalgi prognosis. This work utilizes the interfacial coupling mechanism of intermolecular anchoring as a strategy to develop high-performance piezoelectric composites for wearable electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions

K 2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K 2P s is unknown. Here, combining K 2P 2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K 2P C-type gating. These asymmetric order-disorder transitions, enabled by the K 2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K 2P SF2-M4 loop and conserved “M3 glutamate network,” and are suppressed by the K 2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K 2P channel modulator development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation

While drug resistance mutations can often be attributed to the loss of direct or solvent-mediated protein−ligand interactions in the drug-mutant complex, in this study we show that a resistance mutation for the picomolar HIV-1 capsid (CA)-targeting antiviral (GS-6207) is mainly due to the free energy cost of the drug-induced protein side chain reorganization in the mutant protein. Among several mutations, M66I causes the most suppression of the GS-6207 antiviral activity (up to ~84,000-fold), and only 83- and 68-fold reductions for PF74 and ZW-1261, respectively. To understand the molecular basis of this drug resistance, we conducted molecular dynamics free energy simulations to study the structures, energetics, and conformational free energy landscapes involved in the inhibitors binding at the interface of two CA monomers. To minimize the protein−ligand steric clash, the I66 side chain in the M66I−GS-6207 complex switches to a higher free energy conformation from the one adopted in the apo M66I. In contrast, the binding of GS-6207 to the wild-type CA does not lead to any significant M66 conformational change. Based on an analysis that decomposes the absolute binding free energy into contributions from two receptor conformational states, it appears that it is the free energy cost of side chain reorganization rather than the reduced protein−ligand interaction that is largely responsible for the drug resistance against GS-6207.

Sun, Qinfang (ORCID:0000000173621543)↗