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At least 181 records · Page 10

Comment on “Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy”

This paper presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev et al., 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D 2 -tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Furthermore, once these spectral effects are taken into account, we show that both clustering approaches yields similar clusters structures for the small GlyH + (H 2 O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298K is explored using a series of model polyalanine chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics

The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is an essential lipid A biosynthetic enzyme that is conserved in the majority of gram-negative bacteria. It has emerged as an attractive novel antibiotic target due to the recent discovery of an LpxH-targeting sulfonyl piperazine compound (referred to as AZ1) by AstraZeneca. However, the molecular details of AZ1 inhibition have remained unresolved, stymieing further development of this class of antibiotics. In this paper we report the crystal structure of Klebsiella pneumoniae LpxH in complex with AZ1. We show that AZ1 fits snugly into the L -shaped acyl chain-binding chamber of LpxH with its indoline ring situating adjacent to the active site, its sulfonyl group adopting a sharp kink, and its N -CF 3 –phenyl substituted piperazine group reaching out to the far side of the LpxH acyl chain-binding chamber. Intriguingly, despite the observation of a single AZ1 conformation in the crystal structure, our solution NMR investigation has revealed the presence of a second ligand conformation invisible in the crystalline state. Together, these distinct ligand conformations delineate a cryptic inhibitor envelope that expands the observed footprint of AZ1 in the LpxH-bound crystal structure and enables the design of AZ1 analogs with enhanced potency in enzymatic assays. These designed compounds display striking improvement in antibiotic activity over AZ1 against wild-type K. pneumoniae , and coadministration with outer membrane permeability enhancers profoundly sensitizes Escherichia coli to designed LpxH inhibitors. Remarkably, none of the sulfonyl piperazine compounds occupies the active site of LpxH, foretelling a straightforward path for rapid optimization of this class of antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗

Frank–Kasper Phases of Diblock Copolymer Melts: Self-Consistent Field Results of Two Commonly Used Models

We constructed phase diagrams of conformationally asymmetric diblock copolymer A-B melts using the polymer self-consistent field (SCF) calculations of both the dissipative particle dynamics chain (DPDC) model (i.e., compressible melts of discrete Gaussian chains with the DPD non-bonded potential) and the “standard” model (i.e., incompressible melts of continuous Gaussian chains with the Dirac δ-function non-bonded potential) in the χN-ε plane, where χN and ε characterize, respectively, the repulsion and conformational asymmetry between the A and B blocks, at the A-block volume fraction f = 0.2 and 0.3. Consistent with previous SCF calculations of the “standard” model, σ and A15 are the only stable Frank–Kasper (FK) phases among the five FK (i.e., σ, A15, C14, C15 and Z) phases considered. The stability of σ and A15 is due to their delicate balance between the energetic and entropic contributions to the Helmholtz free energy per chain of the system, which, within our parameter range, increases in the order of σ/A15, Z, and C14/C15. While in general the SCF phase diagrams of these two models are qualitatively consistent, A15 is not stable for the DPDC model at the copolymer chain length N = 10 and f = 0.3; any differences in the SCF phase diagrams are solely due to the differences between these two models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of an open K ATP channel reveals tandem PIP 2 binding sites mediating the Kir6.2 and SUR1 regulatory interface

ATP-sensitive potassium (K ATP ) channels, composed of four pore-lining Kir6.2 subunits and four regulatory sulfonylurea receptor 1 (SUR1) subunits, control insulin secretion in pancreatic β-cells. K ATP channel opening is stimulated by PIP 2 and inhibited by ATP. Mutations that increase channel opening by PIP 2 reduce ATP inhibition and cause neonatal diabetes. Although considerable evidence has implicated a role for PIP 2 in K ATP channel function, previously solved open-channel structures have lacked bound PIP 2 , and mechanisms by which PIP 2 regulates K ATP channels remain unresolved. Here, we report the cryoEM structure of a K ATP channel harboring the neonatal diabetes mutation Kir6.2-Q52R, in the open conformation, bound to amphipathic molecules consistent with natural C18:0/C20:4 long-chain PI(4,5)P 2 at two adjacent binding sites between SUR1 and Kir6.2. The canonical PIP 2 binding site is conserved among PIP 2 -gated Kir channels. The non-canonical PIP 2 binding site forms at the interface of Kir6.2 and SUR1. Functional studies demonstrate both binding sites determine channel activity. Kir6.2 pore opening is associated with a twist of the Kir6.2 cytoplasmic domain and a rotation of the N-terminal transmembrane domain of SUR1, which widens the inhibitory ATP binding pocket to disfavor ATP binding. The open conformation is particularly stabilized by the Kir6.2-Q52R residue through cation-π bonding with SUR1-W51. Together, these results uncover the cooperation between SUR1 and Kir6.2 in PIP 2 binding and gating, explain the antagonistic regulation of K ATP channels by PIP 2 and ATP, and provide a putative mechanism by which Kir6.2-Q52R stabilizes an open channel to cause neonatal diabetes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The rhodopsins: structure and function. Introduction

Nature makes use of the propensity of retinal for light-dependent double-bond isomerization in a number of systems and in a variety of ways. The common theme for light receptors based on this kind of chemistry is that (1) the retinal is bound in most cases to a small membrane protein via a protonated lysine-retinal Schiff base, (2) the absorption maximum in the visible is tuned to a suitable wavelength largely by electrostatic interaction with polar protein residues, and (3) the light-induced bond rotations and strains in the retinal set off reaction chains during which at least part of the excess free energy acquired is transferred to the protein and causes pK shifts of acidic residues and/or backbone conformational changes. The physiological consequence of the process initiated by absorption of light is either the activation of an information transfer chain (sensory and visual rhodopsins) or energy transduction which drives the electrogenic movement of ions across the membrane (ion-motive rhodopsins). Rhodopsins with these functions occur in bacteria and in higher organisms; from an evolutionary standpoint they are not related to one another. Nevertheless, all of these proteins are remarkably similar and form a distinct family.

NASA Discipline Number 52-30↗

Multipartite entanglement in the one-dimensional spin- 1 2 Heisenberg antiferromagnet

Multipartite entanglement refers to the simultaneous entanglement between multiple subsystems of a many-body quantum system. While multipartite entanglement can be difficult to quantify analytically, it is known that it can be witnessed through the quantum Fisher information (QFI), a quantity that can also be related to dynamical Kubo response functions. In this work, we first show that the finite temperature QFI can generally be expressed in terms of a static structure factor of the system, plus a correction that vanishes as T→0. This implies that the static structure factor witnesses multipartite entanglement near quantum critical points at temperatures below a characteristic energy scale of the system. Therefore, in systems with a known static structure factor, we can deduce finite temperature scaling of multipartite entanglement and low temperature entanglement depth without knowledge of the full dynamical response function of the system. This is particularly useful to study 1D quantum critical systems in which sub-power-law divergences can dominate entanglement growth, where the conventional scaling theory of the QFI breaks down. Furthermore, the 1D spin- 1 2 antiferromagnetic Heisenberg model is an important example of such a system, and we show that multipartite entanglement in the Heisenberg chain diverges nontrivially as ~ln(1/T) 3/2 . We verify these predictions with calculations of the QFI using conformal field theory and matrix product state simulations. Finally, we discuss the implications of our results for experiments to probe entanglement in quantum materials, comparing to neutron scattering data in KCuF 3 , a material well described by the Heisenberg chain.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Is a Malleable Active Site Loop the Key to High Substrate Promiscuity? Hybrid, Biocatalytic Route to Structurally Diverse Taxoid Side Chains with Remarkable Dual Stereocontrol

Abstract These studies reveal the first structure ofClostridium acetobutylicumalcohol dehydrogenase (CaADH), a protein exhibiting remarkable substrate promiscuity and stereochemical fidelity. The CaADH enzyme is utilized here for synthesizing 20 potential aryl isoserine side chains for the Taxotere family of tubulin‐binding chemotherapeutics. The approach involves dynamic reductive kinetic resolution (DYRKR) upon the corresponding α‐chloro‐β‐keto esters, showing high D‐synstereoselectivity, including those leading to the clinically relevant milataxel (Ar = 2‐furyl) and simotaxel (Ar = 2‐thienyl) side chains. Furthermore, various cross‐coupling chemistries performed on thep‐bromophenyl isoserine side chain significantly enhance the structural diversity of the taxoid side chain library obtained (16 additional taxoid side chains). The CaADH structure is notable: (i) the nicotinamide cofactor is bound in ananti‐conformation, with the amide carbonyl occupying the ketone binding pocket, and (ii) a flexible loop near the active site likely contributes to the remarkable substrate promiscuity observed in CaADH. We present our perspective on the dynamic nature of the CaADH active site through molecular dynamics simulation, proposing a halogen bonding model as a potential mechanism for the remarkable selectivity for an (S)‐configured C─Cl bond, in addition to the D‐facial selectivity, demonstrated across 20 diverse substrates by this remarkable short‐chain dehydrogenase enzyme.

Chemistry↗

Water accelerated self-healing of hydrophobic copolymers

Previous studies have shown that copolymer compositions can significantly impact self-healing properties. This was accomplished by enhancement of van der Waals (vdW) forces which facilitate self-healing in relatively narrow copolymer compositional range. In this work we report the acceleration of self-healing in alternating/random hydrophobic acrylic-based copolymers in the presence of confined water molecules. Under these conditions competing vdW interactions do not allow H 2 O-diester H-bonding, thus forcing nBA side groups to adapt L-shape conformations, generating stronger dipole-dipole interactions resulting in shorter inter-chain distances compared to ‘key-and-lock’ associations without water. The perturbation of vdW forces upon mechanical damage in the presence of controllable amount of confined water is energetically unfavorable leading the enhancement of self-healing efficiency of hydrophobic copolymers by a factor of three. The concept may be applicable to other self-healing mechanisms involving reversible covalent bonding, supramolecular chemistry, or polymers with phase-separated morphologies.

36 MATERIALS SCIENCE↗

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗

Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the submicromolar range was developed. Copyright 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 517-526, 2002.

Evaluation Studies↗

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↗

Conformal field theories are magical

“Magic” is the degree to which a state cannot be approximated by Clifford gates. We study mana, a measure of magic, in the ground state of the Z 3 Potts model, and argue that it is a broadly useful diagnostic for many-body physics. In particular we find that the q = 3 ground state has large mana at the model's critical point, and that this mana resides in the system's correlations. Here, we explain the form of the mana by a simple tensor-counting calculation based on a MERA representation of the state. Because mana is present at all length scales, we conclude that the conformal field theory describing the three-state Potts model critical point is magical. These results control the difficulty of preparing the Potts ground state on an error-corrected quantum computer and constrain tensor network models of AdS-CFT.

1-dimensional spin chains↗

Hybrid-Lipid Bilayers Induce n -Alkyl-Chain Order in Reversed-Phase Chromatographic Surfaces, Impacting their Shape Selectivity for Aromatic Hydrocarbon Partitioning

Shape selectivity is important in reversed-phase liquid chromatographic separations, where stationary phases are capable of separating geometric isomers, thereby resolving solutes based on their three-dimensional structure or shape rather than other chemical differences. Numerous chromatographic studies have been carried out using n-alkyl-chain-modified columns to understand how molecular shape affects retention. For polycyclic aromatic hydrocarbons (PAHs), it was found that planar compounds were selectively retained over non-planar structures of comparable molecular weight on surfaces with longer n-alkyl chains, higher chain-density, or at lower temperatures, where selectivity likely arises with greater ordering of the n-alkyl chains. A limitation of these studies, however, is the small range of chain ordering that can be achieved and lack of a direct measure of the n-alkyl-chain order of the stationary phases. In this work, we employ a C 18 stationary phase modified with a monolayer of phospholipid as a means of significantly varying the n-alkyl chain order. These hybrid-supported lipid bilayers, which have previously been employed as membrane-like stationary phases for measuring lipophilicity, provide a unique approach to control n-alkyl chain ordering by varying the acyl chain length and degree of unsaturation of the phospholipid modifier. The degree of alkyl-chain order of the resulting modified surfaces is determined from the ratio of trans- versus gauche-conformers, measured in situ within individual porous particles by confocal Raman microscopy. This methodology was also used to assess the affinity of these surfaces for planar versus non-planar PAH molecules. The retention selectivity for the planar versus non-planar compounds, thus determined, was found to vary significantly and systematically with the degree of order of the acyl/alkyl chains in the hybrid-supported lipid bilayers. Furthermore, the investigation also demonstrates the utility of confocal Raman microscopy for interrogating the impact of solute partitioning on stationary-phase structure within porous chromatographic particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Verifying the structure-property-performance relationship of Y6-based small molecule acceptors by alkoxy-side chain isomerization and conjugated skeleton asymmetry

Non-fullerene small molecule acceptors (NF-SMAs) such as Y6 derivatives were the current working horse for the top performing polymer solar cells (PSCs). For this reason, numerous chemical modifications have been explored for establishing structure–property-performance relationship for Y6-based NF-SMAs. In this work, we explored the isomerization on asymmetrical Y6 derivatives by varying the position of alkoxy side chain on the thiophene linkage between the core and one of the end groups of Y6. The isomers with differences in conformational restriction raised by noncovalent interactions as well as steric hindrance revealed distinctive behavior in crystallization and polymorphism, which led to a significant contrast in PSC performances. Here the X-TO1 molecule with alkoxy side chain facing the end group (outward) displayed preferred molecular configuration and polymorph, delivering power conversion efficiency (PCE) of 15.63%, while its isomer X-TO2 showed coexisted polymorphs significantly increased the charge recombination in the PSC devices led to a low PCE around 3%. This structure–property-performance relationship not only highlighted the elegancy of isomerization in tuning the photovoltaic performances but also identified polymorphism as one of the causes for impairing photovoltaic performances of PSCs.

36 MATERIALS SCIENCE↗

Supply Chain Research and Analysis for Space Systems

The implementation of NASA GSFC's portfolio of mission projects relies upon inter-connected, multi-tiered supply chains of organizations operating under direct and indirect contracts and other agreements throughout the U.S. and around the world. These supply chains are subject to an inter-related array of technical/production, business, market and security risks that are amplified by the ongoing globalization of industry and technology and which can disrupt or threaten the production and delivery of products and services when needed and in conformance with requirements. In recognition of such risks and associated challenges, GSFC's SMA directorate launched an innovative Supply Chain Research and Analysis capability three years ago to gain greater insight into the operating environment, performance, capabilities and viability of current and prospective suppliers for GSFC projects and proposals. The capability uses business intelligence techniques and primarily open source information resources as part of a cost-effective, non-intrusive methodology to produce several types of research and analysis reports. The reports are based on a holistic analytical framework encompassing key technical/production, business enterprise management, market and security factors, and feature in-depth information, summary information profiles, SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis, and candidate risk concerns in order to pro-actively support SMA and project management needs. The SRA capability, which is designed to complement and support ongoing SMA/project management activities and practices, has produced over 105 reports since its start-up in early 2015.This presentation addresses the approach, methodology and performance of the Supply Chain Research and Analysiscapability and its value in assuring the success of NASA mission projects. In doing so, the presentation provides lessons-learned, best practices, case examples and address how it fits into the development of an enterprise-level Supply Chain Risk Management capability.

supply chain risk management↗

Eigenstate Entanglement: Crossover from the Ground State to Volume Laws

For the typical quantum many-body systems that obey the eigenstate thermalization hypothesis (ETH), we argue that the entanglement entropy of (almost) all energy eigenstates is described by a single crossover function. The ETH implies that the crossover functions can be deduced from subsystem entropies of thermal ensembles and have universal properties. These functions capture the full crossover from the ground-state entanglement regime at low energies and small subsystem size (area or log-area law) to the extensive volume-law regime at high energies or large subsystem size. For critical one-dimensional systems, a universal scaling function follows from conformal field theory and can be adapted for nonlinear dispersions. We use it to also deduce the crossover scaling function for Fermi liquids in d > 1 dimensions. Here, the analytical results are complemented by numerics for large noninteracting systems of fermions in d ≤ 3 dimensions and have also been confirmed for bosonic systems and nonintegrable spin chains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Native Architecture of Wheat Straw Cell Walls: A Unified Model from X-ray Scattering and Solid-State NMR

Plant secondary cell walls constitute the dominant reservoir of renewable biomass, comprising tightly packed cellulose, hemicellulose, and lignin at the nanoscale. Recent advances in solid-state NMR spectroscopy and the availability of small-angle X-ray scattering for biomass characterization have led to an accumulation of experimental data on cell wall organization, yet no explicit structure model has simultaneously satisfied both Xray and NMR observations. Using wheat straw as a model system, we propose a structural framework consistent with current knowledge of cellulose biosynthesis, X-ray scattering data, and one- and two-dimensional 13 C solid-state NMR spectra. In this model, 18-chain elementary fibrils align in parallel and populate the cross-section at random. Arabinose-substituted xylan shows no conformational dependence for cellulose-binding in wheat, and only a minor fraction of 2-fold xylan appears in close proximity to cellulose, unlike in Arabidopsis, where xylan is more tightly attached to the cellulose surface. While NMR data cannot unambiguously resolve the internal arrangement of the 18 glucan chains, X-ray scattering profiles uniquely constrain the fibril size and exclude the possibility of tight bundling in the intact walls. The specific interaction between the matrix polymers and the cellulose elementary fibrils must be reconsidered in light of the small interfibril spaces, which bring the matrix components into spatial proximity with cellulose even in the absence of attractive interactions. These findings provide fundamental molecular-level insight into cellulose fibril architecture and matrix−polymer interactions, resolving longstanding discrepancies between spectroscopic and scattering data and advancing our understanding of biopolymer assembly into structurally and functionally versatile lignocellulosic biomaterials.

Carbohydrates↗