Ionizing radiation shielding properties of metal oxide impregnated conformal coatings
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Chemistry↗
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Results for “conformers”
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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Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease
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99 GENERAL AND MISCELLANEOUS↗
Conformational Plasticity in Human Heme-Based Dioxygenases
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99 GENERAL AND MISCELLANEOUS↗
Conformal electrochemical deposition of intermetallic AuCu thin films for convergent C–N coupling
A compositionally tunable series of AuCu films is active for electrocatalytic urea generation from carbon dioxide and nitrate.
Gerke, Carter S. [Department of Chemistry, Johns H↗
Crystal structure of a far-red–sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism
Significance Phytochromes are well-known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red- and far-red sensing are also critical for cyanobacteria living in the far-red–enriched shade of plants. This work reports the crystal structure of a far-red–sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insights into the molecular basis of far-red-sensing by phycobilin-based photoreceptors. Owing to the deep tissue penetration of far-red light, far-red–sensing cyanobacteriochromes are promising protein scaffolds for developing genetically encoded photoswitches, optoacoustic contrast agents, and fluorescent probes for in situ imaging and optogenetic applications.
59 BASIC BIOLOGICAL SCIENCES↗
Tuning the Conformations of an M4L4 Cage and Their Impact on Catalysis
Enzymes catalyze chemical reactions with remarkable rate enhancements and selectivity. Supramolecular catalysis seeks to understand and emulate these outcomes, leveraging noncovalent interactions, electric fields, and controlled active site microenvironments to enhance catalysis in an enzyme-like fashion. The effects of conformational dynamics on supramolecular catalysts and assemblies are, however, relatively unexplored, despite their crucial role in enzyme rate enhancement. Here, we elucidate the conformational landscape of a model M4L4 supramolecular host through a rational approach: stabilizing a high-energy conformer through distal ligand modification and a transient intermediate state through symmetry-matched guest encapsulation, as well as tuning the conformer distribution through same-charge metal exchange at the host vertices. Each of these structural modifications induces a substantial shift in the host's conformational landscape, offering insights into the rational design of conformationally dynamic cages and enzymes. Although the thermodynamic properties of the dynamic Ga4L412- cage can be influenced by temperature, solvent, and guest binding, we find that conformational change occurs on a time scale that renders it rate-limiting in a model catalytic reaction, precluding rate enhancement through conformational selection. This concept is illustrated by locking the catalytically inactive conformer to a high-energy conformer that is catalytically competent. These findings demonstrate that precise modulation of the conformational landscape of supramolecular hosts provides an effective strategy for controlling their catalytic activity and binding.
Catalysis↗
A high-throughput workflow to analyze sequence-conformation relationships and explore hydrophobic patterning in disordered peptoids
Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using matrix-assisted laser desorption/ionization and tandem mass spectrometry (MALDI-MS/MS), and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived “motifs” to inform a machine-learning algorithm toward conformation prediction. Here, this multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.
data-driven analysis↗
Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions
The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.
Nielson, Felicity F.↗
Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence
G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.
59 BASIC BIOLOGICAL SCIENCES↗
CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM
Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.
47 OTHER INSTRUMENTATION↗
Searching for Conformity Across Cosmic Time with Local Group and Local Volume Star Formation Histories
Conformity denotes the correlation of properties between pairs of galaxies as a function of separation. Correlations between properties such as the star formation rate (SFR), stellar mass, and specific star formation rate (sSFR) have implications for the impact of environment upon galaxy formation and evolution. Conformity between primary galaxies and satellites within the same dark matter halo has been well documented in simulations and observations. However, the existence of conformity at greater distances—known as two-halo conformity—remains uncertain. We investigate whether galaxies in the Local Volume to a distance of 4 Mpc show conformity by examining the SFR, sSFR, stellar mass, and quenched fraction as a function of physical separation. Making use of the star formation histories of these galaxies, we then extend this analysis back in time to offer the first probe of conformity inside our past light cone. At the present day, we find that the stellar mass or sSFR of a galaxy correlates with the median SFR of neighboring galaxies at a separation of 2–3 Mpc. At a lookback time of 1 Gyr, we find a correlation with the quenched fraction of neighboring galaxies, again at a 2–3 Mpc separation. These signals of conformity likely arise from the differences between the recent star formation histories of Local Group dwarf galaxies and those outside the Local Group. As current and future missions including JWST, Rubin, and Roman expand the sample of Local Volume galaxies, tests of conformity using star formation histories will provide an important tool for exploring spatiotemporal correlations between galaxies.
79 ASTRONOMY AND ASTROPHYSICS↗
On the conformal symmetry of exceptional scalar theories
The DBI and special galileon theories exhibit a conformal symmetry at unphysical values of the spacetime dimension. We find the Lagrangian form of this symmetry. The special conformal transformations are non-linearly realized on the fields, even though conformal symmetry is unbroken. Commuting the conformal transformations with the extended shift symmetries, we find new symmetries, which when taken together with the conformal and shift symmetries close into a larger algebra. For DBI this larger algebra is the conformal algebra of the higher dimensional bulk in the brane embedding view of DBI. For the special galileon it is a real form of the special linear algebra. We also find the Weyl transformations corresponding to the conformal symmetries, as well as the necessary improvement terms to make the theories Weyl invariant, to second order in the coupling in the DBI case and to lowest order in the coupling in the special galileon case.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes
Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae
Photosynthetic organisms use pigment–protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment–protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The microwave spectra of the conformers of $\mathcal{n}$-butyl nitrate
We report the microwave spectrum of n-butyl nitrate was recorded in the 5 to 20 GHz frequency range using broadband chirp and narrowband pulse excitation molecular jet Fourier transform microwave spectrometers. A quantum chemistry structural analysis yielded thirteen stable conformers. Among them, the five most energetically stable conformers were observed in the experimental spectra. The most stable conformer features a butyl chain with an anti-gauche-anti conformation (AGA) where the γ-carbon atom is about 64° out of the nitrate plane. For this conformer, spectra of all 13 C and 15 N minor isotopologues could be measured. The conformer with a straight butyl chain (AAA), and three other conformers (GAA, GGA, and AGG) were also observed. Accurate rotational constants, centrifugal distortion constants, and 14 N nuclear quadrupole coupling constants could be deduced and compared to the theoretical values.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational remodeling of an enzyme conformational landscape for altered substrate selectivity
Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗