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Results for “Molecular conformation”

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Poly(cyclosilane) Connectivity Tunes Optical Absorbance

We report herein the influence of skeletal connectivity on the conformation-dependent optical properties of cyclosilane homo- and copolymers. 1,3-Linked cyclosilanes were bathochromically shifted by 20 nm in solution relative to 1,4-linked cyclosilanes, an effect reproduced by quantum chemical calculations on oligomeric model systems. Polysilane optical properties are conformation-dependent, and 1,3-linked cyclosilanes were hypothesized to adopt a favorable conformation unavailable to 1,4-linked cyclosilanes constrained to an endocyclic gauche conformation. Copolymerization of the isomeric cyclosilanes 1,3Si 6 and 1,4Si 6 afforded linear statistical copolymers, as characterized by 1 H and 29 Si NMR spectroscopies. The distinct connectivity of each comonomer was found to give rise to tunable absorption spectra, where the position of the absorption band systematically increased with the increased corporation of 1,3Si 6 . Computational studies pointed to conformation-dependent changes in orbital symmetry in shifting the most intense transition from the low-energy highest occupied molecular orbital (HOMO) → lowest unoccupied molecular orbital (LUMO) transition to a higher-energy HOMO → LUMO + n transition. Here, the results of these studies demonstrate for the first time the role of silicon skeletal connectivity in controlling conformation and optoelectronic properties and provide new insight into the structure-based design of solution-processable silicon-based polymeric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2024

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases (FAPs) to catalyse unnatural photoredox radical C–C bond formation by leveraging strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases (RAPs) to facilitate decarboxylative radical cyclisation with excellent chemo-, enantio-, and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of FAPs. An orthogonal set of RAPs was engineered to access all four possible stereoisomers of stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved RAPs allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclisation. The development of stereoselective RAPs provides unnatural C–C bond forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free radical-mediated reactions.

Ju, Shuyun (ORCID:000000020322104X)↗
DOE OSTI2020

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BP SS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BP SS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BP SS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BP SS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R 0 ) and fluorophore orientation factor (κ 2 ) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

An Archaea 5S rRNA analog is stably expressed in Escherichia coli

Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.

Non-NASA Center↗
NASA NTRS1994

Inventing and improving ribozyme function: rational design versus iterative selection methods

Two major strategies for generating novel biological catalysts exist. One relies on our knowledge of biopolymer structure and function to aid in the 'rational design' of new enzymes. The other, often called 'irrational design', aims to generate new catalysts, in the absence of detailed physicochemical knowledge, by using selection methods to search a library of molecules for functional variants. Both strategies have been applied, with considerable success, to the remodeling of existing ribozymes and the development of ribozymes with novel catalytic function. The two strategies are by no means mutually exclusive, and are best applied in a complementary fashion to obtain ribozymes with the desired catalytic properties.

Review, Tutorial↗
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗
DOE OSTI2022

Switching charge states in quasi-2D molecular conductors

Abstract 2D molecular entities build next-generation electronic devices, where abundant elements of organic molecules are attractive due to the modern synthetic and stimuli control through chemical, conformational, and electronic modifications in electronics. Despite its promising potential, the insufficient control over charge states and electronic stabilities must be overcome in molecular electronic devices. Here, we show the reversible switching of modulated charge states in an exfoliatable 2D-layered molecular conductor based on bis(ethylenedithio)tetrathiafulvalene molecular dimers. The multiple stimuli application of cooling rate, current, voltage, and laser irradiation in a concurrent manner facilitates the controllable manipulation of charge crystal, glass, liquid, and metal phases. The four orders of magnitude switching of electric resistance are triggered by stimuli-responsive charge distribution among molecular dimers. The tunable charge transport in 2D molecular conductors reveals the kinetic process of charge configurations under stimuli, promising to add electric functions in molecular circuitry.

Huang, Yulong (ORCID:0000000296160134)↗
NASA NTRS2001

The gating mechanism of the large mechanosensitive channel MscL

The mechanosensitive channel of large conductance, MscL, is a ubiquitous membrane-embedded valve involved in turgor regulation in bacteria. The crystal structure of MscL from Mycobacterium tuberculosis provides a starting point for analysing molecular mechanisms of tension-dependent channel gating. Here we develop structural models in which a cytoplasmic gate is formed by a bundle of five amino-terminal helices (S1), previously unresolved in the crystal structure. When membrane tension is applied, the transmembrane barrel expands and pulls the gate apart through the S1-M1 linker. We tested these models by substituting cysteines for residues predicted to be near each other only in either the closed or open conformation. Our results demonstrate that S1 segments form the bundle when the channel is closed, and crosslinking between S1 segments prevents opening. S1 segments interact with M2 when the channel is open, and crosslinking of S1 to M2 impedes channel closing. Gating is affected by the length of the S1-M1 linker in a manner consistent with the model, revealing critical spatial relationships between the domains that transmit force from the lipid bilayer to the channel gate.

Non-NASA Center↗
DOE OSTI2023

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia , is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Further Investigations of Racemic and Chiral Molecular Sieves of the STW Topology

Large single crystals of pure-silica STW-type molecular sieves are prepared using 1,2,3,4,5-pentamethylimidazolium (12345PMI) and 2-ethyl-1,3,4-trimethylimidazolium (2E134TMI) as organic structure-directing agents (OSDAs) and α-amino acid additives. The effects of the amount and type of amino acid on the crystallization of pure-silica STW materials are investigated. Room-temperature single-crystal X-ray diffractometry shows that 12345PMI better fits the STW cage than 2E134TMI and is fully consistent with computed simulations. The synthesis of an enantioenriched R-STW-type molecular sieve having a Si/Ge ratio of 2.2 is achieved using a chiral, dicationic OSDA that contains two stereocenters. Furthermore, the conformation of the chiral OSDA in the chiral framework has been obtained from a Rietveld refinement using synchrotron powder diffraction data and is the first structure refinement of an enantioenriched, inorganic molecular sieve prepared from a pure, asymmetric OSDA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗
NASA NTRS1999

Non-unity molecular heritability demonstrated by continuous evolution in vitro

INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

Non-NASA Center↗
DOE OSTI2020

Probing Conformational Evolution and Associated Dynamics of Mg(N(SO 2 CF 3 ) 2 ) 2 ·Dimethoxyethane Adduct Using Solid-State 19 F and 1 H NMR

Bis(trifluoromethanesulfonimide) or TFSI is widely used as a counter anion in electrolyte design due to its structural flexibility and chemical stability. Here we studied the conformational variations and associated dynamics of TFSI in adduct of Mg(TFSI) 2 with dimethoxyethane (DME), a solvate crystalline material using solid-state 1 H and 19 F NMR. TFSI molecular motion in this solvate structure falls within the timescale of the 19 F NMR experiment, yielding spectroscopic signatures for unique TFSI conformers under the coordination environment of Mg 2+ cation. Within the temperature range of -5 to 82 °C, we observe nine distinct TFSI sites in both crystalline and disordered regions using 19 F NMR, reflecting complexity of structural and dynamics of TFS1 anions within solvate structure. The four distinguishable sites in the disordered region for the two CF 3 groups of the same TFSI molecule are identified using chemical shift analysis. The exchange rate constants from site to site are calculated through variable temperature 19 F NMR and two-dimensional (2D) exchange spectroscopy (EXSY) experiments, along with respective activation enthalpies using Eyring's formulation. The flip rate of CF 3 around the S-C bond is estimated as ~ 15 s -1 at 8 °C with ΔH ≠ ~ 22 kJ/mol, but the rotation of the entire TFSI is 4.8 s -1 at 8 °C with a significantly greater ΔH ≠ = 98 ± 10 kJ/mol. Furthermore, the slow conversion of trans to cis conformers at a lower temperature (T ≤ 1 °C) in the crystalline region is monitored, with a conversion rate of ~ 2 x 10 -5 s -1 at -5 °C. Density functional theory (DFT)-based calculations were performed to support further the assignment of experimental chemical shifts, and the activation energy E a = 21.1 kJ/mol obtained for the cis to trans transition is consistent with experimental values. The combined set of 19 F and 1 H under both one-dimensional (1D) and 2D NMR methods demonstrated here can be further used for examining electrode-electrolyte interfaces to probe the motions of various constituents that can enable detailed studies of interfacial processes and dynamics. Ultimately, such studies will aid in the design and discovery of interfacial constructs in which directed defect chemistry, chemical moiety distribution, and nanostructure are employed to drive efficient charge transport.

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

Tracking the protein conformational motions driving HIV-1 membrane fusion

HIV-1 Env (trimeric gp120/gp41) is the surface protein responsible for membrane fusion. The Env binds to the receptor proteins, which induces gp120 shedding leading to conformational changes of gp41 from the pre-fusion to post-fusion state, allowing its fusion peptide to embed in the host cell membrane and bringing the viral and host cell membranes together. The gp41 refolding is a target of several peptide inhibitors. Yet, the molecular mechanism of this dynamic process is still not well understood. In this study, we successfully simulate the conformational change of gp41 from pre-fusion to post-fusion state in atomistic resolution using all-atom structure-based models. We reveal that maintaining the directionality of protomer interactions in both pre-fusion and post-fusion states is crucial for gp41 refolding. Additionally, we find that HR1 inherently extends as a three-helical bundle toward the host-cell membrane without any bias. Importantly, we identify native contacts in the pre-fusion state that are critical for the proper refolding of gp41 towards the post-fusion state. Lastly, by incorporating the membrane-fusion inhibitors, T20 and SFT, we identify the most vulnerable stage in the fusion pathway that exhibits the greatest sensitivity to these drugs, which could aid in a better understanding of drug resistance mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗