Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
Abstract not provided
Olson, Linda J.↗
SEARCH · Engineering Papers
Results for “conformation dynamics”
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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Sixfold Way of Traversable Wormholes in the Sachdev-Ye-Kitaev Model
In the infrared limit, a nearly anti–de Sitter spacetime in two dimensions ( AdS 2 ) perturbed by a weak double trace deformation and a two-site ( q > 2 )-body Sachdev-Ye-Kitaev (SYK) model with N Majoranas and a weak 2 r -body intersite coupling share the same near-conformal dynamics described by a traversable wormhole. We exploit this relation to propose a symmetry classification of traversable wormholes depending on N , q , and r , with q > 2 r , and confirm it by a level statistics analysis using exact diagonalization techniques. Intriguingly, a time-reversed state never results in a new state, so only six universality classes occur—A, AI, BDI, CI, C, and D—and different symmetry sectors of the model may belong to distinct universality classes. Published by the American Physical Society 2024
Physics↗
Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy
Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024
36 MATERIALS SCIENCE↗
FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II
Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Composite entanglement topology and extensional rheology of symmetric ring-linear polymer blends
Extensive molecular simulations are applied to characterize the equilibrium dynamics, entanglement topology, and nonlinear extensional rheology of symmetric ring-linear polymer blends with systematically varied ring fraction ϕR. Chains with degree of entanglement Z≈14 are mixed to produce 10 well-entangled systems with ϕR varying from neat linear to neat ring melts. Z is large enough that except for very large ϕR, the rings are threaded by multiple linear chains in equilibrium. Primitive path analysis is used to visualize and quantify the structure of the composite ring-linear entanglement network. We measure the quantity of ring-linear threading and linear-linear entanglement as a function of ϕR and identify with simple arguments a ring fraction ϕR≈0.4 where the topological constraints of the composite entanglement network are maximized. These topological analyses are used to rationalize the ϕR-dependence of ring and linear chain dynamics, conformations, and rheology. Simulations of startup uniaxial elongation flows demonstrate the extensional stress overshoot observed in recent filament stretching experiments and characterize how it depends on the blend composition and entanglement topology. The overshoot is driven by an overstretching and recoil of ring polymers due to the convective unthreading of rings from linear chains.
O’Connor, Thomas C.↗
Cryo-$\mathrm{EM}$ reveals an entangled kinetic trap in the folding of a catalytic $\mathrm{RNA}$
Functional RNAs fold through complex pathways that can contain misfolded “kinetic traps.” A complete model of RNA folding requires understanding the formation of these misfolded states, but they are difficult to characterize because of their transient and potentially conformationally dynamic nature. We used cryo–electron microscopy (cryo-EM) to visualize a long-lived misfolded state in the folding pathway of the Tetrahymena thermophilagroup I intron, a paradigmatic RNA structure-function model system. The structure revealed how this state forms native-like secondary structure and tertiary contacts but contains two incorrectly crossed strands, consistent with a previous model. This incorrect topology mispositions a critical catalytic domain and cannot be resolved locally as extensive refolding is required. This work provides a structural framework for interpreting decades of biochemical and functional studies and demonstrates the power of cryo-EM for the exploration of RNA folding pathways.
59 BASIC BIOLOGICAL SCIENCES↗
Switchable client specificity in a dual functional chaperone coordinates light-harvesting complex biogenesis
The proper assembly of light-harvesting complexes (LHCs) is critical for photosynthesis and requires the biogenesis of light-harvesting chlorophylla,b-binding proteins (LHCPs) to be coordinated with chlorophyll (Chl) biosynthesis. The mechanism underlying this coordination is not well understood. Here, we show that a conserved molecular chaperone, chloroplast signal recognition particle 43-kDa protein (cpSRP43), provides a molecular thermostat that helps maintain this coordination. cpSRP43 undergoes a conformational rearrangement between a well-folded closed state and a partially disordered open state. Closed cpSRP43 is dedicated to the biogenesis of LHCPs, whereas open cpSRP43 protects multiple Chl biosynthesis enzymes from heat-induced destabilization. Rising temperature shifts cpSRP43 to the open state, enabling it to protect heat-destabilized Chl biosynthesis enzymes. Our results reveal the molecular basis of a posttranslational mechanism for the thermoadaptation of LHC biogenesis. They also demonstrate how an adenosine triphosphate–independent chaperone uses conformational dynamics to switch its activity and client selectivity, thereby adapting to different proteostatic demands under shifting environmental conditions.
Science & Technology - Other Topics↗
Single-molecule infrared spectroscopy with scanning tunneling microscopy
Probing vibrations at the single-molecule level is essential for achieving bond-specific chemical control in realistic heterogeneous environments. Here, we introduce a new measurement scheme that integrates frequency-tunable infrared excitation with scanning tunneling microscopy to characterize vibration-mediated nuclear motions of single molecules. We first validated the technique by monitoring the infrared-induced rotation of the ethynyl radical and then applied it to mapping pyrrolidine’s conformational dynamics. The resulting broadband spectra captured fundamental vibrational modes together with rich overtone and combination bands inaccessible by conventional methods, which we confirmed with isotopic substitutions. Density functional theory calculations showed that delocalized modes coupled with pyrrolidine ring puckering drive the structural transition, revealing altered selection rules compared with traditional infrared spectroscopy. Here, this new experimental platform enables molecular vibrations and transformations to be probed with atomic precision.
Liang, Kangkai [University of California, San Dieg↗
Stochastic equilibrium Raman spectroscopy (STERS)
In this manuscript, we propose a new method for cavity- and surface-enhanced Raman spectroscopy (SERS) with improved temporal resolution in the measurement of stochastic Raman spectral fluctuations. Our approach combines Fourier spectroscopy and photon correlation to decouple the integration time from the temporal resolution. Using statistical optics Monte Carlo simulations, we establish the relationship between time resolution and Raman signal strength, revealing that typical Raman spectral fluctuations, commensurate with molecular conformational dynamics, can theoretically be resolved on micro- to millisecond timescales. The method can further extract average single-molecule dynamics from small sub-ensembles, thereby potentially mitigating challenges in achieving strictly single-molecule isolation on SERS substrates.
Cobb-Bruno, Colburn [University of California, Ber↗
Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis
Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.
09 BIOMASS FUELS↗
Structural mechanisms for VMAT2 inhibition by tetrabenazine
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson’s disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2’s importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington’s chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
59 BASIC BIOLOGICAL SCIENCES↗
Replication Data for: Deconstructing Chirality: Probing Local and Non-local Effects in Azobenzene Derivatives with X-ray Circular Dichroism
Resolving molecular chirality at the atomic scale remains a critical challenge in chemistry. Conventional Optical Circular Dichroism spectroscopy often overlooks subtle and localized structural features. Here, we computationally investigate site-specific X-ray Circular Dichroism (XCD) across a series of trans-azobenzene derivatives to deconstruct and interpret chiroptical signals at the atomic level. Our modeling reveals that XCD is capable of distinguishing dichroic contributions arising from both a local chiral center and global molecular twist, revealing their intricate interplay and potential for constructive or destructive interference. We show that sterically-induced global distortions can dominate the XCD signal in some cases, even suppressing the response from the chiral center itself. This insight suggests a new molecular design principle for tuning chiroptical activity, which we extend by proposing strategies to achieve unidirectional photoisomerization through steric gearing. Altogether, this work establishes a quantitative framework for engineering chiroptical responses, laying the foundation for the design of functional chiral systems utilizing principles of unidirectional molecular motor-like conformational dynamics.
Chemistry↗
Neutrino Dipole Moments and Radiative Signatures from Partial Compositeness
We investigate composite neutrino models where heavy neutrinos emerge as bound states from a near-conformal strongly coupled sector. Standard Model neutrinos mix with these composite singlets via an inverse seesaw mechanism, where the anomalous scaling dimensions of the composite-sector operators naturally suppress light neutrino masses to sub-eV scales. Matching the conformal dynamics onto low-energy theory yields enhanced electromagnetic transition dipole operators with couplings $d_{μN} \sim 10^{-6}$-$10^{-8}\,\mathrm{GeV}^{-1}$, parametrically larger than the loop-level predictions of minimal Dirac or Majorana models. We carry out a dedicated event-level simulation of the production-and-decay chain $νX \to \mathcal{U} X \to νγX$ and compute the resulting event rates at MiniBooNE and MINERvA within the model, accounting for the composite production cross section and decay kinematics in detail. We further present predictions for the photon energy, angular, and multiplicity distributions. For the benchmark scenarios accessible at these experiments the radiative signal is predominantly single-photon; the composite structure additionally permits fragmentation of the up-scattered state into multiple heavy neutrinos, each decaying as $N\toνγ$, with multi-photon final states emerging for lighter compositeness scales or higher beam energies as a qualitatively new probe of the composite dynamics.
Assi, Benoît [Cincinnati U.; Fermilab] (ORCID:0000↗
Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation
The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO 2 C 2 H 7 + and PO 2 CH 4 + , oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO 2 C 2 H 7 + and PO 2 CH 4 + . The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.
59 BASIC BIOLOGICAL SCIENCES↗
MA’AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution
Not provided.
Biochemistry & Molecular Biology↗
Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations
We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.
Do, Hung Nguyen↗
Residue Specific Characterization of Electrostatics, Conformational Heterogeneity, and Dynamics of Electron Transfer Proteins with Linear and Nonlinear Infrared Spectroscopy. Final Report
The goal of this research project was to further our understanding of biological electron transfer through the development and application of new methods for studying proteins and their complexes with high spatial and temporal detail. The approach was based on incorporation of reporter bonds with distinct vibrational frequencies at specific locations in proteins and their characterization through the interaction of the bonds with pulses of infrared light. The project focused on the proteins plastocyanin (Pc) and cytochrome (cyt) f, two electron transfer partners in photosynthesis. The first thrust of the project was the incorporation of carbon deuterium bonds as non-perturbative probes at a ligand to the copper ion of Pc and their use to detect changes in the bonding due to the number of electrons at the metal and how the bonding changes upon association with cyt f. Toward developing more advanced approaches to characterize proteins, we incorporated a stronger reporter, the cyano group of cyanophenylalanine, at several locations in Pc and measured the frequency dynamics in the absence and presence of cyt f. The acquired data improved the current model for the protein complex. Notably, the data indicated that the majority of the population is involved in a loosely bound complex, providing insight into the nature of the ensembles formed by electron transfer protein complexes that is not available via other approaches. In addition to learning about the protein complex, we made strides toward developing and improving the new experimental approach to study highly dynamic behaviors of proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamic, Tunable, and Conformal Wearable Compression Using Active Textiles
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Rachael Granberry↗