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Results for “Conformational switch”

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

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Noncanonical folding of peptoid oligomers: Formation of a closed conformation in nonpolar solvent

Peptoids provide a versatile platform for foldamer design, yet their conformational behavior in low-dielectric media remains poorly understood. The structural characteristics of N-1-phenylethylglycine (Nspe) homo-oligomers were inves-tigated in chloroform, a solvent that mimics the interior of lipid bilayers, using nuclear magnetic resonance (NMR) spec-troscopy and molecular dynamics (MD) simulations. Nspe7 populated two distinct compact conformations, while Nspe10 adopted a single homogeneous conformation related to the previously reported Nspe9 threaded-loop structure. Integrated experimental and computational analysis reveals that these structures are stabilized by cooperative end-to-end intramo-lecular hydrogen bonding, cis-trans backbone isomerism, and hydrophobic side-chain shielding. The resulting structures minimize exposed polar surface area, demonstrating a closed conformation in the low-dielectric environment. These find-ings establish specific chain-length requirements for achieving well-defined closed conformations. This work provides insights into peptoid folding in nonpolar media, enabling rational design strategies for solvent-directed conformational switching systems.

Oh, Jinyoung↗
DOE OSTI2020

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.

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

Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR

Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an α 2 β 2 heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.

Computational biophysics↗
DOE OSTI2020

Electric field stimulates production of highly conductive microbial OmcZ nanowires

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S cm -1 ) and threefold higher stiffness (1.5 GPa) than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modeling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. Overall, these findings of biologically produced, highly conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

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

Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state

Abstract AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH ( Tm FtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length Tm FtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chromatin binding by HORMAD proteins regulates meiotic recombination initiation

The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae , the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix–turn–helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗
DOE OSTI2023

C-terminal conformational changes in SCF-D3/MAX2 ubiquitin ligase are required for KAI2-mediated signaling

Karrikins (KARs) are bioactive molecules derived from burning vegetation. Plants perceive KARs through the hydrolase KARRIKIN INSENSITIVE 2 (KAI2) that interacts with the F-box protein ubiquitin ligase MORE AXILLARY GROWTH 2 (MAX2). MAX2 also plays a role in the perception and signal activation by Strigolactone (SL), a phytohormone controlling various developmental processes in plants. SL also acts as a rhizosphere signal to activate arbuscular mycorrhiza fungi that can be exploited by parasitic plants. kai2 knockouts exhibit distinct developmental defects and therefore KAI2 is hypothesized to perceive an unidentified endogenous ligand provisionally termed KAI2-Ligand (KL). Upon KAR/KL perception, the protein complex of KAI2-MAX2 targets SUPPRESSOR OF MAX2-1/2 (SMAX1)/SMXL2 for proteasomal degradation. Despite the identification of the key components KAI2, MAX2, and SMAX1 in KAR/KL signaling, their mode of interaction and regulation remains elusive. Recently, the regulatory function of the conformational switch of MAX2 C-terminal helix (CTH) in SL signaling has been demonstrated however its role in KAR/KL signaling remained unknown. Here we address the function of MAX2-CTH dynamics both in vitro and in planta and show that the central role of CTH is conserved between SL and KAR/KL signaling pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors

The G12D mutation is among the most common KRAS mutations associated with cancer, in particular, pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM KD values. Deep mutational scanning of a monobody generated hundreds of functional and nonfunctional single-point mutants, which identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Deep learning–driven rare-event sampling reveals an Ala7/d-Ala8 conformational hinge governing amphiphilic switching in cyclosporine A

Passive membrane permeability of N-methylated macrocyclic peptides remains poorly understood because high-energy conformational intermediates are rarely sampled by conventional methods. Using the deep learning–driven rare-event sampling framework ES-CRUMPLE, we show that cyclosporine A accesses transient amphiphilic states via a localized conformational hinge at Ala7/d-Ala8, revealing a kinetic design handle that is invisible to population-based analyses.

Lindberg, Edward T [University of Tennessee, Knoxv↗
DOE OSTI2020

Fundamental limitations on photoisomerization from thermodynamic resource theories

Small, out-of-equilibrium, and quantum systems defy simple thermodynamic expressions. Such systems are exemplified by molecular switches, which exchange heat with a bath. These molecules can photoisomerize, or change conformation, or switch, on absorbing light. The photoisomerization probability depends on kinetic details that couple the molecule’s energetics to its dissipation. Therefore, a simple, general, thermodynamic-style bound on the photoisomerization probability seems out of reach. We derive such a bound using a resource theory. The resource-theory framework is a set of mathematical tools, developed in quantum information theory, used to generalize thermodynamics to small and quantum settings. From this toolkit has been derived a generalization of the second law, the thermomajorization preorder. We use thermomajorization to upper-bound the photoisomerization probability. Then, we compare the bound with an equilibrium prediction and with a Lindbladian model. We identify a realistic parameter regime in which the Lindbladian evolution saturates the thermomajorization bound. We also quantify the energy coherence in the electronic degree of freedom, and we argue that this coherence cannot promote photoisomerization. Overall, this work illustrates how quantum-information-theoretic thermodynamics can elucidate complex quantum processes in nature, experiments, and synthetics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Prehydrodynamic evolution and its signatures in final-state heavy-ion observables

We investigate the effects of prehydrodynamic evolution on final-state observables in heavy-ion collisions using state-of-the art event simulations coupled to different prehydrodynamic scenarios, which include the recently developed effective kinetic transport theory evolution model KøMPøST. Differential flow observables are found to be mostly insensitive to the details of prehydrodynamic evolution. The main effect we observe is in the p T spectra, particularly the mean transverse momentum. However, at least part of this effect is a consequence of the underlying conformal invariance assumption currently present in such approaches, which is known to be violated in the temperature regime probed in heavy-ion collisions. This assumption of early time conformal invariance leads to an artificially large out-of-equilibrium bulk pressure when switching from (conformal) prehydrodynamic evolution to hydrodynamics (using the nonconformal QCD equation of state), which in turn increases the transverse momentum. Our study indicates that a consistent treatment of prehydrodynamic evolution in heavy-ion collisions requires the use of nonconformal models of early time dynamics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch

Post-translational control of PERIOD stability by Casein Kinase 1δ and ε (CK1) plays a key regulatory role in metazoan circadian rhythms. Despite the deep evolutionary conservation of CK1 in eukaryotes, little is known about its regulation and the factors that influence substrate selectivity on functionally antagonistic sites in PERIOD that directly control circadian period. Here we describe a molecular switch involving a highly conserved anion binding site in CK1. This switch controls conformation of the kinase activation loop and determines which sites on mammalian PER2 are preferentially phosphorylated, thereby directly regulating PER2 stability. Integrated experimental and computational studies shed light on the allosteric linkage between two anion binding sites that dynamically regulate kinase activity. We show that period-altering kinase mutations from humans to Drosophila differentially modulate this activation loop switch to elicit predictable changes in PER2 stability, providing a foundation to understand and further manipulate CK1 regulation of circadian rhythms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering Structural Transitions in a Multilevel Molecular Switch via Intermolecular Coupling

Controlling molecular conformations with atomic precision is essential for advancing molecular functional electronics, as well as our understanding of molecular dynamics. While switching between bistable molecular conformers is common in nature, creating systems with multiple, addressable states remains synthetically challenging. Here, we demonstrate a bottom-up strategy in which intermolecular interactions give rise to multilevel functionality within a simple two-molecule assembly. Using low-temperature scanning tunneling microscopy, we show that a pyrrolidine dimer on Cu(100) exhibits six distinct adsorption conformations, exceeding the four expected from two independent bistable units. This unusual complexity arises from the interplay between intermolecular van der Waals attraction and steric repulsion, which reshapes the potential energy landscape and changes a single high-energy transition into a sequential two-step pathway. Each step is driven by low-energy inelastic electron excitations, achieving a switching efficiency an order of magnitude higher than that of the monomer. Here, by tuning the bias voltage and tip–molecule distance, we achieve deterministic control over multiple stable states, establishing a general design principle for on-demand engineering of collective molecular behavior and energy-efficient multilevel molecular devices.

Molecular interactions↗