Search NASA⌕ Search

SEARCH · Search NASA

Results for “binding modes”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural insights into VRC01-class bnAb precursors with diverse light chains elicited in the IAVI G001 human vaccine trial

The development of germline-targeting vaccines represents a potentially transformative strategy to elicit broadly neutralizing antibodies (bnAbs) against HIV and other antigenically diverse pathogens. Here, we report on structural characterization of vaccine-elicited VRC01-class bnAb precursors in the IAVI G001 Phase 1 clinical trial with the eOD-GT8 60mer nanoparticle as immunogen. High-resolution X-ray structures of eOD-GT8 monomer complexed with Fabs of five VRC01-class bnAb precursors with >90% germline identity revealed a conserved mode of binding to the HIV CD4-binding site via IGHV1-2-encoded heavy chains, mirroring mature bnAb interactions. The light-chain V-gene diversity emulated VRC01 bnAbs and stabilized antigen engagement, while their conserved five-residue LCDR3 motifs prevented steric clashes. Notably, the VRC01-class bnAb precursors accommodated the N276 glycan, a key barrier in HIV Env recognition, through structural rearrangements in HCDR3 or LCDR1, despite its absence in the immunogen. Surface plasmon resonance analysis showed that 87% of elicited antibodies retained glycan binding capacity, albeit with reduced affinity. These findings validate the ability of eOD-GT8 60mer nanoparticles to prime VRC01-class bnAb precursors with native-like paratopes but with intrinsic glycan adaptability. Structural mimicry of mature bnAbs was observed even with limited somatic hypermutation, indicating that critical features are encoded in the germline repertoire. The structures highlight how germline-encoded features drive bnAb-like recognition at early stages. This work provides molecular evidence supporting germline targeting in humans and provides guidance for designing booster immunogens to shepherd affinity maturation toward broad neutralization.

Science & Technology - Other Topics↗
DOE OSTI2020

Structural basis of broad HIV neutralization by a vaccine-induced cow antibody

Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo–electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP.664. The exceptionally long (60 residues) third complementarity-determining region of the heavy chain (CDR H3) of NC-Cow1 forms a mini domain (knob) on an extended stalk that navigates through the dense glycan shield on Env to target a small footprint on the gp120 CD4 receptor binding site with no contact of the other CDRs to the rest of the Env trimer. These findings illustrate, in molecular detail, how an unusual vaccine-induced cow bnAb to HIV Env can neutralize with high potency and breadth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Quantitative Prediction of Uranium Speciation and Amidoxime Binding in Seawater from Advanced Simulation Techniques

The goal of this project was to quantitatively predict stability of uranium species and thermochemistry of uranium binding with amidoxime ligands in realistic seawater conditions. The specific aims of the project were: (i) determine the stable species of uranium and its solvation structure in realistic seawater conditions; also speciation and solvation of uranium's major competing species in seawater, vanadium; (ii) accurately predict the free energies (and thereby stability constants) of binding between uranium and amidoxime; (iii) accurately predict the reaction enthalpies and entropies of binding between uranium and amidoxime as well as between vanadium and amidoxime. Main results and conclusions are as follows. First-principles molecular dynamic simulations found that the structure of the Ca 2 UO 2 (CO 3 ) 3 complex is very stable and that one Ca ion binds to the center UO 2 (CO 3 ) 3 4- anion stronger than the other Ca ion. This finding suggests that using time-resolved EXAFS spectra may confirm the asymmetry in binding of the two Ca ions in the aqueous Ca 2 UO 2 (CO 3 ) 3 complex. To consider the common ions, solvation of the Ca 2 UO 2 (CO 3 ) 3 complex in seawater was simulated by classical molecular dynamics simulation. It was found that the structure of the Ca 2 UO 2 (CO 3 ) 3 complex is very stable in the model seawater. A Na+ ion was found to be closely associated with the Ca 2 UO 2 (CO 3 ) 3 complex by indirectly interacting with one axial oxygen atom of the UO 2 group bridged by a water molecule. In addition, the Na + ion interacts closely with one Ca 2+ ion than the other. The present simulations revealed the key role of common ions such as Na + in impacting the solvation, structure, and apparent charge of the Ca 2 UO 2 (CO 3 ) 3 complex in seawater. The sequential processes of UO 2 2+ binding with the three CO 3 2- groups and the two Ca 2+ ions in pure water and in 0.1 M NaCl were simulated by classical molecular dynamics with both the non-constrained brute-force approach and umbrella sampling. The simulated free energies show excellent agreement with the experiment. The coordination structures of UO 2 (CO 3 ) 3 4- and CaUO 2 (CO 3 ) 3 2- were found to be significantly affected by the presence of Na + ions, leading to a monodentate binding of a carbonate group to U and a water molecule entering the first coordination shell of U. To shed light on the binding between uranyl and glutardiamidoxime (H 2 B), an important model and state-of-the-art ligand for seawater uranium extraction, a suite of computational methods was employed. From molecular dynamics (MD) simulations, it was found that the binding configurations of B 2- with uranyl favor the twofold distorted η 2 binding between the oximate ends (C=N-O-) and U, while HB - prefers the chelating mode for the oximate end with the neutral end being solvated by water. The free energies of sequential ligand binding to form UO 2 B, [UO 2 B 2 ] 2- , and [UO 2 (HB)B] - were simulated with umbrella sampling and very good agreement with the experimental values was achieved, which corroborates the structural insights into the binding mode. State-of-the-art polymeric sorbents employ both amidoximate and carboxylate groups on the side chains to achieve optimal U uptake and selectivity, so we simulated the binding of a model amidoximate–carboxylate bifunctional ligand with uranyl. Classical MD and free-energy simulations in 0.5 M NaCl showed that the carboxylate group binds first to uranyl, leading to a loose intermediate state, and then, the amidoximate group binds, resulting in a more stable and tight chelate state. Binding of the second bifunctional ligand follows a similar process, and the two ligands prefer a trans configuration around the uranyl group. The simulated free energies indicate that the two bifunctional ligands bind with uranyl 14 kcal/mol stronger than the two ligands with only amidoximate groups, confirming an important synergy between amidoximate and carboxylate groups in binding uranyl.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors

The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, receptor-associated protein (RAP) was described as a molecular chaperone for LDLR-related protein 1 (LRP1), a prominent member of the LDLR family. We aimed to verify this role of RAP for LRP1 and two other LDLR family receptors, LDLR and vLDLR, and to investigate the mechanisms of respective interactions using a cell culture model system, purified system, and in silico modelling. Upon coexpression of RAP with clusters of the ligand-binding complement repeats (CRs) of the receptors in secreted form in insect cells culture, the isolated proteins had increased yield, enhanced folding, and improved binding properties compared with proteins expressed without RAP, as determined by circular dichroism and surface plasmon resonance. Within LRP1 CR-clusters II and IV, we identified multiple sites comprised of adjacent CR doublets, which provide alternative bivalent binding combinations with specific pairs of lysines on RAP. Mutational analysis of these lysines within each of isolated RAP D1/D2 and D3 domains having high affinity to LRP1 and of conserved tryptophans on selected CR-doublets of LRP1, as well as in silico docking of a model LRP1 CR-triplet with RAP, indicated a universal role for these residues in interaction of RAP and LRP1. Consequently, we propose a new model of RAP interaction with LDLR family receptors based on switching of the bivalent contacts between molecules over time in a dynamic mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center

Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O 2 -binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme–substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.

36 MATERIALS SCIENCE↗
DOE OSTI2018

An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors

Polycomb repressive complex 2 (PRC2) mediates trimethylation of histone H3K27 (H3K27me3), an epigenetic hallmark for repressed chromatin. Overactive mutants of the histone lysine methyltransferase subunit of PRC2, Ezh2, are found in various types of cancers. Pyridone-containing inhibitors such as GSK126 compete with S-adenosylmethionine (SAM) for Ezh2 binding and effectively inhibit PRC2 activity. PRC2 from the thermophilic fungus Chaetomium thermophilum (ct) is functionally similar to the human version in several regards and has the added advantage of producing high-resolution crystal structures, although inhibitor-bound structures of human or human/chameleon PRC2 are also available at up to 2.6 Å resolution. We solved crystal structures of both human and ctPRC2 bound to GSK126 and the structurally similar inhibitor GSK343. While the two organisms feature a disparate degree of inhibitor potency, surprisingly, GSK126 binds in a similar manner in both structures. Structure-guided protein engineering of the drug binding pocket allowed us to introduce humanizing mutations into ctEzh2 to produce a ctPRC2 variant that is more susceptible to GSK126 inhibition. Additional analysis indicated that an evolutionarily conserved structural platform dictates a unique mode of GSK126 binding, suggesting a mechanism of drug selectivity. The existing drug scaffold may thus be used to probe the function and cellular regulation of PRC2 in a wide spectrum of organisms, ranging from fungi to humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Surface Termination of CsPbBr 3 Perovskite Quantum Dots Determined by Solid-State NMR Spectroscopy

Cesium lead halide perovskite quantum dots (QDs) have gained significant attention as next-generation optoelectronic materials; however, their properties are highly dependent on their surface chemistry. The surfaces of cuboidal CsPbBr 3 QDs have been intensively studied by both theoretical and experimental techniques, but fundamental questions still remain about the atomic termination of the QDs. The surface binding sites and modes of ligands at the surface remain unproven. Herein, we demonstrate that solid-state NMR spectroscopy allows the unambiguous assignment of organic surface ligands via 1 H, 13 C, and 31 P NMR. Surface-selective 133 Cs solid-state NMR spectra show the presence of an additional 133 Cs NMR signal with a unique chemical shift that is attributed to Cs atoms terminating the surface of the particle and which are likely coordinated by carboxylate ligands. Dipolar dephasing curves that report on the distance between the surface ammonium ligands and Cs and Pb were recorded using double resonance 1 H{ 133 Cs} and 1 H{ 207 Pb} RESPDOR experiments. Model QD surface slabs with different possible surface terminations were generated from the CsPbBr 3 crystal structure and theoretical RESPDOR dipolar dephasing curves considering all possible 1 H- 133 Cs/ 207 Pb spin pairs were then calculated. Comparison of the calculated and experimental RESPDOR curves indicates the particles are CsBr terminated (not PbBr 2 terminated) with alkylammonium ligands substituting into some surface Cs sites, consistent with the surface-selective 133 Cs NMR experiments. Lastly, these results highlight the utility of high-resolution solid-state NMR spectroscopy for studying ligand binding and the surface structure of nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The Role of Evolving Interfacial Substrate Properties on Heterogeneous Cellulose Hydrolysis Kinetics

Interfacial enzyme reactions require formation of an enzyme–substrate complex at the surface of a heterogeneous substrate, but often multiple modes of enzyme binding and types of binding sites complicate analysis of their kinetics. Excess heterogeneous substrate is often used as a justification to model the substrate as unchanging, but using the study of the enzymatic hydrolysis of insoluble cellulose as an example, we argue that reaction rates are dependent on evolving substrate interfacial properties. We hypothesize that the relative abundance of binding sites on cellulose where hydrolysis can occur (productive binding sites) and binding sites where hydrolysis cannot be initiated or is inhibited (nonproductive binding sites) contribute to rate limitations. We show that the initial total number of productive binding sites (the productive binding capacity) determines the magnitude of the initial burst phase of cellulose hydrolysis, while productive binding site depletion explains overall hydrolysis kinetics. Furthermore, we show that irreversibly bound surface enzymes contribute to the depletion of productive binding sites. Our model shows that increasing the ratio of productive to nonproductive binding sites promotes hydrolysis, while maintaining an elevated productive binding capacity throughout conversion is key to preventing hydrolysis slowdown.

09 BIOMASS FUELS↗
DOE OSTI2024

Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore

The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans–cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65—an evolutionary convergence that deepens our understanding of visual system diversity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage

Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain

Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Network construction of non-Abelian chiral spin liquids

We use a network of chiral junctions to construct a family of topological chiral spin liquids in two spatial dimensions. The chiral spin liquid phase harbors SU(2) _k k anyons, which stem from the underlying SU(2) _k k WZW models that describe the constituent spin chains of the network. The network exhibits quantized spin and thermal Hall conductances. We illustrate our construction by inspecting the topological properties of the SU(2) _2 2 model. We find that this model has emergent Ising anyons, with spinons acting as vortex excitations that bind Majorana zero modes. We also show that the ground state of this network is threefold degenerate on the torus, asserting its non-Abelian character. Our results shed new light on the stability of non-Abelian topological phases in artificial quantum materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads

Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis (M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. Overall, the outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterizing inhibitors of human AP endonuclease 1

AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg 2+ -bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Synthesis and molecular structures of Yb{sup II} and Ca bis(amidinate) complexes containing the tridentate amidinate ligand [2,6-Pr{sup i}{sub 2}C{sub 6}H{sub 3}NC(But)NC{sub 6}H{sub 4}OMe-2]

New bis(amidinate) complexes of calcium, [2,6-Pr{sup i}{sub 2}C{sub 6}H{sub 3}NC(But)NC{sub 6}H{sub 4}OMe-2]{sub 2}Ca(DME) (2), and divalent ytterbium, [2,6-Pr{sup i}{sub 2}C{sub 6}H{sub 3}NC(But)NC{sub 6}H{sub 4}OMe-2]{sub 2}Yb (4), were synthesized by the transamination of the bis(amide) derivatives [(Me{sub 3}Si){sub 2}N]{sub 2}M(THF){sub 2} (M = Ca, Yb) with two equivalents of amidine 2,6-Pr{sup i}{sub 2}C{sub 6}H{sub 3}N=C(But)N(H)C{sub 6}H{sub 4}OMe-2, in which one nitrogen atom bears an o-methoxyphenylene moiety capable of coordinating a metalion. An X-ray diffraction study showed that, despite very similar ionic radii of Ca{sup 2+} and Yb{sup 2+}, the amidinate ligands in complexes 2 and 4 bind to these ions in different coordination modes. In the calcium complex, both ligands adopt a κ{sup 2}-N, O-chelating coordination mode. In the divalent ytterbium compound, one ligand is chelating and binds to the metalion in a κ{sup 2}-N, O-coordination mode, while the second ligand is coordinated via both the N and O (κ{sup 2}) atoms and the arene ring of the 2,6-Pr{sup i}{sub 2}C{sub 6}H{sub 3} moiety (η{sup 6}-coordination mode).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

cAMP binding to closed pacemaker ion channels is non-cooperative

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Hierarchical Majoranas in a programmable nanowire network

We propose a hierarchical architecture for building “logical” Majorana zero modes using “physical” Majorana zero modes at the Y-junctions of a hexagonal network of semiconductor nanowires. Each Y-junction contains three “physical” Majoranas, which hybridize when placed in close proximity, yielding a single effective Majorana mode near zero energy. The hybridization of effective Majorana modes on neighboring Y-junctions is controlled by applied gate voltages on the links of the honeycomb network. This gives rise to a tunable tight-binding model of effective Majorana modes. We show that selecting the gate voltages that generate a Kekule vortex pattern in the set of hybridization amplitudes yields an emergent “logical” Majorana zero mode bound to the vortex core. The position of a logical Majorana can be tuned adiabatically, without moving any of the “physical” Majoranas or closing any energy gaps, by programming the values of the gate voltages to change as functions of time. Furthermore, a nanowire network supporting multiple such “logical” Majorana zero modes provides a physical platform for performing adiabatic non-Abelian braiding operations in a fully controllable manner.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Temperature-Responsive Competitive Inhibition of CRISPR-Cas9

CRISPR-Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory "anti-CRISPR" (Acr) proteins, including six inhibitors (AcrIIA1-AcrIIA6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its more potent homolog, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. Finally, these findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally.

59 BASIC BIOLOGICAL SCIENCES↗