Search NASA⌕ Search

SEARCH · Search NASA

Results for “Helical structures”

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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
NASA NTRS1979

The 13th Aerospace Mechanisms Symposium

Technological areas covered include propulsion, motion compensation, instrument pointing and adjustment, centrifuge testing, bearing design, vehicle braking, and cargo handling. Devices for satellite, missile, and hypersonic-wind-tunnel applications; space shuttle mechanical and thermal protection systems; and techniques for building large space structures are described. In addition, a fluid drop injector device for a Spacelab experiment, a helical grip for cable cars, and applications of rare earth permanent magnets are discussed.

Bond, A. C.↗
DOE OSTI2024

Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non‐natural substrate specificity

Abstract Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic “isoprenol pathways,” which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non‐natural alkyl‐monophosphates (alkyl‐Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non‐natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non‐natural substrates using the IPK homolog fromThermococcus paralvinellae(TcpIPK). Four such structures were solved, each bound to a different non‐natural alkyl‐P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures ofTcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl‐P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures ofTcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non‐natural substrates.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Deeply virtual Compton scattering off the neutron

The three-dimensional structure of nucleons (protons and neutrons) is embedded in so-called generalized parton distributions, which are accessible from deeply virtual Compton scattering. In this process, a high-energy electron is scattered off a nucleon by exchanging a virtual photon. Then, a highly energetic real photon is emitted from one of the quarks inside the nucleon, which carries information on the quark's transverse position and longitudinal momentum. By measuring the cross-section of deeply virtual Compton scattering, Compton form factors related to the generalized parton distributions can be extracted. Here, we report the observation of unpolarized deeply virtual Compton scattering off a deuterium target. From the measured photon-electroproduction cross-sections, we have extracted the cross-section of a quasifree neutron and a coherent deuteron. Due to the approximate isospin symmetry of quantum chromodynamics, we can determine the contributions from the different quark flavours to the helicity-conserved Compton form factors by combining our measurements with previous ones probing the proton's internal structure. These results advance our understanding of the description of the nucleon structure, which is important to solve the proton spin puzzle. The internal structure of the neutron has now been probed by highly energetic photons scattering off it. Combined with previous results for protons, these measurements reveal the contributions of quark flavours to the nucleon structure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Tuning the many-body interactions in a helical Luttinger liquid

In one-dimensional (1D) systems, electronic interactions lead to a breakdown of Fermi liquid theory and the formation of a Tomonaga-Luttinger Liquid (TLL). The strength of its many-body correlations can be quantified by a single dimensionless parameter, the Luttinger parameter K, characterising the competition between the electrons’ kinetic and electrostatic energies. Recently, signatures of a TLL have been reported for the topological edge states of quantum spin Hall (QSH) insulators, strictly 1D electronic structures with linear (Dirac) dispersion and spin-momentum locking. Here we show that the many-body interactions in such helical Luttinger Liquid can be effectively controlled by the edge state’s dielectric environment. This is reflected in a tunability of the Luttinger parameter K, distinct on different edges of the crystal, and extracted to high accuracy from the statistics of tunnelling spectra at tens of tunnelling points. The interplay of topology and many-body correlations in 1D helical systems has been suggested as a potential avenue towards realising non-Abelian parafermions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach

Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to previous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament

By virtue of their native structures, tubulin dimers are protein building blocks that are naturally pre-programmed to assemble into cytoskeletal polymers known as microtubules (MTs). Here we demonstrate polycation-directed (i.e. electrostatically tunable) assembly of tubulins through tubulin protofilament conformational changes in the longitudinal and lateral directions, creating novel tubulin double helices and various tubular architectures. Synchrotron small angle X-ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single- and double-layered double-helix tubulin tubules. The phase transitions from MTs into the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and MT diameter (≈25 nm). This work suggests the feasibility of “programmable breakdown” of protein nanotubes, tearing MTs into double-stranded tubulins and building up previously undiscovered nanostructures, by using polycations with scissor- and glue-like properties. Importantly, we define a new role of tubulins as two-dimensionally shape-controllable building blocks for novel supramolecular architectures. Furthermore, these findings provide insight into the design of protein-based functional materials, for example, as metallization templates for nanoscale electronic devices, kinesin motor-driving molecular screws, and anticancer drug delivery vehicles.

2D shape‐control↗
NASA NTRS1988

Observations of electron beam structure in space experiments

Observations of a 100-mA, 1-keV electron beam were made with a low light level TV system and other instruments aboard the space shuttle STS 3 in March 1982. When fired at a moderate pitch angle with respect to the magnetic field, the beam electrons initially moved outward along a classical helical trajectory. Within a short distance, however, the beam electrons were deflected away from the helical trajectory into paths parallel to magnetic field lines threading the primary helix. This resulted in the formation of a thin-walled, cylindrical electron beam structure having a radius equal to the primary beam gyroradius. This structure, which is consistent with earlier laboratory vacuum chamber observations and recent two-dimensional computer electrostatic plasma simulations, has important implications for determining the extent to which pulsed electron beams can radiate electromagnetic energy in the ionosphere.

Banks, Peter M.↗
DOE OSTI2026

Omnigenous umbilic stellarators

To better understand the dependence of the magnetic field structure in the plasma edge on the plasma boundary shape, in the context of X-point and island divertor designs, we define and develop a class of stellarators called umbilic stellarators. These equilibria are characterised by a single continuous high-curvature edge on the plasma boundary that goes around multiple times toroidally before meeting itself. We develop a technique that allows us to simultaneously optimise the plasma boundary along with a curve lying on the boundary on which we impose a high curvature while imposing omnigenity – a property of the magnetic field that ensures trapped particle confinement throughout the plasma volume. We find that umbilic stellarators naturally tend to favour piecewise omnigenity instead of omnigenity with a specific helicity. After generating omnigenous umbilic stellarators, we design coil sets for some of them and explore the fieldline structure in the edge and its sensitivity to small fluctuations in the plasma. Finally, using single-stage optimisation, we simultaneously modify the plasma and coil shape and propose an experiment to modify an existing tokamak to a finite-𝛽 stellarator using this technique and explore a potentially simpler way to convert a limited tokamak into a diverted stellarator.

fusion plasma↗
DOE OSTI2024

Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures

Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by “hydrogen bond enhanced halogen bonds” (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. Finally, this research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.

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

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T m ) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [ (-6) MPro H41A and (-6*) MPro H41A , respectively], and its corresponding mature MPro H41A were systematically examined. While the H41A mutation exerts negligible effect on T m and dimer dissociation constant (K dimer ) of MPro H41A , relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in T m and > 85-fold increase in K dimer as compared to MPro H41A . The K d for the binding of the covalent inhibitor GC373 to (-6*) MPro H41A increases ~12-fold, relative to MPro H41A , concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Finally, disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The structural basis of promiscuity in small multidrug resistance transporters

By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family’s extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo-EM analysis of S. aureus TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance

Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the Staphylococcus aureus WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo–electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate–ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plasma Wall Interaction with 3-D Plasma Boundaries

The interaction of the edge plasma and the material surfaces is one of the most critical challenges on the path to harness fusion power as new, fundamental energy source. This challenge typically combines the thrust to reach high density, low temperature (detached) plasmas in front of the divertor target plates as well as understanding the plasma material interaction (PMI) in particular in this regime. The combination of both research thrusts represents an extraordinarily challenging subject encompassing spatial scales spanning nanometers to meters in all states of matter and across a broad energy range. Modeling capabilities, which help to interpret data from nowadays experiments and enable extrapolation to future devices are urgently required. This is in particular true for toroidal magnetic confinement devices with three-dimensional (3D) plasma boundaries. Such plasma boundary geometries occur in tokamaks, when small amplitude magnetic perturbations are used to stabilize the unruly edge plasma or in stellarators, that are inherently 3D plasma confinement devices. In this project, the impact of 3D plasma boundaries on the plasma material interaction (PMI) was assessed. This work focused on plasma boundary conditions, in which high-density conditions at the material surfaces yield mitigation of the otherwise immense heat and particle loads that these materials would see. These so-called high recycling and eventually detached plasma regimes are of great interest for future reactor operation. In the project, key features that are unique to 3D boundaries were explored in comparison to canonically assumed axisymmetric plasma edge situations in tokamaks. In particular, the relevance of the 3D boundary situation in the extrapolation to the plasma boundary solution at ITER, the next step fusion energy experiment under construction as a multi-national, world-wide large-science experiment in southern France, has been explored. The EMC3-EIRENE plasma edge fluid and kinetic neutral transport code has been advanced to cope with the challenging and unprecedented conditions in the ITER boundary plasma including 3D fields that are planned to be used to suppress harmful edge instabilities, the so-called edge localized modes. This is a vital integration challenge for ITER and the results from this grant have provide a leading capability for this assessment. It was shown that the detachment process in a 3D edge solution for ITER follows the recycling regimes that are known from axisymmetric solutions, but that multiple plasma exhaust channels connected to the material surfaces are established which feature individual recycling characteristics. Because these channels touch the material surfaces in the divertor in a 3D geometry, the compatibility with the plasma material interaction (PMI), including erosion and impurity generation has been found to be an important part of the integration challenge. To address this, the fully 3D plasma material interaction code ERO2 has been adapted to these ITER specific geometries and a homogeneous mixing model was implemented, that allows to consider the mixing of Be and Was used at ITER in the PMI modeling. This model enhancement has been used to study non-local migration of Be in the JET ITER like wall configuration and it has been shown that with this model such complex migration processes in ITER relevant plasma shapes and with ITER relevant plasma boundary conditions can be addressed. The combined modeling approach using EMC3-EIRENE as a plasma boundary transport code and the ERO2 specialized PMI model will be an asset for the continued preparations of ITER operation as well as for Fusion Pilot Plant efforts that have emerged in the U.S. during the evolution of this grant. The predictive capability of this numerical tool has been validated at the DIII-D US national fusion facility. Here, dedicated plasma edge diagnostics were implemented to measure the impurity household around a 3D edge plasma during ELM suppression by 3D fields. Dedicated experiments with local material probes using these diagnostics and the state-of-the-art suite of boundary measurements at DIII-D have shown that the 3D perturbation of the plasma edge that is excreted by such 3D control fields yield a perturbation of the plasma boundary flux structure and hence also of the resulting PMI. The 3D boundary plasma is composed out of helical magnetic flux channels that intersect the divertor targets at an angle relative to the main guiding field, i.e., the toroidal magnetic field component of the tokamak. A similar effect has been measured as well on limiter surfaces during the startup campaign at the new stellarator experiment Wendelstein 7-X. These experiments ad initial analysis with the ERO plasma material interaction model, suggested that the place of erosion for a given particle from the surface and its re-deposition can be different in such 3D field geometries yielding potentially a significant level of net-erosion. This is not the case for axisymmetric solutions, where it was shown in the past that the eroded particles are effectively re-deposited into gaps produced by erosion at the same position and hence the net-erosion levels are small. For ITER, the quest to suppress the ELMs and at the same time maintain the integrity of the divertor is an issue, which these fundamental findings will help to resolve. The coupling of this work to the extrapolation in the ITER program has been addressed by both the PI and the lead numerical scientist being ITER Science Fellows in the duration of the contract and forward. A second focus in the exploration of 3D boundary effects on tokamaks and stellarators has been set on the measurement of helium exhaust features with such 3D fields. This is important because He represents the ash of the fusion process and needs to be exhausted. It was shown that 3D field application compatible with suppression of ELMs yields an increase of the helium exhaust performance. The ratio of the effective helium confinement time over the energy confinement time was reduced by almost 50% which demonstrated that the impact of helium accumulation in the plasma core with respect to the confinement of energy to sustain the fusion reaction is significantly improved with such 3D control fields. It was shown that this is the case for tokamaks as well as stellarators. At the Large helical Device in Japan, a similar enhancement of the helium exhaust features when small amplitude additional 3D fields were applied was measured. This is an important additional function of 3D field application and its impact on ITER is presently being studied in combination with investigations of helium exhaust in 3D field geometries of stellarator devices.

3D plasma edge transport↗
NASA NTRS2002

Evolutionary Optimization of a Quadrifilar Helical Antenna

Automated antenna synthesis via evolutionary design has recently garnered much attention in the research literature. Evolutionary algorithms show promise because, among search algorithms, they are able to effectively search large, unknown design spaces. NASA's Mars Odyssey spacecraft is due to reach final Martian orbit insertion in January, 2002. Onboard the spacecraft is a quadrifilar helical antenna that provides telecommunications in the UHF band with landed assets, such as robotic rovers. Each helix is driven by the same signal which is phase-delayed in 90 deg increments. A small ground plane is provided at the base. It is designed to operate in the frequency band of 400-438 MHz. Based on encouraging previous results in automated antenna design using evolutionary search, we wanted to see whether such techniques could improve upon Mars Odyssey antenna design. Specifically, a co-evolutionary genetic algorithm is applied to optimize the gain and size of the quadrifilar helical antenna. The optimization was performed in-situ in the presence of a neighboring spacecraft structure. On the spacecraft, a large aluminum fuel tank is adjacent to the antenna. Since this fuel tank can dramatically affect the antenna's performance, we leave it to the evolutionary process to see if it can exploit the fuel tank's properties advantageously. Optimizing in the presence of surrounding structures would be quite difficult for human antenna designers, and thus the actual antenna was designed for free space (with a small ground plane). In fact, when flying on the spacecraft, surrounding structures that are moveable (e.g., solar panels) may be moved during the mission in order to improve the antenna's performance.

Lohn, Jason D.↗
NASA NTRS2008

Topological Origins of the Slow Solar Wind

Although the slow solar wind has been studied for decades with both in situ and remote sensing observations, its origin is still a matter of intense debate. In the standard quasi-steady model, the slow wind is postulated to originate near coronal hole boundaries that define topologically well-behaved separatrices between open and closed field regions. In the interchange model, on the other hand, the slow wind is postulated to originate on open flux that is dynamically diffusing throughout the seemingly closed-field corona. We argue in favor of the quasi-steady scenario and propose that the slow wind is due to two effects: First, the open-closed boundary is highly complex due to the complexity of the photospheric flux distribution. Second, this boundary is continuously driven by the transport of magnetic helicity from the closed field region into the open. The implications of this model for the structure and dynamics of the corona and slow wind are discussed, and observational tests of the mode

Antiochos, Spiro↗
DOE OSTI2023

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans

Abstract O-Phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal step of selenocysteine (Sec) synthesis in archaea and eukaryotes. How the Sec synthetic machinery recognizes and discriminates tRNASec from the tRNA pool is essential to the integrity of the selenoproteome. Previously, we suggested that SepSecS adopts a competent conformation that is pre-ordered for catalysis. Herein, using high-resolution X-ray crystallography, we visualized tRNA-dependent conformational changes in human SepSecS that may be a prerequisite for achieving catalytic competency. We show that tRNASec binding organizes the active sites of the catalytic protomer, while stabilizing the N- and C-termini of the non-catalytic protomer. Binding of large anions to the catalytic groove may further optimize the catalytic site for substrate binding and catalysis. Our biochemical and mutational analyses demonstrate that productive SepSecS•tRNASec complex formation is enthalpically driven and primarily governed by electrostatic interactions between the acceptor-, TΨC-, and variable arms of tRNASec and helices α1 and α14 of SepSecS. The detailed visualization of the tRNA-dependent activation of SepSecS provides a structural basis for a revised model of the terminal reaction of Sec formation in archaea and eukaryotes.

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↗