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At least 163 records · Page 9

The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

99 GENERAL AND MISCELLANEOUS↗

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

The interplay between spatial and heliconical orientational order in twist-bend nematic materials

The helical pitch formed by organic molecules, such as the α-helix of proteins, usually requires hydrogen bonding between chiral units and long-range positional order. It was recently found that certain liquid crystal oligomers can have a twist-bend nematic (NTB) phase with nanoscale heliconical structure without hydrogen bonding, molecular chirality or positional order. To understand the nature of this unique structure, here we present hard and resonant tender X-ray scattering studies of two novel sulfur containing dimer materials. We simultaneously measure the temperature dependences of the helical pitch and the correlation length of both the helical and positional order. In addition to an unexpected strong variation of the pitch with the length of the spacer connecting the monomer units, we find that at the transition to the NTB phase the positional correlation length drops. Additionally, the helical structure was found not only in the NTB phase but observed even in the upper range of a smectic phase that forms just below the NTB state. The coexistence of smectic layering and the heliconical order indicates a layered (SmATB) phase wherein the rigid units of the dimers are tilted with respect to the smectic layer normal in order to accommodate the bent conformation of the dimers and the tilt direction rotates along the heliconical axis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

Kory, Carol L.↗

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional (3-D) electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

Kory, Carol L.↗

Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase

The ability to sense and respond to environmental cues is essential for adaptation and survival in living organisms. In bacteria, this process is accomplished by multidomain sensor histidine kinases that undergo autophosphorylation in response to specific stimuli, thereby triggering downstream signaling cascades. However, the molecular mechanism of allosteric activation is not fully understood in these important sensor proteins. Here, we report the full-length crystal structure of a blue light photoreceptor LOV histidine kinase (LOV-HK) involved in light-dependent virulence modulation in the pathogenic bacterium Brucella abortus. Joint analyses of dark and light structures determined in different signaling states have shown that LOV-HK transitions from a symmetric dark structure to a highly asymmetric light state. The initial local and subtle structural signal originated in the chromophore-binding LOV domain alters the dimer asymmetry via a coiled-coil rotary switch and helical bending in the helical spine. These amplified structural changes result in enhanced conformational flexibility and large-scale rearrangements that facilitate the phosphoryl transfer reaction in the HK domain.

59 BASIC BIOLOGICAL SCIENCES↗

The Origins of Magnetic Structure in the Corona and Wind

One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at two special locations: photospheric polarity inversions lines. (non-potentiality observed as a filament channel) and coronal hole boundaries, (observed as the slow solar wind). This characteristic feature of the closed-field corona is highly unexpected given that its magnetic field is continuously tangled by photospheric motions. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. I propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries inversion lines and coronal holes, creating both filament channels and the slow wind. We describe how the helicity is injected and transported and calculate the relevant rates. I argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field. This work has been supported by the NASA HTP, SR&T, and LWS programs.

Antiochos, Spiro K.↗

Formation of helices with controllable chirality in gel-fiber composites

While microscale helices with specified chirality are pervasive in biological systems, driving purely synthetic materials to self-organize into such useful structures remains a significant challenge. Through theory and simulations, we model the behavior of initially flat ribbons of gel-fiber composites and show that these materials self-organize into three-dimensional helices with the application of heat. We specifically focus on thermo-responsive gels, which shrink when heated to a point near the lower critical solubility temperature (LCST). Within the composite, regions of the LCST gel that lie far from the fibers can readily shrink in response to the increased temperature; however, near the fibers the network is inhibited from undergoing the heat-induced collapse. This competition between the constrained and the unconstrained regions of the heated sample plays a vital role in the structural evolution of the material. Additionally, we find that this dynamic process can be controlled through the careful placement of the fibers on the outer surface of the gel. We specifically identify fiber arrangements that lead to the formation of helical structures with controlled chirality. Moreover, we isolate scenarios where constraining the movement of one or both the free ends of the sample promotes and stabilizes the formation of helical structures with specified handedness. Such structurally tailored composites are useful for creating mechanically robust actuators, and “appendages” for soft robots that can controllably curl and uncurl with variations in temperature.

36 MATERIALS SCIENCE↗

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional (3-D) electromagnetic computer code, MAxwell's equations by the Finite Integration Algorithm (MAFIA). Cold-test parameters have been calculated for several helical traveLing-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making It possible, for the first time, to design complete TWT via computer simulation.

Kory, Carol L.↗

Folding Coarse-Grained Oligomer Models with PyRosetta

Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta’s ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. Here, we show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.

36 MATERIALS SCIENCE↗

Suppression of antiferromagnetic order and strong ferromagnetic spin fluctuations in Ca(Co 1-x Ni x ) 2-y As 2 single crystals

CaCo 2–y As 2 is a unique itinerant system having strong magnetic frustration. Here, we report the effect of electron doping on the physical properties resulting from Ni substitutions for Co. The single crystals of Ca(Co 1–x Ni x ) 2–y As 2 were characterized by single-crystal x-ray diffraction, energy-dispersive x-ray spectroscopy, magnetization M versus temperature T, magnetic field H, time t, and heat capacity C p (H, T) measurements. The A-type antiferromagnetic (AFM) transition temperature T N = 52 K for x = 0 decreases to 22 K with only 3% Ni substitution and is completely suppressed for x > 0.16. For 0.11 ≤ x ≤ 0.52 strong ferromagnetic (FM) fluctuations develop as revealed by magnetic susceptibility χ(T) = M(T) / H measurements. For x = 0.11 and 0.16 competing AFM and FM interactions result in a reentrant spin-glass behavior below T N , as evidenced by the observations of thermomagnetic hysteresis and magnetic relaxation. Enhanced FM fluctuations are also found for the x = 0.21 and 0.31 crystals, where χ c increases significantly at low T. A large χ anisotropy in these compositions where χ c is up to a factor of two larger than χ ab suggests that the FM spin fluctuations are quasi-1D in nature. Weak ferromagnetic contributions to the magnetization are found at T = 2 K for x = 0.11 –0.31. Heat-capacity Cp(T) measurements reveal the presence of FM quantum spin fluctuations for 0.11 ≤ x ≤ 0.52, where a logarithmic T dependence of Cp(T) / T is observed at low T. Here, the suppression of AFM order by the development of strong FM fluctuations in Ca(Co 1–x Ni x ) 2–y As 2 crystals suggests the presence of a FM quantum-critical point at x ≈ 0.20. Our density-functional theory (DFT) calculations confirm that FM fluctuations are enhanced by Ni substitutions for Co in CaCo 2–y As 2 . The Sommerfeld electronic heat-capacity coefficient is enhanced for x = 0, 0.21, and 0.42 by about a factor of two compared to DFT calculations of the density of states (DOS) at the Fermi energy, suggesting an enhancement of the DOS from electron-phonon and/or electron-electron interactions. The crystals with x > 0.52 do not exhibit FM spin fluctuations or magnetic order at T ≥ 1.8 K, which was found from the DFT calculations to arise from a Stoner transition. Superconductivity is not observed above 1.8 K for any of the compositions. Neutron-diffraction studies of crystals with x = 0.11 and 0.16 in the crossover regime (0.1 ≲ x ≲ 0.2) show no evidence of A-type ordering as observed in the parent compound with x = 0. Furthermore, no other common magnetic structures, such as ferromagnetic (FM), helical stacking of in-plane FM layers, or in-plane AFM structure, are found with an ordered moment greater than the uncertainty of 0.05 μ B per transition-metal atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Helicity and Filament Channels? The Straight Twist!

One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at special locations, photospheric polarity inversions lines where the non-potentiality is observed as a filament channel. This characteristic feature of the closed-field corona is highly unexpected given that photospheric motions continuously tangle its magnetic field. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. We propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries, polarity inversion lines, creating filament channels. We describe how the helicity is injected and transported and calculate the relevant rates. We argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field.

Antiochos, Spiro K.↗

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

Non-NASA Center↗

Three-State Electrochiroptical Switches Derived from Chiral Stable Carbenes

Chiral redox switches have been used to develop stimuli-responsive materials and organic electronics wherein small molecule chirality produces new functionality. Despite the widespread use of stable carbenes in redox-active materials and asymmetric synthesis, their integration into chiral redox switches remains largely unexplored. Herein, we show that chiral stable carbenes can be used to construct helically chiral overcrowded alkenes which function as three-state electrochiroptical switches. Redox-driven (de)aromatization triggers the reversible exchange of helical and axial chirality via a helically chiral π-radical cation. Due to dramatic changes in both electronic and geometric structure, including the inversion of helical chirality, each state exhibits distinct chiroptical properties. As a proof of concept, we demonstrate multiple cycles of electrochemical ON–OFF switching and sign inversion of the electronic circular dichroism response. Overall, this work establishes chiral stable carbenes as promising building blocks for chiral and redox-switchable materials.

Chirality↗

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗

Solution of the Schrödinger equation for quasi-one-dimensional materials using helical waves

We formulate and implement a spectral method for solving the Schrödinger equation, as it applies to quasi-one-dimensional materials and structures. This allows for computation of the electronic structure of important technological materials such as nanotubes (of arbitrary chirality), nanowires, nanoribbons, chiral nanoassemblies, nanosprings and nanocoils, in an accurate, efficient and systematic manner. Our work is motivated by the observation that one of the most successful methods for carrying out electronic structure calculations of bulk/crystalline systems — the plane-wave method — is a spectral method based on eigenfunction expansion. Our scheme avoids computationally onerous approximations involving periodic supercells often employed in conventional plane-wave calculations of quasi-one-dimensional materials, and also overcomes several limitations of other discretization strategies, e.g., those based on finite differences and atomic orbitals. The basis functions in our method — called helical waves (or twisted waves) — are eigenfunctions of the Laplacian with symmetry adapted boundary conditions, and are expressible in terms of plane waves and Bessel functions in helical coordinates. We describe the setup of fast transforms to carry out discretization of the governing equations using our basis set, and the use of matrix-free iterative diagonalization to obtain the electronic eigenstates. Miscellaneous computational details, including the choice of eigensolvers, use of a preconditioning scheme, evaluation of oscillatory radial integrals and the imposition of a kinetic energy cutoff are discussed. We have implemented these strategies into a computational package called HelicES (Helical Electronic Structure). We demonstrate the utility of our method in carrying out systematic electronic structure calculations of various quasi-one-dimensional materials through numerous examples involving nanotubes, nanoribbons and nanowires. We also explore the convergence properties of our method, and assess its accuracy and computational efficiency by comparison against reference finite difference, transfer matrix method and plane-wave results. We anticipate that our method will find applications in computational nanomechanics and multiscale modeling, for carrying out transport calculations of interest to the field of semiconductor devices, and for the discovery of novel chiral phases of matter that are of relevance to the burgeoning quantum hardware industry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Computational Study of a Phenolic Based Polymer with a Spring-Like Structure

We report the stretching potentials for a helical phenolic-based polymer with high symmetry and a spring-like structure that can be stretched by a factor of 4 along the spring direction and still return to its original structure. We hope that synthetic polymer chemists assess if this polymer or a similar one can be synthesized and tested.

Charles W Bauschlicher↗