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At least 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A biophysical framework for double-drugging kinases

Selective orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as “double-drugging”, has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Förster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing cooperativity. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the double-drugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe a fully closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light on the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of double-drugging strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The spread of technological innovations: effects of psychology, culture and policy interventions

Technological innovations drive the evolution of human societies. The success of innovations depends not only on their actual benefits but also on how potential adopters perceive them and how their beliefs are affected by their social and cultural environment. To deepen our understanding of socio-psychological processes affecting the new technology spread, we model the joint dynamics of three interlinked processes: individual learning and mastering the new technology, changes in individual attitudes towards it, and changes in individual adoption decisions. We assume that the new technology can potentially lead to a higher benefit but achieving it requires learning. We posit that individual decision-making process as well as their attitudes are affected by cognitive dissonance and conformity with peers and an external authority. Individuals vary in different psychological characteristics and in their attitudes. We investigate both transient dynamics and long-term equilibria observed in our model. We show that early adopters are usually individuals who are characterized by low cognitive dissonance and low conformity with peers but are sensitive to the effort of an external authority promoting the innovation. We examine the effectiveness of five different intervention strategies aiming to promote the diffusion of a new technology: training individuals, providing subsidies for early adopters, increasing the visibility of peer actions, simplifying the exchange of opinions between people, and increasing the effort of an external authority. We also discuss the effects of culture on the spread of innovations. Finally, we demonstrate that neglecting the cognitive forces and the dynamic nature of individual attitudes can lead to wrong conclusions about adoption of innovations. Our results can be useful in developing more efficient policies aiming to promote the spread of new technologies in different societies, cultures and countries.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2026

Towards a Quintic Ginzburg-Landau Description of the (2,7) Minimal Model

We discuss dimensional continuation of the massless scalar field theory with the 𝑖⁢𝜙 5 interaction term. It preserves the so-called 𝒫⁢𝒯 symmetry, which acts by 𝜙 →−𝜙 accompanied by 𝑖 →−𝑖. Below its upper critical dimension 10/3, this theory has interacting infrared fixed points. We argue that the fixed point in 𝑑 = 2 describes the nonunitary minimal conformal model 𝑀⁡(2,7). We identify the operators 𝜙 and 𝜙 2 with the Virasoro primaries 𝜙 1,2 and 𝜙 1,3 , respectively, and 𝑖⁢𝜙 3 with a quasiprimary operator, which is a Virasoro descendant of 𝜙 1,3 . Our identifications appear to be consistent with the operator product expansions and with considerations based on integrability. Using constrained Padé extrapolations, we provide estimates of the critical exponents in 𝑑 = 3. We also comment on possible lattice descriptions of 𝑀⁡(2,7) and discuss RG flows to and from this conformal field theory (CFT). Finally, we conjecture that the minimal models 𝑀⁡(2,2⁢𝑛 +1) are described by the massless scalar field theories with the 𝑖⁢𝜙 2⁢𝑛−1 interaction terms.

Conformal field theory↗
DOE OSTI2022

Entanglement phase transitions in random stabilizer tensor networks

Here we explore a class of random tensor network models with “stabilizer” local tensors which we name random stabilizer tensor networks (RSTNs). For RSTNs defined on a two-dimensional square lattice, we perform extensive numerical studies of entanglement phase transitions between volume-law and area-law entangled phases of the one-dimensional boundary states. These transitions occur when either (a) the bond dimension D of the constituent tensors is varied or (b) the tensor network is subject to random breaking of bulk bonds, implemented by forced measurements. In the absence of broken bonds, we find that the RSTN supports a volume-law entangled boundary state with bond dimension D ≥ 3 where D is a prime number, and an area-law entangled boundary state for D = 2. Upon breaking bonds at random in the bulk with probability p, there exists a critical measurement rate p c for each D ≥ 3 above which the boundary state becomes area-law entangled. To explore the conformal invariance at these entanglement transitions for different prime D, we consider tensor networks on a finite rectangular geometry with a variety of boundary conditions, and extract universal operator scaling dimensions via extensive numerical calculations of the entanglement entropy, mutual information, and mutual negativity at their respective critical points. Our results at large D approach known universal data of percolation conformal field theory, while showing clear discrepancies at smaller D, suggesting a distinct entanglement transition universality class for each prime D. We further study universal entanglement properties in the volume-law phase and demonstrate quantitative agreement with the recently proposed description in terms of a directed polymer in a random environment.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multipartite entanglement in two-dimensional chiral topological liquids

The multipartite entanglement structure for the ground states of two-dimensional (2D) topological phases is an interesting albeit not well-understood question. Utilizing the bulk-boundary correspondence, the calculation of tripartite entanglement in 2D topological phases can be reduced to that of the vertex state, defined by the boundary conditions at the interfaces between spatial regions. In this paper, we use the conformal interface technique to calculate entanglement measures in the vertex state, which include area-law terms, corner contributions, and topological pieces, and a possible additional order-one contribution. Furthermore, this explains our previous observation of the Markov gap ℎ = $\frac{c}{3}$ ⁢ln⁡2 in the three-vertex state, and generalizes this result to the p-vertex state, general rational conformal field theories, and more choices of subsystems. Finally, we support our prediction by numerical evidence, finding precise agreement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Application of dilaton chiral perturbation theory to N f = 8 , SU(3) spectral data

We extend dilaton chiral perturbation theory (dChPT) to include the taste splittings in the Nambu-Goldstone sector observed in lattice simulations of near-conformal theories with staggered fermions. We then apply dChPT to a recent simulation by the LSD collaboration of the SU(3) gauge theory with 8 fermions in the fundamental representation, which is believed to exhibit near-conformal behavior in the infrared, and in which a light singlet scalar state, nearly degenerate with the pions, has been found. We find that the mesonic sector of this theory can be successfully described by dChPT, including, in particular, the mesonic taste splittings found in the simulation. We confirm that current simulations of this theory are in the "large-mass" regime.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Crossing Symmetric Dispersion Relations for Mellin Amplitudes

We consider manifestly crossing symmetric dispersion relations for Mellin amplitudes of scalar four point correlators in conformal field theories. This allows us to set up the nonperturbative Polyakov bootstrap for the conformal field theories in Mellin space on a firm foundation, thereby fixing the contact term ambiguities in the crossing symmetric blocks. Our new approach employs certain “locality” constraints replacing the requirement of crossing symmetry in the usual fixed-t dispersion relation. Using these constraints, we show that the sum rules based on the two channel dispersion relations and the present dispersion relations are identical. Our framework allows us to connect with the conceptually rich picture of the Polyakov blocks being identified with Witten diagrams in anti-de Sitter space. We also give two sided bounds for Wilson coefficients for effective field theories in anti-de Sitter space.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Molecular-dynamics simulation methods for macromolecular crystallography

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein–solvent interface. To address this limitation, a set of MD–MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

FTR for: Reducing plug-load electricity footprint of residential buildings through low-cost, non-intrusive sub-metering and personalized feedback technology

The project started in October 2016 and ended in December 2022. The project's principal goals and achievements were: (i) Measure real and reactive electric power consumption in ~400 apartments in multifamily settings of varying size and vintage and publish the data; data was published according to New York State's recommended 15x15 rule continuously from Jan 2019 through December 2022 (10 second time resolution); with the combination of large number of apartments, real and reactive power, as well as high time resolution (10-seconds), the dataset is first of its kind worldwide; because the dataset New York City apartment consumption pre, during, and post pandemic, it further offers unique insights into changes in residential electricity consumption during lockdowns and after modified work from home schedules. (ii) Measure effectiveness of different feedback types to prompt residents to lower their electricity consumption; achieved 11% (kWh-weighted) reduction versus baseline consumption; confirmed previous studies that social comparisons elicit above average responses; showed, for the first time, that the so called boomerang effect in power consumption feedback projects can be explained by a previously hypothesized norm-conforming "magnet effect" (rather than a non-conforming defiance effect), thus substantially advancing the research in the field. (iii) Disaggregate apartment-level consumption to appliance level; because the hardware for electricity consumption unexpectedly allowed only for 10-second time resolution (rather than the 1-second resolution we had planned on), the disaggregation algorithms we developed on sample data could not be applied to the actual field data we collected. The project has yielded high visibility, with a total of 17 publications, from peer reviewed journals, published data sets (free access), blog posts, NY Times, National Public Radio, and CNN.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The differing effects of a dual acting regulator on SIRT1

SIRT1 is an NAD + -dependent protein deacetylase that has been shown to play a significant role in many biological pathways, such as insulin secretion, tumor formation, lipid metabolism, and neurodegeneration. There is great interest in understanding the regulation of SIRT1 to better understand SIRT1-related diseases and to better design therapeutic approaches that target SIRT1. There are many known protein and small molecule activators and inhibitors of SIRT1. One well-studied SIRT1 regulator, resveratrol, has historically been regarded as a SIRT1 activator, however, recent studies have shown that it can also act as an inhibitor depending on the identity of the peptide substrate. The inhibitory nature of resveratrol has yet to be studied in detail. Understanding the mechanism behind this dual behavior is crucial for assessing the potential side effects of STAC-based therapeutics. Here, we investigate the detailed mechanism of substrate-dependent SIRT1 regulation by resveratrol. We demonstrate that resveratrol alters the substrate recognition of SIRT1 by affecting the K M values without significantly impacting the catalytic rate k cat ). Furthermore, resveratrol destabilizes SIRT1 and extends its conformation, but the conformational changes differ between the activation and inhibition scenarios. We propose that resveratrol renders SIRT1 more flexible in the activation scenario, leading to increased activity, while in the inhibition scenario, it unravels the SIRT1 structure, compromising substrate recognition. Our findings highlight the importance of substrate identity in resveratrol-mediated SIRT1 regulation and provide insights into the allosteric control of SIRT1. This knowledge can guide the development of targeted therapeutics for diseases associated with dysregulated SIRT1 activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Frank–Kasper Phases of Diblock Copolymer Melts: Self-Consistent Field Results of Two Commonly Used Models

We constructed phase diagrams of conformationally asymmetric diblock copolymer A-B melts using the polymer self-consistent field (SCF) calculations of both the dissipative particle dynamics chain (DPDC) model (i.e., compressible melts of discrete Gaussian chains with the DPD non-bonded potential) and the “standard” model (i.e., incompressible melts of continuous Gaussian chains with the Dirac δ-function non-bonded potential) in the χN-ε plane, where χN and ε characterize, respectively, the repulsion and conformational asymmetry between the A and B blocks, at the A-block volume fraction f = 0.2 and 0.3. Consistent with previous SCF calculations of the “standard” model, σ and A15 are the only stable Frank–Kasper (FK) phases among the five FK (i.e., σ, A15, C14, C15 and Z) phases considered. The stability of σ and A15 is due to their delicate balance between the energetic and entropic contributions to the Helmholtz free energy per chain of the system, which, within our parameter range, increases in the order of σ/A15, Z, and C14/C15. While in general the SCF phase diagrams of these two models are qualitatively consistent, A15 is not stable for the DPDC model at the copolymer chain length N = 10 and f = 0.3; any differences in the SCF phase diagrams are solely due to the differences between these two models.

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

Application of transport-based metric for continuous interpolation between cryo-EM density maps

Cryogenic electron microscopy (cryo-EM) has become widely used for the past few years in structural biology, to collect single images of macromolecules "frozen in time". As this technique facilitates the identification of multiple conformational states adopted by the same molecule, a direct product of it is a set of 3D volumes, also called EM maps. To gain more insights on the possible mechanisms that govern transitions between different states, and hence the mode of action of a molecule, we recently introduced a bioinformatic tool that interpolates and generates morphing trajectories joining two given EM maps. This tool is based on recent advances made in optimal transport, that allow efficient evaluation of Wasserstein barycenters of 3D shapes. As the overall performance of the method depends on various key parameters, including the sensitivity of the regularization parameter, we performed various numerical experiments to demonstrate how MorphOT can be applied in different contexts and settings. Finally, we discuss current limitations and further potential connections between other optimal transport theories and the conformational heterogeneity problem inherent with cryo-EM data.

3D shapes↗
NASA NTRS2002

Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the submicromolar range was developed. Copyright 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 517-526, 2002.

Evaluation Studies↗
NASA NTRS2000

A semiempirical study for the ground and excited states of free-base and zinc porphyrin-fullerene dyads

The ground and excited states of a covalently linked porphyrin-fullerene dyad in both its free-base and zinc forms (D. Kuciauskas et al., J. Phys. Chem. 100 (1996) 15926) have been investigated by semiempirical methods. The excited-state properties are discussed by investigation of the character of the molecular orbitals. All frontier MOs are mainly localized on either the donor or the acceptor subunit. Thus, the absorption spectra of both systems are best described as the sum of the spectra of the single components. The experimentally observed spectra are well reproduced by the theoretical computations. Both molecules undergo efficient electron transfer in polar but not in apolar solvents. This experimental finding is explained theoretically by explicitly considering solvent effects. The tenth excited state in the gas phase is of charge-separated character where an electron is transferred from the porphyrin donor to the fullerene acceptor subunit. This state is stabilized in energy in polar solvents due to its large formal dipole moment. The stabilization energy for an apolar environment such as benzene is not sufficient to lower this state to become the first excited singlet state. Thus, no electron transfer is observed, in agreement with experiment. In a polar environment such as acetonitrile, the charge-separated state becomes the S, state and electron transfer takes place, as observed experimentally. The flexible single bond connecting both the donor and acceptor subunits allows free rotation by ca. +/- 30 degrees about the optimized ground-state conformation. For the charge-separated state this optimized geometry has a maximum dipole moment. The geometry of the charge-separated state thus does not change relatively to the ground-state conformation. The electron-donating properties of porphyrin are enhanced in the zinc derivative due to a reduced porphyrin HOMO-LUMO energy gap. This yields a lower energy for the charge-separated state compared to the free-base dyad.

Bridged Compounds/chemistry↗
NASA NTRS1999

Left-handed Z-DNA: structure and function

Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-stranded RNA adenosine deaminase type I (ADAR1) has motifs specific for the Z-DNA conformation. Editing by ADAR1 requires a double-stranded RNA substrate. In the cases known, the substrate is formed by folding an intron back onto the exon that is targeted for modification. The use of introns to direct processing of exons requires that editing occurs before splicing. Recognition of Z-DNA by ADAR1 may allow editing of nascent transcripts to be initiated immediately after transcription, ensuring that editing and splicing are performed in the correct sequence. Structural characterization of the Z-DNA binding domain indicates that it belongs to the winged helix-turn-helix class of proteins and is similar to the globular domain of histone-H5.

Review↗
NASA NTRS1999

Non-unity molecular heritability demonstrated by continuous evolution in vitro

INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

Non-NASA Center↗
NASA NTRS2000

Database of non-canonical base pairs found in known RNA structures

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

NASA Discipline Exobiology↗