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

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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Tropical Intraseasonal Air-Sea Exchanges during the 1997 Pacific Warming

The Madden Julian Oscillations (MJO) and associated westerly wind (WW) events account for much of the tropical intraseasonal variability (TISV). The TISV has been suggested as an important stochastic forcing that may be one of the underlying causes for the observed irregularities of the El Nino-Southern Oscillation (ENSO). Recent observational studies and theories of interannual to interdecadal-scale variability suggest that ENSO may arise from different mechanisms depending on the basic states. The Pacific warming event of 1997, being associated with a period of strong MJO and WW events, serves as a natural experiment for studying the possible role of TISV in triggering an ENSO event. We have performed a combined statistical and composite analysis of surface WW events based on the assimilated surface wind and sea level pressure for the period of 1980-1993, the SSM/I wind for the period of 1988-1997, and OLR. Results indicates that extratropical forcing contribute significantly to the evolution of MJO and establishment of WW events over the Pacific warm pool. Following the major WW events, there appeared an eastward extension of equatorial warm SST anomalies from the western Pacific warm pool. Such tropical-extratropical interaction is particularly clear in the winter of 96-97 that leads to the recent warming event in 1997/98. From the above discussion, our current study on this subject is based on the hypothesis that 1) there is an enhanced air-sea interaction associated with TISV and the northerly surges from the extratropics in the initial phase of the 97/98 warming event, and 2) the relevant mechanisms are functions of the basic state of the coupled system (in terms of SST distribution and atmospheric mean circulation) that varies at the interannual and interdecadal time scale. We are analyzing the space-time structure of the northerly surges, their association with air-sea fluxes and upper ocean responses during the period of September 1996 to June 1997. The estimate of daily values of latent heat fluxes is based on NSCAT wind, SST, and ECMWF surface air temperature and SSM/I water vapor data (Chou et al. 1997). To understand the relevant mechanisms, we will analyze the origin of the northerly surges in terms of atmospheric instability associated with the extratropical circulation, and the mutual influence between the tropical heating and the extratropical circulation. In this meeting, we will report the analysis addressing the first part of the above hypothesis.

Sui, C.-H.↗
DOE OSTI2017

Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter

Human glucose-6-phosphatase plays a vital role in blood glucose homeostasis and holds promise as a therapeutic target for diabetes. Expression of its catalytic subunit gene 1 (G6PC1) is tightly regulated by metabolic-response transcription factors such as FoxO1 and CREB. Although at least three potential FoxO1 binding sites (insulin response elements, IREs) and one CREB binding site (cAMP response element, CRE) within the proximal region of the G6PC1 promoter have been identified, the interplay between FoxO1 and CREB and between FoxO1 bound at multiple IREs has not been well characterized. Here we present the crystal structures of the FoxO1 DNA binding domain in complex with the G6PC1 promoter. Here, these complexes reveal the presence of a new non-consensus FoxO1 binding site that overlaps the CRE, suggesting a mutual exclusion mechanism for FoxO1 and CREB binding at the G6PC1 promoter. Additional findings include (i) non-canonical FoxO1 recognition sites, (ii) incomplete FoxO1 occupancies at the available IRE sites, and (iii) FoxO1 dimeric interactions that may play a role in stabilizing DNA looping. These findings provide insight into the regulation of G6PC1 gene transcription by FoxO1, and demonstrate a high versatility of target gene recognition by FoxO1 that correlates with its diverse roles in biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking

Microbial-mediated utilization of particulate organic matter (POM) during its downward transport from the surface to the deep ocean constitutes a critical component of the global ocean carbon cycle. However, it remains unclear as to how high hydrostatic pressure (HHP) and low temperature (LT) with the sinking particles affects community structure and network interactions of the particle-attached microorganisms (PAM) and those free-living microorganisms (FLM) in the surrounding water. In this study, we investigated microbial succession and network interactions in experiments simulating POM sinking in the ocean. Diatom-derived 13C- and 12C-labeled POM were used to incubate surface water microbial communities from the East China Sea (ECS) under pressure (temperature) of 0.1 (25 °C), 20 (4 °C), and 40 (4 °C) MPa (megapascal). Our results show that the diversity and species richness of the PAM and FLM communities decreased significantly with HHP and LT. Microbial community analysis indicated an increase in the relative abundance of Bacteroidetes at high pressure (40 MPa), mostly at the expense of Gammaproteobacteria, Alphaproteobacteria, and Gracilibacteria at atmospheric pressure. Hydrostatic pressure and temperature affected lifestyle preferences between particle-attached (PA) and free-living (FL) microbes. Ecological network analysis showed that HHP and LT enhanced microbial network interactions and resulted in higher vulnerability to networks of the PAM communities and more resilience of those of the FLM communities. Most interestingly, the PAM communities occupied most of the module hubs of the networks, whereas the FLM communities mainly served as connectors of the modules, suggesting their different ecological roles of the two groups of microbes. These results provided novel insights into how HHP and LT affected microbial community dynamics, ecological networks during POM sinking, and the implications for carbon cycling in the ocean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Proceedings of RIKEN BNL Research Center Workshop: Brookhaven Summer Program on Quarkonium Production in Elementary and Heavy Ion Collisions

Understanding the structure of the hadron is of fundamental importance in subatomic physics. Production of heavy quarkonia is arguably one of the most fascinating subjects in strong interaction physics. It offers unique perspectives into the formation of QCD bound states. Heavy quarkonia are among the most studied particles both theoretically and experimentally. They have been, and continue to be, the focus of measurements in all high energy colliders around the world. Because of their distinct multiple mass scales, heavy quarkonia were suggested as a probe of the hot quark-gluon matter produced in heavy-ion collisions; and their production has been one of the main subjects of the experimental heavy-ion programs at the SPS and RHIC. However, since the discovery of J/psi at Brookhaven National Laboratory and SLAC National Accelerator Laboratory over 36 years ago, theorists still have not been able to fully understand the production mechanism of heavy quarkonia, although major progresses have been made in recent years. With this in mind, a two-week program on quarkonium production was organized at BNL on June 6-17, 2011. Many new experimental data from LHC and from RHIC were presented during the program, including results from the LHC heavy ion run. To analyze and correctly interpret these measurements, and in order to quantify properties of the hot matter produced in heavy-ion collisions, it is necessary to improve our theoretical understanding of quarkonium production. Therefore, a wide range of theoretical aspects on the production mechanism in the vacuum as well as in cold nuclear and hot quark-gluon medium were discussed during the program from the controlled calculations in QCD and its effective theories such as NRQCD to various models, and to the first principle lattice calculation. The scientific program was divided into three major scientific parts: basic production mechanism for heavy quarkonium in vacuum or in high energy elementary collisions; the formation of quarkonium in nuclear medium as well as the strong interacting quark-gluon matter produced in heavy ion collisions; and heavy quarkonium properties from the first principle lattice calculations. The heavy quarkonium production at a future Electron-Ion Collider (EIC) was also discussed at the meeting. The highlight of the meeting was the apparent success of the NRQCD approach at next-to-leading order in the description of the quarkonium production in proton-proton, electron-proton and electron positron collisions. Still many questions remain open in lattice calculations of in-medium quarkonium properties and in the area of cold nuclear matter effects.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

HALO: A full-orbit model of nonlinear interaction of fast particles with eigenmodes

HALO (HAgis LOcust) solves the initial value Vlasov-Maxwell problem perturbatively for application to certain nonlinear wave-particle problems in tokamak plasmas. It uses the same basic approach as the HAGIS code for wave evolution but is built on the LOCUST-GPU full-orbit code for the solution of the Hamiltonian fast particle motion in cylindrical coordinates. The wave amplitude and particle evolution include all finite Larmour radius effects. We describe and benchmark the currently implemented Alfvén eigenmode workflow, demonstrating correct particle motion, linear and nonlinear power transfer. Here, the formulation and numerical scheme are sufficiently general as to allow easy future implementation of different kinds of eigenmodes, such as modes close to the ion-cyclotron frequency. The code can model multiple eigenmodes and multiple fast ion species simultaneously, and supports the general form of the equilibrium distribution in constants of motion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

G-protein coupled receptors: advances in simulation and drug discovery

G-protein coupled receptors (GPCRs), the largest family of human membrane proteins, mediate cellular signaling and represent primary targets of about one third of currently marketed drugs. GPCRs undergo highly dynamic structural transitions during signal transduction, from binding of extracellular ligands to coupling with intracellular effector proteins. Molecular dynamics (MD) simulations have been utilized to investigate GPCR signaling mechanisms (such as pathways of ligand binding and receptor activation/deactivation) and to design novel small-molecule drug candidates. Future research directions point towards modeling cooperative binding of multiple orthosteric and allosteric ligands to GPCRs, GPCR oligomerization and interactions of GPCRs with different intracellular signaling proteins. Lastly, through methodological and supercomputing advances, MD simulations will continue to provide important insights into GPCR signaling mechanisms and further facilitate structure-based drug design.

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

Role Evaluation of Active Groups in Lignin on UV-Shielding Performance

The contribution of the active groups in lignin to ultraviolet (UV)-shielding performance still remains unclear. In this study, we employed 16 lignin model compounds and theoretical calculations to ascertain the contribution of different functional groups to UV-shielding performance. These results showed that the order of UV-shielding performance on functional groups was -C=C–CHO > -C=C–COOH > -C=C–CH 2 OH > --C=C > quinone > -COOH > -OCH 3 ≈ -OH. Moreover, the synergism between the para-substituted electron-donating group -OH and the electron-withdrawing group allyl on the aromatic ring played a major role in UV-shielding performance of lignin models, whereas the additive effect of meta/ortho-substituted -OCH 3 played a secondary role. Furthermore, we found that the hydrophile–lipophile balance (HLB) value of lignin models also greatly affected the sunscreen protection factor (SPF) of lignin model-based sunscreens. A closer HLB value of lignin to 8.89 corresponded with a higher SPF of the lignin model-based sunscreen. The commercial photoprotective ingredient ethylhexyl methoxycinnamate (EHMC) and lignin models had a synergistic effect on UV-shielding performance caused by the π–π stacking interaction between the parallel-displaced stacked aromatic rings of lignin models and EHMC. Additionally, the UV irradiation test showed that these sunscreens prepared using lignin models and EHMC exhibited good photostability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Drug Delivery Through the Skin: Molecular Simulations of Barrier Lipids to Design more Effective Noninvasive Dermal and Transdermal Delivery Systems for Small Molecules Biologics and Cosmetics

The delivery of drugs through the skin provides a convenient route of administration that is often preferable to injection because it is noninvasive and can typically be self-administered. These two factors alone result in a significant reduction of medical complications and improvement in patient compliance. Unfortunately, a significant obstacle to dermal and transdermal drug delivery alike is the resilient barrier that the epidermal layers of the skin, primarily the stratum corneum, presents for the diffusion of exogenous chemical agents. Further advancement of transdermal drug delivery requires the development of novel delivery systems that are suitable for modern, macromolecular protein and nucleotide therapeutic agents. Significant effort has already been devoted to obtain a functional understanding of the physical barrier properties imparted by the epidermis, specifically the membrane structures of the stratum corneum. However, structural observations of membrane systems are often hindered by low resolutions, making it difficult to resolve the molecular mechanisms related to interactions between lipids found within the stratum corneum. Several models describing the molecular diffusion of drug molecules through the stratum corneum have now been postulated, where chemical permeation enhancers are thought to disrupt the underlying lipid structure, resulting in enhanced permeability. Recent investigations using biphasic vesicles also suggested a possibility for novel mechanisms involving the formation of complex polymorphic lipid phases. In this review, we discuss the advantages and limitations of permeation-enhancing strategies and how computational simulations, at the atomic scale, coupled with physical observations can provide insight into the mechanisms of diffusion through the stratum corneum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Molecular ecological network analyses

Background: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Effect of Ion (Ar{sup +}) Irradiation on Cluster Magnetism and Magnetic Interactions in Fe{sub 67}Cr{sub 18}B{sub 15} Amorphous Alloy

The comparison of the resonance magnetic absorption spectra with the data on structure and magnetic properties of Fe{sub 67}Cr{sub 18}B{sub 15} amorphous samples has shown that a randomly inhomogeneous medium of amorphous alloy is multiphase. Two types of samples with the same chemical composition, but with a different clusterized structure, and the use of (Ar{sup +}) ion irradiation in the experiment made it possible to separate four basic phases with different magnetic properties. The basic phase α-(Fe,Cr) contains large clusters of D < 400 Å in size with a tendency to phase separation of iron (α-Fe) and chromium (α-Cr), which under irradiation, enhances the competing FM and AFM magnetic interactions and increases the intensity of the resonance magnetic absorption lines associated with α-Fe and α-Cr. The phase Fe{sub 3}B (D < 100 Å) is detected by independent line in the resonance absorption spectra only when its groupings are isolated from the α-(Fe,Cr) metal phase clusters. The fourth phase contains precluster groupings and disappears when the sample is irradiated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analogue of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form {pi}-stacking interactions with the catalytic Tyr{sup 24} have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19-24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Force transduction and lipid binding in MscL: A continuum-molecular approach

The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, and identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10–13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.

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

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗
DOE OSTI2015

Forecasting the response of Earth's surface to future climatic and land use changes: A review of methods and research needs

In the future, Earth will be warmer, precipitation events will be more extreme, global mean sea level will rise, and many arid and semiarid regions will be drier. Human modifications of landscapes will also occur at an accelerated rate as developed areas increase in size and population density. We now have gridded global forecasts, being continually improved, of the climatic and land use changes (C&LUC) that are likely to occur in the coming decades. However, besides a few exceptions, consensus forecasts do not exist for how these C&LUC will likely impact Earth-surface processes and hazards. In some cases, we have the tools to forecast the geomorphic responses to likely future C&LUC. Fully exploiting these models and utilizing these tools will require close collaboration among Earth-surface scientists and Earth-system modelers. This paper assesses the state-of-the-art tools and data that are being used or could be used to forecast changes in the state of Earth's surface as a result of likely future C&LUC. We also propose strategies for filling key knowledge gaps, emphasizing where additional basic research and/or collaboration across disciplines are necessary. The main body of the paper addresses cross-cutting issues, including the importance of nonlinear/threshold-dominated interactions among topography, vegetation, and sediment transport, as well as the importance of alternate stable states and extreme, rare events for understanding and forecasting Earth-surface response to C&LUC. Five supplements delve into different scales or process zones (global-scale assessments and fluvial, aeolian, glacial/periglacial, and coastal process zones) in detail.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

A Three-Dimensional Dynamic Supramolecular “Sticky Fingers” Organic Framework

Engineering high-recognition host-guest materials is a burgeoning area in basic and applied research. The challenge of exploring novel porous materials with advanced functionalities prompted us to develop dynamic crystalline structures promoted by soft interactions. The first example of a pure molecular dynamic crystalline framework is demonstrated, which is held together by means of weak "sticky fingers" van der Waals interactions. The presented organic-fullerene-based material exhibits a non-porous dynamic crystalline structure capable of undergoing single-crystal-to-single-crystal reactions. Exposure to hydrazine vapors induces structural and chemical changes that manifest as toposelective hydrogenation of alternating rings on the surface of the [60]fullerene. To conclude, control experiments confirm that the same reaction does not occur when performed in solution. Easy-to-detect changes in the macroscopic properties of the sample suggest utility as molecular sensors or energy-storage materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase

Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. In conclusion, these results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Analytic, non-perturbative, gauge-invariant quantum chromodynamics: Nucleon scattering and binding potentials

Removal of the quenched approximation in the mechanism which produced an analytic estimate of quark-binding potentials, along with a reasonable conjecture of the color structure of the nucleon formed by such a binding potential, is shown to generate an effective nucleon scattering and binding potential. The mass-scale factor on the order of the pion mass, previously introduced to define the transverse imprecision of quark coordinates, is again used, while the strength of the potential is proportional to the square of a renormalized quantum chromodynamics (QCD) coupling constant. The potential so derived does not include corrections due to spin, angular momentum, nucleon structure, and electroweak interactions; rather, it is qualitative in nature, showing how Nuclear Physics can arise from fundamental QCD. -- Highlights: •Nucleon–nucleon forces are derived qualitatively from basic realistic quantum chromodynamics. •An effective nucleon binding is obtained from the simplest unquenched approximation. •A model deuteron binding energy of −2.2 MeV follows with α{sub s,R}=12.5.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 – a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution – reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1–3 regions ‘sense’ nucleic acids, ‘regulate’ the HNH conformational transition, and ultimately ‘lock’ the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1–3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.

59 BASIC BIOLOGICAL SCIENCES↗