Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Clas
Explore the source record for details and available documents.
Kemp, M. Trent↗
SEARCH · Search NASA
Results for “AsP”
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.
Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase)
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. In this paper, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors.
60 APPLIED LIFE SCIENCES↗
Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp{sup 143} and Arg{sup 232} play divergent roles toward different substrates
YfeX from Escherichia coli O157 is a bacterial dye-decolorizing peroxidase that represents both dye-decoloring activity and typical peroxidase activity. We reported the crystal structure of YfeX bound to heme at 2.09 Å resolution. The YfeX monomer resembles a ferredoxin-like fold and contains two domains. The three conserved residues surrounding the heme group are His{sup 215}, Asp{sup 143} and Arg{sup 232}. His{sup 215} functions as the proximal axial ligand of the heme iron atom. Biochemical data show that the catalytic significance of the conserved Asp{sup 143} and Arg{sup 232} depends on the substrate types and that YfeX may adopt various catalytic mechanisms toward divergent substrates. In addition, it is observed that an access tunnel spans from the protein molecular surface to the heme distal region, it serves as the passageway for the entrance and binding of the H{sub 2}O{sub 2}. - Highlights: • We determined the crystal structure of YfeX bound to heme at 2.09 Å resolution. • The conserved Asp{sup 143} and Arg{sup 232} play different roles toward divergent substrates. • The H{sub 2}O{sub 2} access tunnel spans from the protein molecular surface to the heme distal region.
60 APPLIED LIFE SCIENCES↗
An Application of ASP in Nuclear Engineering: Explaining the Three Mile Island Nuclear Accident Scenario
Abstract The paper describes an ongoing effort in developing a declarative system for supporting operators in the Nuclear Power Plant (NPP) control room. The focus is on two modules: diagnosis and explanation of events that happened in NPPs. We describe an Answer Set Programming (ASP) representation of an NPP, which consists of declarations of state variables, components, their connections, and rules encoding the plant behavior. We then show how the ASP program can be used to explain the series of events that occurred in the Three Mile Island, Unit 2 (TMI-2) NPP accident, the most severe accident in the USA nuclear power plant operating history. We also describe an explanation module aimed at addressing answers to questions such as “why an event occurs?” or “what should be done?” given the collected data.
Computer Science↗
AmeriFlux FLUXNET-1F US-Mo1 LTAR CMRB Field 1 (CMRB ASP)
This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP). This is the FLUXNET version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP) produced by applying the standard ONEFlux (1F) software. Site Description - Site is in a 36 ha agricultural research field near Centralia, MO on a broad, slightly sloped landscape. Currently farmed in a corn-soybean-wheat-hay rotation. Used for research since 1991; prior to that was managed for commercial crop production.
Schreiner-McGraw, Adam↗
Nanostructure Growth in the Ga(In)AsP–GaAs System under Quasi-Equilibrium Conditions
The formation of nanostructures on the surface of GaAs under quasi-equilibrium conditions in a quasi-closed volume from saturated phosphor and indium vapors in the presence of a Au catalyst with growth according to the “vapor–liquid–crystal” mechanism is considered for the first time. The influence of the growth temperature and size of Au drops on the morphology and composition of the fabricated nanostructures is studied. Experimental data on the formation of Ga(In)AsP nanocrystals on GaAs substrates with various orientations are presented. It is established that the temperature growth range of the nanostructures when using this method is 540–640°C with a drop size from 30 to 120 nm. It is shown that the size of the catalyst drops substantially affects the morphology and growth rate of the fabricated nanostructures while their composition weakly depends on both the drop size and the substrate orientation.
36 MATERIALS SCIENCE↗
AmeriFlux US-Mo1 LTAR CMRB Field 1 (CMRB ASP)
This is the AmeriFlux version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP). Site Description - Site is in a 36 ha agricultural research field near Centralia, MO on a broad, slightly sloped landscape. Currently farmed in a corn-soybean-wheat-hay rotation. Used for research since 1991; prior to that was managed for commercial crop production.
Schreiner-McGraw, Adam↗
AmeriFlux US-LMA Mississippi ARS Arant ASP
This is the AmeriFlux version of the carbon flux data for the site US-LMA Mississippi ARS Arant ASP. Site Description - Field
Witthaus, Lindsey [USDA ARS]↗
Comparison of Response Times for the Thermo ASP-2S1/NRD and Ludlum 30-7B Neutron Instruments
Health Physics Services (HPS) received feedback from a customer service survey regarding the difference in response times between the Thermo ASP-2S1/NRD (Thermo) and Ludlum Model 30-7B (Ludlum). In response to the feedback, tests were performed in the field and duplicated in a laboratory to evaluate and compare each instrument’s response time to reach an applied exposure. The results of the tests showed that optimizing its screen refresh rate by updating the Ludlum’s firmware improves response time, making it more comparable to the Thermo.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Materials Data on AsP by Materials Project
PAs crystallizes in the monoclinic C2/m space group. The structure is one-dimensional and consists of two PAs ribbons oriented in the (0, 1, 0) direction. As3+ is bonded in an L-shaped geometry to two equivalent P3- atoms. Both As–P bond lengths are 2.38 Å. P3- is bonded in a trigonal non-coplanar geometry to two equivalent As3+ and one P3- atom. The P–P bond length is 2.22 Å.
36 MATERIALS SCIENCE↗
Materials Data on AsP by Materials Project
PAs is Halite, Rock Salt structured and crystallizes in the trigonal R3m space group. The structure is two-dimensional and consists of three PAs sheets oriented in the (0, 0, 1) direction. As3+ is bonded in a 6-coordinate geometry to three equivalent P3- atoms. All As–P bond lengths are 2.45 Å. P3- is bonded in a 6-coordinate geometry to three equivalent As3+ atoms.
36 MATERIALS SCIENCE↗
Advanced Synchrophasor Protocol (ASP) Development and Demonstration Project
The Advanced Synchrophasor Protocol Project had two main objectives: To develop, document, and demonstrate a new standard communications protocol (that became named the Streaming Telemetry Transport Protocol, or STTP) to overcome the issues being encountered in large-scale synchrophasor data system deployments using existing protocols – specifically with issues of scalability, data loss, bandwidth utilization, data access control, transport security options, and cost of configuration management, and to work with standards bodies to put STTP on a track for consideration as a standard protocol.
42 ENGINEERING↗
Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His 3 Asp Site
Calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is a host-defense protein that sequesters nutrient transition metals from microbes. Each S100A8/S100A9 heterodimer contains four EF-hand domains and two transition-metal-binding sites. We investigate the effect of Ca(II) ions on the structure and Ni(II)-binding properties of human CP. By employing energy dispersive X-ray (EDX) spectroscopy, we evaluate the metal content of Ni(II)-bound CP-Ser [oligomer of S100A8(C42S) and S100A9(C3S)] crystals obtained in the absence and presence of Ca(II). We present a 2.1 Å resolution crystal structure of Ni(II)-bound CP-Ser and compare this structure to a reported Ni(II)- and Ca(II)-bound CP-Ser structure [Nakashige, T. G., et al. (2017) J. Am. Chem. Soc.139, 8828–8836]. This analysis reveals conformational changes associated with coordination of Ca(II) to the EF-hands of S100A9 and that Ca(II) binding affects the coordination number and geometry of the Ni(II) ion bound to the His3Asp site. In contrast, negligible differences are observed for the Ni(II)-His6 site in the absence and presence of Ca(II). Biochemical studies show that, whereas the His6 site has a thermodynamic preference for Ni(II) over Zn(II), the His3Asp site selects for Zn(II) over Ni(II), and relatively rapid metal exchange occurs at this site. Furthermore, these observations inform the working model for how CP withholds nutrient metals in the extracellular space.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and Function of the β-Asp-Arg Polymerase Cyanophycin Synthetase 2
Not provided.
Biochemistry & Molecular Biology↗
Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE
Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca 2+ , Mn 2+ , Fe 2+ /Fe 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ , but not monovalent metal ions, Cr 3+ , Mg 2+ , Y 3+ , Sr 2+ or Ba 2+ . Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
59 BASIC BIOLOGICAL SCIENCES↗
Exploiting an Asp-Glu “switch” in glycogen synthase kinase 3 to design paralog-selective inhibitors for use in acute myeloid leukemia
Abstract not provided
Wagner, Florence F. (ORCID:0000000189810330)↗
ASP (Adaptive Splines for Prediction) [SWR-22-66]
This software package provides functionality to fit piecewise cubic splines to model the relationship between a univariate X (independent variable) and a univariate Y (dependent variable). The output is akin to linear regression but has higher "capacity" in that it can learn more complicated relationships despite leveraging only a single predictor. It thus can learn very reasonable relationships between X and Y with minimal effort. The canonical intended use case is for predicting electric demand (Y) from temperature (X). There can be complicated, non-linear relationships between these two variables, but these can be reasonably approximated by the sum of: 1) an "aggregate" relationship between daily average temperature and daily average demand, and 2) intra-day patterns represented as hourly offsets from the daily average load. The spline functionality is used for learning a robust "aggregate" relationship without the inconvenience of manual feature engineering while still ensuring robust results. The model fitting workhorse is R's built-in smooth.spline. This package provides a suite of options for controlling how smooth.spline fits a spline to the data. In particular, it is designed to return a model with a single critical point (i.e., a single location along the domain/support where the first derivative is zero). This is to ensure that predicted changes in electric demand are always positive as temperatures become more extreme. This helps to prevent overfitting, particularly when the input data has few observations or has significant uncertainty from other sources.
Murphy, Sinnott↗