Results for “BASIC INTERACTIONS” — Page 61

DOE OSTI2023

TRACER-CAT-LANL Aerosol Optics and Chemical Speciation - SPAMS

Aerosol size distribution, optical properties, and speciation data collected in La Port TX, during TRACER-CAT-LANL, July 2022, with basic trace gas measurements. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by Los Alamos National Laboratory (TRACER-CAT-LANL, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-LANL is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol and trace gas data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments Include: Picarro GHG Photoacoustic Soot Spectrometer (PASS-3) Humidified-cavity attenuated phase shift-single scattering albedo particulate matter monitor (H-CAPS-PMSSA) Soot Particle Aerosol Mass Spectrometer (SPAMS) Single-Particle Soot Photometer (SP2) Cloud Condensation Nuclei Counter (CCNc) Aerodynamic Particle Sizer (APS) Scanning Mobility Particle Sizer (SMPS)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-LANL Aerosol Optics and Chemical Speciation - SMPS

Aerosol size distribution, optical properties, and speciation data collected in La Port TX, during TRACER-CAT-LANL, July 2022, with basic trace gas measurements. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by Los Alamos National Laboratory (TRACER-CAT-LANL, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-LANL is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol and trace gas data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments Include: Picarro GHG Photoacoustic Soot Spectrometer (PASS-3) Humidified-cavity attenuated phase shift-single scattering albedo particulate matter monitor (H-CAPS-PMSSA) Soot Particle Aerosol Mass Spectrometer (SPAMS) Single-Particle Soot Photometer (SP2) Cloud Condensation Nuclei Counter (CCNc) Aerodynamic Particle Sizer (APS) Scanning Mobility Particle Sizer (SMPS)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-LANL Aerosol Optics and Chemical Speciation - CAPS-SSA

Aerosol size distribution, optical properties, and speciation data collected in La Port TX, during TRACER-CAT-LANL, July 2022, with basic trace gas measurements. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by Los Alamos National Laboratory (TRACER-CAT-LANL, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-LANL is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol and trace gas data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments Include: Picarro GHG Photoacoustic Soot Spectrometer (PASS-3) Humidified-cavity attenuated phase shift-single scattering albedo particulate matter monitor (H-CAPS-PMSSA) Soot Particle Aerosol Mass Spectrometer (SPAMS) Single-Particle Soot Photometer (SP2) Cloud Condensation Nuclei Counter (CCNc) Aerodynamic Particle Sizer (APS) Scanning Mobility Particle Sizer (SMPS)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-LANL Aerosol Optics and Chemical Speciation - PASS

Aerosol size distribution, optical properties, and speciation data collected in La Port TX, during TRACER-CAT-LANL, July 2022, with basic trace gas measurements. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by Los Alamos National Laboratory (TRACER-CAT-LANL, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-LANL is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol and trace gas data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments Include: Picarro GHG Photoacoustic Soot Spectrometer (PASS-3) Humidified-cavity attenuated phase shift-single scattering albedo particulate matter monitor (H-CAPS-PMSSA) Soot Particle Aerosol Mass Spectrometer (SPAMS) Single-Particle Soot Photometer (SP2) Cloud Condensation Nuclei Counter (CCNc) Aerodynamic Particle Sizer (APS) Scanning Mobility Particle Sizer (SMPS)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

TRACER-CAT-LANL Aerosol Optics and Chemical Speciation - CCN

Aerosol size distribution, optical properties, and speciation data collected in La Port TX, during TRACER-CAT-LANL, July 2022, with basic trace gas measurements. All sampling was conducted with an identical aerosol inlet as the standard ARM-AOS systems. The TRacking Aerosol Convection interactions ExpeRiment Carbonaceous Aerosols Thrust by Los Alamos National Laboratory (TRACER-CAT-LANL, July 2022) was designed to complement the larger ARM TRACER science goals to understand convective cloud lifecycles and aerosol-convection interactions. TRACER-CAT-LANL is focused on understanding the relationship between particle composition and light absorption and the influence of water uptake on this relationship. This aerosol and trace gas data can be used to understand the relationship between particle composition and light absorption and the influence of water uptake on this relationship. Instruments Include: Picarro GHG Photoacoustic Soot Spectrometer (PASS-3) Humidified-cavity attenuated phase shift-single scattering albedo particulate matter monitor (H-CAPS-PMSSA) Soot Particle Aerosol Mass Spectrometer (SPAMS) Single-Particle Soot Photometer (SP2) Cloud Condensation Nuclei Counter (CCNc) Aerodynamic Particle Sizer (APS) Scanning Mobility Particle Sizer (SMPS)

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2011

Structures of Bacterial Biosynthetic Arginine Decarboxylases

Biosynthetic arginine decarboxylase (ADC; also known as SpeA) plays an important role in the biosynthesis of polyamines from arginine in bacteria and plants. SpeA is a pyridoxal-5'-phosphate (PLP)-dependent enzyme and shares weak sequence homology with several other PLP-dependent decarboxylases. Here, the crystal structure of PLP-bound SpeA from Campylobacter jejuni is reported at 3.0 {angstrom} resolution and that of Escherichia coli SpeA in complex with a sulfate ion is reported at 3.1 {angstrom} resolution. The structure of the SpeA monomer contains two large domains, an N-terminal TIM-barrel domain followed by a {beta}-sandwich domain, as well as two smaller helical domains. The TIM-barrel and {beta}-sandwich domains share structural homology with several other PLP-dependent decarboxylases, even though the sequence conservation among these enzymes is less than 25%. A similar tetramer is observed for both C. jejuni and E. coli SpeA, composed of two dimers of tightly associated monomers. The active site of SpeA is located at the interface of this dimer and is formed by residues from the TIM-barrel domain of one monomer and a highly conserved loop in the {beta}-sandwich domain of the other monomer. The PLP cofactor is recognized by hydrogen-bonding, {pi}-stacking and van der Waals interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Characterization of CO2 behavior on rutile TiO2 (110) surface

The dynamic behavior of carbon dioxide (CO2) adsorbed on the rutile TiO2 (110) surface is studied by dispersion-corrected density functional theory (DFT) and combined ab initio molecular dynamics (AIMD). Understanding he behavior of CO2 is important regarding possible applications for treating CO2 in current environmental problems along with the consideration as a renewable energy source. Concerning the ability as a redusible support of TiO2 surface, a fundamental understanding of the interaction between CO2 and TiO2 surface will help extending the possibile applications. In the current study, CO2 interaction and dynamics behavior on the TiO2 surface is characterized including he effect of the oxygen vacancy (OV) defect. Also the coverage dependence of CO2 behavior is investigated since more contribution of the intermolecular interaction among CO2 molecules can be expected as the coverage increasing. This work is supported by the US Department of Energy (DOE), Office of Basic Science, Division of Chemical Sciences, Geosicences and Biosciences. Pacific Northwest National Laboratory (PNNL) is multiprogram national laboratory operated for DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

ab initio molecular dynamics↗

DOE OSTI2016

Three-Beam Instabilily in the LHC

In the LHC, a transverse instability has been regularly observed at 4 TeV right after the beta-squeeze, when the beams are separated by ten transverse rms sizes, and only one of the two beams is seen as oscillating. According to the author, only a single hypothesis appeared to be consistent with all the observations and basic concepts, one about a third beam - an electron cloud, generated by the two proton beams in the high-beta areas of the interaction regions. The instability results from a combined action of the cloud nonlinear focusing and impedance.

43 PARTICLE ACCELERATORS↗

DOE OSTI2013

Speculations about e-cloud instabilities in the LHC

In the LHC, a transverse instability is regularly observed at 4TeV right after the beta-squeeze, when the beams are separated by about their ten transverse rms sizes [1-3], and only one of the two beams is seen as oscillating. So far only a single hypothesis is consistent with all the observations and basic concepts, one about a third beam - an electron cloud, generated by the two proton beams in the high-beta areas of the interaction regions.

Burov, Alexey↗

DOE OSTI2015

Targeting diverse protein–protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold

Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. In this paper, we describe a strategy for designing oligomers containing both α- and β-amino acid residues (“α/β-peptides”) that mimic several peptides derived from the three-helix bundle “Z-domain” scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF 165 -induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain–mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Finally, such reagents would be useful for diagnostic and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity

High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Structures of Coxsackievirus, Rhinovirus, and Poliovirus Polymerase Elongation Complexes Solved by Engineering RNA Mediated Crystal Contacts

RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2–2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight base-pairs of the nascent duplex, a fully prepositioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Peptide design by optimization on a data-parameterized protein interaction landscape

Many applications in protein engineering require optimizing multiple protein properties simultaneously, such as binding one target but not others or binding a target while maintaining stability. Such multistate design problems require navigating a high-dimensional space to find proteins with desired characteristics. A model that relates protein sequence to functional attributes can guide design to solutions that would be hard to discover via screening. In this work, we measured thousands of protein–peptide binding affinities with the high-throughput interaction assay amped SORTCERY and used the data to parameterize a model of the alpha-helical peptide-binding landscape for three members of the Bcl-2 family of proteins: Bcl-x L , Mcl-1, and Bfl-1. We applied optimization protocols to explore extremes in this landscape to discover peptides with desired interaction profiles. Computational design generated 36 peptides, all of which bound with high affinity and specificity to just one of Bcl-x L , Mcl-1, or Bfl-1, as intended. We designed additional peptides that bound selectively to two out of three of these proteins. The designed peptides were dissimilar to known Bcl-2–binding peptides, and high-resolution crystal structures confirmed that they engaged their targets as expected. Excellent results on this challenging problem demonstrate the power of a landscape modeling approach, and the designed peptides have potential uses as diagnostic tools or cancer therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

A Small Covalent Allosteric Inhibitor of Human Cytomegalovirus DNA Polymerase Subunit Interactions

Human cytomegalovirus DNA polymerase comprises a catalytic subunit, UL54, and an accessory subunit, UL44, the interaction of which may serve as a target for the development of new antiviral drugs. Using a high-throughput screen, we identified a small molecule, (5-((dimethylamino)methylene-3-(methylthio)-6,7-dihydrobenzo[c]thiophen-4(5H)-one), that selectively inhibits the interaction of UL44 with a UL54-derived peptide in a time-dependent manner, full-length UL54, and UL44-dependent long-chain DNA synthesis. A crystal structure of the compound bound to UL44 revealed a covalent reaction with lysine residue 60 and additional noncovalent interactions that cause steric conflicts that would prevent the UL44 connector loop from interacting with UL54. Analyses of the reaction of the compound with model substrates supported a resonance-stabilized conjugation mechanism, and substitution of the lysine reduced the ability of the compound to inhibit UL44-UL54 peptide interactions. Furthermore, this novel covalent inhibitor of polymerase subunit interactions may serve as a starting point for new, needed drugs to treat human cytomegalovirus infections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and Its Interaction with Contactin 2 (CNTN2)

Not Available

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Protein extraction into the bicontinuous microemulsion phase of a Water/SDS/pentanol/dodecane winsor-III system: Effect on nanostructure and protein conformation

Bicontinuous microemulsions (BμEs), consisting of water and oil nanodomains separated by surfactant monolayers of near-zero curvature, are potentially valuable systems for purification and delivery of biomolecules, for hosting multiphasic biochemical reactions, and as templating media for preparing nanomaterials. We formed Winsor-III systems by mixing aqueous protein and sodium dodecyl sulfate (SDS) solutions with dodecane and 1-pentanol (cosurfactant) to efficiently extract proteins into the middle (BμE) phase. Bovine serum albumin (BSA) and cytochrome c partitioned to the BμE phase at 64% and 81% efficiency, respectively, producing highly concentrated protein solutions (32 and 44 g L –1 , respectively), through release of water and oil from the BμEs. Circular dichroism spectroscopic analysis demonstrated that BSA underwent minor secondary structural changes upon incorporation into BμEs, while the secondary structure of cytochrome c and pepsin underwent major changes. Small-angle x-ray scattering (SAXS) results show that proteins promoted an increase of the interfacial fluidity and surface area per volume for the BμE surfactant monolayers, and that each protein uniquely altered self-assembly in the Winsor-III systems. Cytochrome c partitioned via electrostatic attractions between SDS and the protein’s positively-charged groups, residing near the surfactant head groups of BμE monolayers, where it decreased surfactant packing efficiency. BSA partitioned through formation of SDS-BSA complexes via hydrophobic and electrostatic attractive interactions. As the BSA-SDS ratio increased, complexes’ partitioning favored BμEs over the oil excess phase due to the increased hydrophilicity of the complexes. In conclusion, this study demonstrates the potential utility of BμEs to purify proteins and prepare nanostructured fluids possessing high protein concentration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

PerCon SFA project data dentification of spatially resolved biomarkers of drought in Sorghum bicolor rhizosphere molecular-microbe interactions using a novel root cartography "RhizoGrid" system for sampling plants under drought and control conditions across 10 equally sized root zone environments (4 quadrants each). Each quadrant was sampled and processed for 16S amplicon, metabolomics, and X-ray computed tomography (XCT). Data download includes experimental metadata and results files for 16S rRNA sequence analysis of microbial community assembly (processed data files), liquid chromatography mass spectrometry (LC-MS) metabolomics analysis of microbial community root exudates (processed data files), X-ray computed tomography (XCT) spatial gradient analysis (raw and processed data files) of microbial community composition, and related computational modeling outputs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut

Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.

59 BASIC BIOLOGICAL SCIENCES↗