Search NASA⌕ Search

SEARCH · Search NASA

Results for “loop chaining”

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.

At least 289 records · Page 16

Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies

Antibodies provide a broad defense against a vast array of antigens; however, the structural features that contribute to this diverse antigen recognition vary in different vertebrates. In cows, a subset of antibodies have an exceptionally long third heavy-chain complementarity-determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. We have determined crystal structures of three bovine Fabs to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, whereas the knob regions share a conserved β sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the structural diversity of the knob. Finally, the unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems and may inform efforts in antibody engineering.

60 APPLIED LIFE SCIENCES↗

Development of a Techno-Economic Analysis Framework for a Solar Thermochemical Fuel Production Process

Synthetic liquid fuels can provide a drop-in substitute for fossil-based fuels in sectors such as aviation and maritime, where electrification is not a viable option due to the need for high specific energy density. However, for these alternative fuels to be adopted at a commercial scale, their price must be competitive compared to their fossil-based counterparts. The reverse water-gas shift (RWGS) reaction offers a promising pathway, using hydrogen (sourced from electrolysis) and carbon dioxide as the feed and reacting to produce syngas - a mixture of H2 and CO at a specific ratio. Syngas is a useful precursor that can be converted into fuels and chemicals via known downstream processes, such as liquid transportation fuels via Fischer-Tropsch (FT) synthesis. The RWGS reaction is currently not applied in commercial scale, unlike the rest of the components in the process chain (electrolyzers and syngas-to-fuel synthesis units). The RWGS reaction poses several challenges due to its restrictive thermodynamics. Being an equimolar reaction, high temperatures and a large excess of H2 are needed to achieve reasonable CO2 conversion at equilibrium. This has detrimental effects on practical process implementation and the quality of syngas that can be produced, with direct effect on the energy and capital requirements, as well as the need for expensive downstream separation. In this work, we are proposing to develop a new concentrating solar thermal (CST) compatible RWGS reactor, performing the reaction in a 2-step chemical looping process using metal oxide at a temperature range of 600-800 degrees Celsius. By decoupling the reactor from the solar receiver, the Generation 3 (Gen3) CST technology could be utilized, together with its proposed thermal energy storage (TES) technology, benefitting from a good match to the required temperatures. CST technology is a viable option for supplying the heat that could be rapidly deployed in scale, thus being a good match to the gas-to-liquid (GTL) process which requires a large minimal scale to be commercially viable. The integration of TES with CST also allows operating the plant at large annual capacity factors and avoids multiple shutdown/startup cycles, thus fitting into the steady-state operation mode that most GTL processes require. The main innovation in the proposed design hinges on a countercurrent reaction design using a packed bed reactor. In 2019 Metcalfe et al. showed the benefits of countercurrent species exchange could be realized in a redox chemical-looping processes, by storing the favorable countercurrent chemical potential profiles in a packed bed of non-stoichiometric oxide. Metcalfe et al. applied this breakthrough concept to the WGS reaction, which is conventionally a co-feed catalytic process, showing a dramatic improvement. Bulfin et al. (2023) performed a similar proof-of-concept demonstration for the RWGS reaction using CeO2, achieving cumulative and peak CO2 conversions of 88% and 95%, respectively, compared to a thermodynamic limit of 58% for the co-feed catalytic process at the same conditions. In our new REGENLOOP project, we are developing a reactor prototype from the heat-exchange packed bed reactor-type, a commonly used reactor in the chemical industry. The endothermic heat of reduction will be supplied to the reactor using CST, while the same heat transfer fluid (HTF) mechanism will be used to extract the exothermic heat of oxidation. An array of multiple reactors is used to supply constant high-purity CO stream, that is then mixed with H2 from electrolysis to produce a high-purity syngas at the required composition. By removing the CO-CO2 separation after the RWGS process, significant energy and cost reduction can be achieved. A physics-based TEA framework is currently being developed, covering all the major plant processes, from the solar collection through storage, chemical looping RWGS, GTL, and auxiliary unit operations, up to the liquid hydrocarbon product. This modeling framework will utilize reduced-order models for the chemical looping RWGS and TES, CST modeling using SolarPILOT, and Aspen Plus for the GTL. By using this combined physics-based approach, the effects of design/operating parameters on the performance and cost can be elucidated. In our presentation, the modeling framework will be presented in detail, including preliminary cost predictions of using this plant configuration under a few selected relevant case studies. This study will be used to identify the major cost drivers, informing further system design and optimization needed to chart the way for a commercially viable pathway.

14 SOLAR ENERGY↗

Automatic Differentiation in MetaPhysicL and Its Applications in MOOSE

Efficient solution via Newton’s method of nonlinear systems of equations requires an accurate representation of the Jacobian, corresponding to the derivatives of the component residual equations with respect to the degrees of freedom. In practice these systems of equations often arise from spatial discretization of partial differential equations used to model physical phenomena. These equations may involve domain motion or material equations that are complex functions of the systems’ degrees of freedom. Computing the Jacobian by hand in these situations is arduous and prone to error. Finite difference approximations of the Jacobian or its action are prone to truncation error, especially in multiphysics settings. Symbolic differentiation packages may be used, but often result in an excessive number of terms in realistic model scenarios. An alternative to symbolic and numerical differentiation is automatic differentiation (AD), which propagates derivatives with every elementary operation of a computer program, corresponding to continual application of the chain rule. Automatic differentiation offers the guarantee of an exact Jacobian at a relatively small overhead cost. In this work, we outline the adoption of AD in the Multiphysics Object Oriented Simulation Environment (MOOSE) via the MetaPhysicL package. We describe the application of MOOSE’s AD capability to several sets of physics that were previously infeasible to model via hand-coded or Jacobian-free simulation techniques, including arbitrary Lagrangian-Eulerian and level-set simulations of laser melt pools, phase-field simulations with free energies provided through neural networks, and metallic nuclear fuel simulations that require inner Newton loop calculation of nonlinear material properties.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Precision Labeling of Native Antibodies with Lock Coupling

The formation of stable protein complexes enables much of biotechnology, but even high-affinity complexes can dissociate, limiting potential applications in biomaterials, bioimaging, nanomedicine, and other protein-based technologies. Here, in this study, we describe lock coupling, a simple and selective one-step reaction between interfacial lysine and glutamate or aspartate side chains to form stable isopeptide bonds and be used for the precise labeling of native antibodies. We identify conditions in which short-lived activated esters formed by the aqueous carbodiimide EDC promote isopeptide bond formation specifically at preassociated amine-acid pairs. Indiscriminate cross-linking is minimized by formation of protein complexes before addition of catalyst, use of acidic pH to suppress exposed Lys reactivity, and limiting the aqueous stability of activated esters. For native antibody (Ab) labeling, we show that the small IgG-binding protein GB1 can be covalently attached to the Ab Fc domain and that introduction of Cys into GB1 loops allows for facile conjugation of fluorophores, micelles, or inorganic nanocrystals for imaging in live cells and animals. By varying Cys substituents and protein stoichiometry, a defined number of probes can be uniformly attached without the need for extensive purification. In live-cell confocal microscopy, labeled GB1 serves as a stable replacement for secondary Abs, enabling simple multicolor immunostaining and imaging. Lock coupling requires just a single reagent in aqueous buffer and leverages both the innate ability of proteins to form high-affinity complexes and the widespread presence of Lys-Glu/Asp pairs at their interfaces, with the potential for precision synthesis of protein-based probes for imaging, biomaterials, biophysics, and medicine.

antibody↗

BOTTLE 2 - Analysis

The use of analysis is foundational to BOTTLE. In particular, we conduct techno-economic analysis (TEA), life cycle assessment (LCA), and supply chain modeling for each new BOTTLE innovation, spanning new deconstruction and upcycling technologies to redesigned polymers. These critical analysis tools are used in parallel with laboratory research to ensure that BOTTLE technologies can ultimately meet our key metrics. The BOTTLE team used analysis early in the current 3-year project cycle to identify research priorities from a scale, energy, and economics perspective (Nicholson et al., Joule 2021), and recently we presented a comprehensive framework for comparing new circularity-focused approaches to linear, incumbent practices (Nicholson et al., Ann. Rev. Chem. Biomolec. Eng. 2022). This presentation will also review case studies in analysis for closed-loop PET recycling across a range of recycling methods, baseline studies that we have conducted for plastics pyrolysis and gasification as another comparator for BOTTLE technologies, and a comprehensive study of existing closed-loop recycling technologies from a full suite of environmental impacts and feedstock quality metrics. We have undertaken studies of circular polymers being developed in the Redesign task, and we will present an exemplary case for a bio-based acrylic polymer that can replace polymethyl methacrylate. Overall, analysis is critical to enable the BOTTLE Consortium to focus on impactful, realistic technologies.

BIOMASS FUELS↗

The role of Ile87 of CYP158A2 in oxidative coupling reaction

Both CYP158A1 and CYP158A2 are able to catalyze an oxidative C-C coupling reaction producing biflaviolin or triflaviolin in Streptomyces coelicolor A3(2). The substrate-bound crystal structures of CYP158A2 and CYP158A1 reveal that the side chain of Ile87 in CYP158A2 points to the active site contacting the distal flaviolin molecule, however, the bulkier side chain of Lys90 in CYP158A1 (corresponding to Ile87 in CYP158A2) is toward the distal surface of the protein. These results suggest that these residues could be important in determining product regiospecificity. In order to explore the role of the two residues in catalysis, the reciprocal mutants, Ile87Lys and Lys90Ile, of CYP158A2 and CYP158A1, respectively, were generated and characterized. The mutant Ile87Lys enzyme forms two isomers of biflaviolin instead of three isomers of biflaviolin in wild-type CYP158A2. CYP158A1 containing the substitution of lysine with isoleucine has the same catalytic activity compared with the wild-type CYP158A1. The crystal structure of Ile87Lys showed that the BC loop in the mutant is in a very different orientation compared with the BC loop in both CYP158A1/A2 structures. These results shed light on the mechanism of the oxidative coupling reaction catalyzed by cytochrome P450.

Zhao, Bin↗

Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection

ABSTRACT Elucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection. IMPORTANCE Understanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.

36 MATERIALS SCIENCE↗

Circ-UBR5: An exonic circular RNA and novel small nuclear RNA involved in RNA splicing

Highlights: • Low expression of circ-UBR5 in NSCLC was significantly related with tumor poor differentiation. • A highly efficient strategy for finding specific circRNA binding proteins using HuprotTM Protoarray was first be presented. • Circ-UBR5 could bind splicing regulatory factors QKI, and NOVA1 and U1 snRNA in the nucleus. • Our research first revealed the potential function of a non-functional phenotype circRNA in NSCLC cells. Circular RNAs (circRNAs) are class of non-coding RNAs formed by back-splicing events as loops, and could be found in all types of organisms. They play important and diverse roles in cell development, growth, and tumorigenesis, but functions of the majority of circRNAs remain enigmatic. Particularly functional phenotypes of great majority of circRNAs are not obvious. Here we randomly selected a circRNA circ-UBR5, which has no obvious functional phenotype in non-small cell lung cancer (NSCLC) cells from our previous research findings, to explore its potential function in cells. Differential expression of circ-UBR5 was detected in paired samples of tumorous tissues and adjacent nontumorous tissues from 59 patients with NSCLC by real-time quantitative reverse transcription-polymerase chain reactions (qRT-PCRs). Results showed circ-UBR5 expression was significantly downregulated in NSCLC tissues (p (p = 0.00126), suggesting circ-UBR5 might serve as an index of NSCLC differentiation. Our findings indicated circ-UBR5 could bind splicing regulatory factor QKI, KH domain containing RNA binding (QKI) and NOVA alternative splicing regulator 1 (NOVA1) and U1 small nuclear RNA (snRNA) in the nucleus, revealing circ-UBR5 might be a novel snRNA involved in RNA splicing regulatory process. Moreover, we first presented a highly efficient strategy for finding specific circRNA binding proteins using Human Protein Microarray (Huprot™ Protoarray).

60 APPLIED LIFE SCIENCES↗

Electrochemically Initiated Depolymerization of Poly(Methyl Methacrylate)

Efficient depolymerization of polymers with all-carbon backbones under mild conditions would be valuable in chemically recycling commodity plastics. Poly(methyl methacrylate) (PMMA) is a commodity thermoplastic that is currently depolymerized under temperatures in excess of 400 °C. Herein, we lower the temperatures needed to achieve depolymerization of PMMA by performing radical generation and depropagation with orthogonal stimuli. This first demonstration of electrochemically initiated PMMA depolymerization relies on reduction of phthalimide esters that, upon subsequent decarboxylation, generate polymer-centered radicals. These radicals then spontaneously unzip the polymer back to its monomeric constituents at temperatures as low as 105 °C. We studied the mechanism and efficiency of this transformation as a function of phthalimide ester placement, incorporation density, and polymer molecular weight. We found that chain-end activation is effective for modest molecular weights but suffers diminished efficiency at higher degrees of polymerization. In contrast, pendent-group activation is more effective for depolymerizing higher molecular weight species. Integrating higher molar amounts of phthalimide ester pendants leads to more effective depolymerization, with >95% depolymerization in copolymers with 5 mol% phthalimide ester incorporation. We leveraged this understanding to create a custom electro-distillation apparatus that allowed us to simultaneously electrochemically depolymerize PMMA and directly distill methyl methacrylate in >22% yield, which could ultimately be repolymerized. These findings establish electrochemistry as a versatile and orthogonal stimulus for vinyl polymer depolymerization and provide a foundation for closed-loop electrochemical recycling of widely used plastics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First evidence of P2{sub 1}/n to P2{sub 1}/c structural transformation in pyroxene-type LiAlGe{sub 2}O{sub 6} under high-pressure conditions

The high-pressure behavior of the pyroxene-type compound LiAlGe{sub 2}O{sub 6}, the unique representative of a P2{sub 1}/n-pyroxene, was investigated by in-situ X-ray diffraction and Raman spectroscopy on single-crystal samples hydrostatically pressurized in a diamond-anvil cell. The structure was found to undergo a first-order phase transition on compression, with a critical transition at 5.23±0.02 GPa. Together with a strong volume discontinuity of −ΔV/V{sub 0}=−4.1% the transition shows a remarkable hysteresis loop over at least 0.70 GPa pressure interval. The bulk modulus of the low- and high-pressure polymorphs corresponds to K{sub 0}=114(1) and 123(2) GPa, respectively, as described by a 2{sup nd} order Birch–Murnaghan equation of state. Based on the systematic extinctions the transition was identified as a P2{sub 1}/n-to-P2{sub 1}/c transformation. The mechanism of structural transformation was identified to be controlled by the stereochemistry of the Li atoms at the M2 site, which changes its coordination number from 5 to 6. The formation of new Li–O bonds involves the co-operative folding of Ge{sub 2}O{sub 6}-chains, which explains the anisotropy of axial elasticities and the spontaneous strain across the transformation. Simultaneously the distortion correction of AlO{sub 6} units associated with the transition further explains the preference of the P2{sub 1}/c structure under pressure. - Graphical abstract: Detail of the crystal structures of LP-LAG at 3.48 GPa (left) and HP-LAG at 4.51 GPa (right). Li on M2 are green; AlO{sub 6} octahedra (Al at M1) are orange; tetrahedra sites in LP-LAG: T1 (yellow) and T2 (blue); tetrahedra sites in HP-LAG: A-chains (yellow), B-chains (blue). - Highlights: • A new high-pressure phase transition P2{sub 1}/n–P2{sub 1}/c was found for LaAlGe{sub 2}O{sub 6}. • The transition was also followed by micro-Raman spectroscopy. • The high-pressure polymorph shows a higher bulk modulus. • The structural evolution of the two symmetries was determined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time-Periodic Solutions of Driven-Damped Trimer Granular Crystals

We consider time-periodic structures of granular crystals consisting of alternate chrome steel (S) and tungsten carbide (W) spherical particles where each unit cell follows the pattern of a 2 : 1 trimer: S-W-S. The configuration at the left boundary is driven by a harmonic in-time actuation with given amplitude and frequency while the right one is a fixed wall. Similar to the case of a dimer chain, the combination of dissipation, driving of the boundary, and intrinsic nonlinearity leads to complex dynamics. For fixed driving frequencies in each of the spectral gaps, we find that the nonlinear surface modes and the states dictated by the linear drive collide in a saddle-node bifurcation as the driving amplitude is increased, beyond which the dynamics of the system becomes chaotic. While the bifurcation structure is similar for solutions within the first and second gap, those in the first gap appear to be less robust. We also conduct a continuation in driving frequency, where it is apparent that the nonlinearity of the system results in a complex bifurcation diagram, involving an intricate set of loops of branches, especially within the spectral gap. The theoretical findings are qualitatively corroborated by the experimental full-field visualization of the time-periodic structures.

36 MATERIALS SCIENCE↗

Nuclear Spin Relaxation and Molecular Interactions of a Novel Triazolium-Based Ionic Liquid

Nuclear spin relaxation, small-angle X-ray scattering (SAXS), and electrospray ionization mass spectrometry (ESI-MS) techniques are used to determine supramolecular arrangement of 3-methyl-1-octyl-4-phenyl-1H-triazol-1,2,3-ium bis(trifluoromethanesulfonyl)imide [OMPhTz][Tf{sub 2}N], an example of a triazolium-based ionic liquid. The results obtained showed first-order thermodynamic dependence for nuclear spin relaxation of the anion. First-order relaxation dependence is interpreted as through-bond dipolar relaxation. Greater than first-order dependence was found in the aliphatic protons, aromatic carbons (including nearest neighbors), and carbons at the end of the aliphatic tail. Greater than first order thermodynamic dependence of spin relaxation rates is interpreted as relaxation resulting from at least one mechanism additional to through-bond dipolar relaxation. In rigid portions of the cation, an additional spin relaxation mechanism is attributed to anisotropic effects, while greater than first order thermodynamic dependence of the octyl side chain’s spin relaxation rates is attributed to cation–cation interactions. Little interaction between the anion and the cation was observed by spin relaxation studies or by ESI-MS. No extended supramolecular structure was observed in this study, which was further supported by MS and SAXS. nuclear Overhauser enhancement (NOE) factors are used in conjunction with spin–lattice relaxation time (T{sub 1}) measurements to calculate rotational correlation times for C–H bonds (the time it takes for the vector represented by the bond between the two atoms to rotate by one radian). The rotational correlation times are used to represent segmental reorientation dynamics of the cation. A combination of techniques is used to determine the segmental interactions and dynamics of this example of a triazolium-based ionic liquid.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Heavy Chain-Only IgG2b Llama Antibody Effects Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes Elements of Coreceptor- and CD4-Binding Sites

The conserved HIV-1 site of coreceptor binding is protected from antibody-directed neutralization by conformational and steric restrictions. While inaccessible to most human antibodies, the coreceptor site has been shown to be accessed by antibody fragments. In this study, we used X-ray crystallography, surface plasmon resonance, and pseudovirus neutralization to characterize the gp120-envelope glycoprotein recognition and HIV-1 neutralization of a heavy chain-only llama antibody, named JM4. We describe full-length IgG2b and IgG3 versions of JM4 that target the coreceptor-binding site and potently neutralize over 95% of circulating HIV-1 isolates. Contrary to established trends that show improved access to the coreceptor-binding region by smaller antibody fragments, the single-domain (VHH) version of JM4 neutralized less well than the full-length IgG2b version of JM4. The crystal structure at 2.1-Å resolution of VHH JM4 bound to HIV-1 YU2 gp120 stabilized in the CD4-bound state by the CD4-mimetic miniprotein, M48U1, revealed a JM4 epitope that combined regions of coreceptor recognition (including the gp120 bridging sheet, V3 loop, and β19 strand) with gp120 structural elements involved in recognition of CD4 such as the CD4-binding loop. The structure of JM4 with gp120 thus defines a novel CD4-induced site of vulnerability involving elements of both coreceptor- and CD4-binding sites. Here, the potently neutralizing JM4 IgG2b antibody that targets this newly defined site of vulnerability adds to the expanding repertoire of broadly neutralizing antibodies that effectively neutralize HIV-1 and thereby potentially provides a new template for vaccine development and target for HIV-1 therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel

Prokaryotic orthologs of eukaryotic Cys-loop receptor channels recently emerged as structural and mechanistic surrogates to investigate this superfamily of intercellular signaling proteins. Here, we examine proton activation of the prokaryotic ortholog GLIC using patch clamp electrophysiology, mutagenesis, and molecular dynamics (MD) simulations. Whole-cell current recordings from human embryonic kidney (HEK) 293 cells expressing GLIC show half-maximal activation at pH 6, close to the p$K_a$ of histidine, implicating the three native His residues in proton sensing linked to activation. The mutation H235F abolishes proton activation, H277Y is without effect, and all nine mutations of His-127 prevent expression on the cell surface. In the GLIC crystal structure, His-235 on transmembrane (TM) $α$-helix 2, hydrogen bonds to the main chain carbonyl oxygen of Ile-259 on TM α-helix 3. MD simulations show that when His-235 is protonated, the hydrogen bond persists, and the channel remains in the open conformation, whereas when His-235 is deprotonated, the hydrogen bond dissociates, and the channel closes. Mutations of the proximal Tyr-263, which also links TM α-helices 2 and 3 via a hydrogen bond, alter proton sensitivity over a 1.5 pH unit range. MD simulations show that mutations of Tyr-263 alter the hydrogen bonding capacity of His-235. The overall findings show that His-235 in the TM region of GLIC is a novel proton binding site linked to channel activation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and specificity of several triclocarban-binding single domain camelid antibody fragments

The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. Here, a high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed “CDR4”. A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.

59 BASIC BIOLOGICAL SCIENCES↗

A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization

Epitope III, a highly conserved amino acid motif of 524 APTYSW 529 on the hepatitis C virus (HCV) E2 glycoprotein, resides in the critical loop that binds to the host receptor CD81, thus making it one of the most important antibody targets for blocking HCV infections. Here, we have determined the X-ray crystal structure of epitope III at a 2.0-Å resolution when it was captured by a site-specific neutralizing antibody, monoclonal antibody 1H8 (mAb1H8). The snapshot of this complex revealed that epitope III has a relatively rigid structure when confined in the binding grooves of mAb1H8, which confers the residue specificity at both ends of the epitope. Such a high shape complementarity is reminiscent of the “lock and key” mode of action, which is reinforced by the incompatibility of an antibody binding with an epitope bearing specific mutations. By subtly positioning the side chains on the three residues of Tyr 527 , Ser 528 , and Trp 529 while preserving the spatial rigidity of the rest, epitope III in this cocrystal complex adopts a unique conformation that is different from previously described E2 structures. With further analyses of molecular docking and phage display–based peptide interactions, we recognized that it is the arrangements of two separate sets of residues within epitope III that create these discrete conformations for the epitope to interact selectively with either mAb1H8 or CD81. These observations thus raise the possibility that local epitope III conformational dynamics, in conjunction with sequence variations, may act as a regulatory mechanism to coordinate “mAb1H8-like” antibody-mediated immune defenses with CD81-initiated HCV infections.

59 BASIC BIOLOGICAL SCIENCES↗

CD26-mediated regulation of periostin expression contributes to migration and invasion of malignant pleural mesothelioma cells

Highlights: • CD26-expressing MPM cells upregulate production of periostin. • The intracytoplasmic region of CD26 mediates the upregulation of periostin. • CD26 expression leads to nuclear translocation of Twist1 via phosphorylation of Src. • Secreted periostin enhances migration and invasion of MPM cells. - Abstract: Malignant pleural mesothelioma (MPM) is an aggressive malignancy arising from mesothelial lining of pleura. It is generally associated with a history of asbestos exposure and has a very poor prognosis, partly due to the lack of a precise understanding of the molecular mechanisms associated with its malignant behavior. In the present study, we expanded on our previous studies on the enhanced motility and increased CD26 expression in MPM cells, with a particular focus on integrin adhesion molecules. We found that expression of CD26 upregulates periostin secretion by MPM cells, leading to enhanced MPM cell migratory and invasive activity. Moreover, we showed that upregulation of periostin expression results from the nuclear translocation of the basic helix-loop-helix transcription factor Twist1, a process that is mediated by CD26-associated activation of Src phosphorylation. While providing new and profound insights into the molecular mechanisms involved in MPM biology, these findings may also lead to the development of novel therapeutic strategies for MPM.

60 APPLIED LIFE SCIENCES↗

Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli

Abstract The Escherichia coli cytochrome bo 3 ubiquinol oxidase is a four‐subunit heme‐copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts—the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo 3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo‐EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67–74).

59 BASIC BIOLOGICAL SCIENCES↗