Search NASA⌕ Search

SEARCH · Search NASA

Results for “coordination complex”

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 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Entropic control of the free-energy landscape of an archetypal biomolecular machine

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). Here, we propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Science & Technology - Other Topics↗
DOE OSTI2022

Understanding Metal–Organic Framework Nucleation from a Solution with Evolving Graphs

A mechanistic understanding of metal–organic framework (MOF) synthesis and scale-up remains underexplored due to the complex nature of the interactions of their building blocks. In this work, we investigate the collective assembly of building units at the early stages of MOF nucleation, using MIL-101(Cr) as a prototypical example. Using large-scale molecular dynamics simulations, we observe that the choice of solvent (water and N,N-dimethylformamide), the introduction of ions (Na+ and F–) and the relative populations of MIL-101(Cr) half-secondary building unit (half-SBU) isomers have a strong influence on the cluster formation process. Additionally, the shape, size, nucleation and growth rates, crystallinity, and short and long-range order largely vary depending on the synthesis conditions. We evaluate these properties as they naturally emerge when interpreting the self-assembly of MOF nuclei as the time evolution of an undirected graph. Solution-induced conformational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly. While pure solvents lead to the rapid formation of a small number of large clusters, the presence of ions in aqueous solutions results in smaller clusters and slower nucleation. This diversity is captured by the key features of the graph representation. Principle component analysis on graph properties reveals that only a small number of molecular descriptors is needed to deconvolute MOF self-assembly. Furthermore, descriptors such as the average coordination number between half-SBUs and fractal dimension are of particular interest as they can be can be followed experimentally by techniques like by time-resolved spectroscopy. Ultimately, graph theory emerges as an approach that can be used to understand complex processes revealing molecular descriptors accessible by both simulation and experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C 60 : Synthesis, Supramolecular Formation and Excited-State Processes

Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin–zinc porphyrin dyad, H 2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 10 4 m -1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H 2 P, and electron transfer to the coordinated ImC 60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×10 9 s -1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex photochemical events occurring in natural photosynthesis and its implications in building light energy harvesting devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Multimodal Perception and Multicriterion Control of Nested Systems: Coordination of Postural Control and Vehicular Control - 1

The purpose of this report is to identify the essential characteristics of goal-directed whole-body motion. The report is organized into three major sections (Sections 2, 3, and 4). Section 2 reviews general themes from ecological psychology and control-systems engineering that are relevant to the perception and control of whole-body motion. These themes provide an organizational framework for analyzing the complex and interrelated phenomena that are the defining characteristics of whole-body motion. Section 3 of this report applies the organization framework from the first section to the problem of perception and control of aircraft motion. This is a familiar problem in control-systems engineering and ecological psychology. Section 4 examines an essential but generally neglected aspect of vehicular control: coordination of postural control and vehicular control. To facilitate presentation of this new idea, postural control and its coordination with vehicular control are analyzed in terms of conceptual categories that are familiar in the analysis of vehicular control.

Riccio, Gary E.↗
NASA NTRS1986

Investigation of the effects of cobalt ions on epoxy properties

The effects of Co(acac)sub x complexes on MY-720 epoxy properties have been investigated. It appears that Co2(+) ions form antibonding or nonbonding orbitals which increase the free volume and also reduce the cohesiveness of the host epoxy. The effects of Co2(+) ions, on the other hand, seem to result in increased Cohesiveness of the epoxy. The experimental values of magnetic moments of both types of ions in MY-720 suggest that the orbital momentum contributions of the (3d) electrons are partially conserved, though the effect is more pronounced for Co2(+) ions. The coordination environment of the cobalt ions in the host epoxy does not appear to be uniquely defined. These results indicate that the effects of metal ions on resin properties cannot be easily predicted on the basis of ligand field theory argument alone. Complex interactions between metal ions and host epoxy molecular structure suggest the desirability of parallel experimental investigations of electronic, magnetic, and mechanical properties of metal ion-containing epoxy samples for comparison with theory.

Singh, J. J.↗
DOE OSTI2026

Multibody for Everybody (M4E): A Symbolic Dynamics Modeling Tool with Applications in Simulation, Control, and Optimization

Developing the analytical model of a multibody system is often the initial step in control and optimization. The analytical model (equations of motion) describes a system’s time evolution under specified forcing conditions. Although developing these equations is easy for simple systems, this process becomes more complex for systems composed of multiple bodies. Deriving equations of motion for complex multibody systems requires specialized expertise in multibody dynamics, is time-consuming, and is susceptible to error. To address this issue, this paper presents an open-source, easy-to-use, systematic framework to derive symbolic equations of motion in both Python and MATLAB using the joint coordinate formulation. This formulation results in a set of ordinary differential equations that use the minimum set of coordinates needed to model a system. The symbolic representation provides better insight into the influence of design parameters on system performance, facilitates sensitivity analysis and parameter studies, and supports direct implementation of control and optimization routines. The tool enables numerical simulation for specified parameter sets, is modular for straightforward integration with other tools and libraries, and allows incorporation of hydrodynamics, mooring, and other external forces. The result is a reproducible, extensible pipeline for modeling, simulation, and design of complex multibody systems. The proposed tool is versatile and can be applied to domains such as robotics, control, and design. In addition, we integrated external libraries that provide capabilities for modeling offshore systems such as underwater robots and marine energy converters.

16 TIDAL AND WAVE POWER↗
DOE OSTI2016

A Solid of Revolution Time Study using COG11.1 and MCNP6.1

The performance of two continuous energy Monte Carlo transport codes, COG11.1 and MCNP6.1, has been compared for the {sup 239}Pu Jezebel Benchmark using cross sections based on the ENDF/B-VII.1 evaluated nuclear data library. The purpose of this study is to determine the length of time it takes each code to complete a series of criticality calculations, using two different methods to model a solid of revolution. A solid of revolution is essential in many fields of engineering and mathematics, and has been a standard feature in computer-aided design and manufacturing since the 1970's. In the field of criticality safety, a solid of revolution can be used to reproduce and simplify complex engineering drawings and systems that would otherwise require excessive use of geometric primitives and computational resources to achieve a comparable level of fidelity. There are two basic methods to model a solid of revolution: Method 1 (COG) specifies a set of x-y pairs or polar coordinates and rotate the curve about the x-axis. Method 2 (COG and MCNP) creates a set of end-to-end conical frustums and/or cylinders. Method 1 is only available in COG and can be implemented using one surface and sector specification. Method 2 can be implemented in both COG and MCNP. This time study was initially conceived as a result of criticality safety analysis performed for a complex system with a high degree of rotational symmetry. Each COG input deck typically took 1-2 days to run in serial mode. COG input decks were then converted to MCNP format and run on the same computer cluster. Instead of expected 1-2 day runtimes, it took MCNP6.1 more than one week to complete each run. Since MCNP typically runs faster than many codes, these lengthy runtimes were considered unusual. This study attempts to investigate the runtime discrepancy between the two codes. The methods and benchmark in this time study were selected to provide a consistent, generalized approach to modeling an arbitrary solid of revolution. While there are many different ways to model the {sup 239}Pu Jezebel Benchmark, the focus of this study is on investigating the practical difference between the two basic methods to model a surface of revolution. Throughout this study, the only code that maintains reasonably low runtimes is COG11.1 (Method 1). Based on the observed performance of each code and method, it is likely that the divergent runtimes are the result of tracking particles across planes that lie between conical frustums, as opposed to defining the object boundary as a single surface. Slight fluctuations in graphed results were also observed, due to random sampling and CPU loading. This was confirmed by re-running input decks and comparing average runtimes to a preliminary curve fit. From the perspective of a criticality safety analyst, the results of this study are expected to contribute towards understanding one of the practical trade-offs between codes and methods as they apply to real-world analysis. Ultimately, it's about choosing the right tool for the job.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Effect of the Precursor Chemistry on the Crystallization of Triple Cation Mixed Halide Perovskites

Triple cation, mixed halide perovskite compositions have been reported to be more thermally stable, exhibit fewer phase impurities, and show higher power conversion efficiency and better reproducibility than single cation perovskites. In this work, we explain the formation of Cs0.05FA0.81MA0.14Pb(I0.85Br0.15)3 via a multimodal in situ study combining structural information from synchrotron grazing-incidence wide-angle X-ray scattering (GIWAXS) and optical properties from photoluminescence (PL) spectroscopy with density functional theory calculations (DFT). The focus here is on the effects of the solvent and antisolvent during crystallization. The predominantly used solvents N,N-dimethylformamide (DMF), dimethyl sulfoxide (DMSO), and the antisolvent chlorobenzene (CB) as well as the solvent-antisolvent-precursor interactions are investigated. Given the high elemental complexity and mutual interdependencies between solvent, antisolvent, and perovskite precursors, we found significant differences in the crystallization pathways. DMF-pure precursors show the formation of the DMF-containing intermediate phase and the nucleation of compositionally distinct perovskite phases, while when DMSO is added, only crystalline α- and δ-phases were found. In addition, the presence of DMSO helps the formation of α-perovskite. Coordination energy and bond order (BO) calculations support our experimental findings. Dripping of CB induces nucleation at room temperature, slows the α-phase formation rate, and appears to reduce the nucleation radius. These findings provide novel insights into solvent, antisolvent, and perovskite precursor interactions and their formation pathways. The complexity of interactions between solvents and reagents highlights the importance of understanding these effects to further improve the reproducibility and optimize processing conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Science of the Van Allen Probes Science Operations Centers

The Van Allen Probes mission operations materialized through a distributed model in which operational responsibility was divided between the Mission Operations Center (MOC) and separate instrument specific SOCs. The sole MOC handled all aspects of telemetering and receiving tasks as well as certain scientifically relevant ancillary tasks. Each instrument science team developed individual instrument specific SOCs proficient in unique capabilities in support of science data acquisition, data processing, instrument performance, and tools for the instrument team scientists. In parallel activities, project scientists took on the task of providing a significant modeling tool base usable by the instrument science teams and the larger scientific community. With a mission as complex as Van Allen Probes, scientific inquiry occurred due to constant and significant collaboration between the SOCs and in concert with the project science team. Planned cross-instrument coordinated observations resulted in critical discoveries during the seven-year mission. Instrument cross-calibration activities elucidated a more seamless set of data products. Specific topics include post-launch changes and enhancements to the SOCs, discussion of coordination activities between the SOCs, SOC specific analysis software, modeling software provided by the Van Allen Probes project, and a section on lessons learned. One of the most significant lessons learned was the importance of the original decision to implement individual team SOCs providing timely and well-documented instrument data for the NASA Van Allen Probes Mission scientists and the larger magnetospheric and radiation belt scientific community.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

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

Estimation of pipe failure frequencies in the absence of operational experience data: A pilot study

Probabilistic failure metrics such as leak frequency and rupture frequency are commonly used to characterize piping reliability. The methodologies for calculating the failure metrics rely on a complex set of input parameters. Operating experience data and experimental data play an important role in informing the different input parameters. The paper describes results and conclusions of a coordinated research project to benchmark three different reliability models using a four-step procedure: reference case definition of relevance to advanced reactor designs, input parameter calibration, validation of results, and application of different methodologies upon completion of the calibration and validation steps. The reference case is a weld consisting of nickel-base alloy 152/52 and located within a primary pressure boundary of an advanced reactor. This alloy is a class of structural materials known to be highly resistant to stress corrosion cracking. Synergies between the different methods are noted and the importance of a multi-disciplinary approach to input parameter development is underscored. A key conclusion is that the three methods are equally suitable for estimating failure frequencies. In any specific application, a selection of the most practical or effective computational tool can be considered. The comparison of alternative models confirms and helps to gain confidence in the computed failure frequency estimates. The study was part of a coordinated research project organized by the International Atomic Energy Agency.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Rare Earth Element-Induced Condensation of the Block V of the Repeats-in-Toxin Domain from CyaA from Bordetella pertussis for Separations

Rare earth elements (REEs) are critical for the development of a range of new technologies. However, the current industrial separation processes of these metals from natural sources, recycled materials, and industrial effluents involve the large consumption of organic solvents, resulting in a sizable environmental footprint. We aim to exploit the high affinity of the block V peptide of the repeats-in-toxin (RTX) domain of the adenylate cyclase protein from Bordetella pertussis for the separation of REEs. This peptide selectively binds with lanthanide (Ln) cations and can undergo Ln-induced phase separation, which can be used in bioseparation processes. Here, we evaluated the self-assembling structures of complexes of the RTX domain peptide folded in the presence of Ln 3+ cations. Size distribution and surface potential measurements of complexes were taken to understand the Ln-induced changes in the complexed peptide. Transmission electron microscopy imaging was used to explore the structures of complexes, while anomalous small-angle X-ray scattering measurements were used to determine the distribution of Ln 3+ ions within the protein-based macrostructures. In the presence of excess Ln 3+ , we observed the formation of coral-like cylindrical structures comprised of Ln 3+ -RTX complexes, with approximately eight trivalent metals per peptide within the nanosized assemblies. These findings provide new insights into the structural organization of assembled RTX domains and their ability to coordinate with REEs, forming nanosized, metal-rich structures that naturally condense, providing a proof-of-concept for protein-based separation processes of these critical materials.

chemical structure↗
DOE OSTI2016

Impacts of Surface Site Coordination on Arsenate Adsorption: Macroscopic Uptake and Binding Mechanisms on Aluminum Hydroxide Surfaces

Aluminum hydroxides play important roles in regulating the fate and transport of contaminants and nutrients in soils and aquatic systems. Like many metal oxides, these minerals display surface functional groups in a series of coordination states, each of which may differ in its affinity for adsorbates. The distribution of functional group types varies among distinct surfaces of aluminum hydroxides, and we thus hypothesize that the adsorption behavior and mechanisms will show a dependence on particle morphology. To test this hypothesis, we investigate arsenate adsorption on two aluminum hydroxide polymorphs with distinct particle morphologies, gibbsite [γ-Al(OH) 3 ] and bayerite [α-Al(OH) 3 ], at pH 4 and 7. Synthetic gibbsite platelets expose large (001) basal surfaces predicted to be terminated by doubly coordinated functional groups (>Al 2 OH). In contrast, synthetic bayerite microrods display mainly edge surfaces (parallel to the c axis) containing abundant singly coordinated functional groups (>AlOH 2 ). Macroscopic adsorption studies show that gibbsite adsorbs less arsenate per unit surface area than bayerite at both pH values and suggest that two surface complexes form on each material. Similar electrokinetic behavior is displayed at the same relative coverages of arsenate, suggesting that similar reactive surface groups (>AlOH 2 ) control the surface charging on both particles. EXAFS spectroscopy shows that there is no variation in arsenate surface speciation on a given mineral with surface coverage or pH. Whereas bidentate binuclear inner-sphere species are the dominant complexes present, the EXAFS result suggest that outer-sphere species also occur on both minerals, with a greater abundance on gibbsite. This binding mode likely involves adsorption to >Al 2 OH sites, which have a slow ligand exchange rate that inhibits inner-sphere binding. Lastly, these results demonstrate that adsorption mechanisms and capacity, even when normalized for specific surface area, vary with metal oxide particle morphology because of the distribution of distinct functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases

Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10 12 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry

The type III CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) systems are bacterially encoded adaptive immune systems for defense against invading nucleic acids. They accomplish this task through the coordinated cleavage of invading substrates of single-stranded RNA and DNA (ssDNA and ssRNA) by the Csm (type III-A) or Cmr (type III-B) effector complexes. The ssRNA is complementarily bound to the CRISPR RNA (crRNA). However, the structural basis for the DNase and RNase activation of the Csm nucleoprotein complex is largely unknown. Here we report cryo-EM structures of the Csm-crRNA complex, with or without target ssRNA, at near-atomic resolution. Our cryo-EM maps allow us to build atomic models of the key macromolecular components, including Cas10, Csm2, Csm3, Csm4, crRNA and the invading ssRNA. Our structure resolves unambiguously the stoichiometry and tertiary structures of the Csm protein complex and the interactions between protein components and the crRNA/ssRNA. Interestingly, the new atomic structures of the Csm proteins presented here are similar to those of previously known Csm proteins in other species despite their low sequence similarity. Our combined structural and biochemical data suggest that ssRNA cleavage is preferentially carried out near its 5’-end, that the extent of interactions among the ssRNA, crRNA and the protein components regulates the DNase activity of the Csm complex, and that the 3’ flanking sequence of ssRNA activates the Cas10 DNase activity allosterically.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease

Abstract RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.

Science & Technology - Other Topics↗