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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.

Yanagawa, Evan S. K. [University of Pennsylvania ,↗
DOE OSTI2020

Iron(III)–Oxo Cluster Chemistry with Dimethylarsinate Ligands: Structures, Magnetic Properties, and Computational Studies

A program has been initiated to develop Fe III /oxo cluster chemistry with the ‘pseudo-carboxylate’ ligand dimethylarsinate (Me 2 AsO 2 - ) for comparison with the well investigated Fe III /oxo/carboxylate cluster area. The synthesis and characterization of three polynuclear Fe III complexes are reported, [Fe 12 O 4 (O 2 C t Bu) 8 (O 2 AsMe 2 ) 17 (H 2 O) 3 ]Cl 3 (1), Na 2 [Fe 12 Na 2 O 4 (O 2 AsMe 2 ) 20 (NO 3 ) 6 (Me 2 AsO 2 H) 2 (H 2 O) 4 ](NO 3 ) 6 (2) and [Fe 3 (O 2 AsMe 2 ) 6 (Me 2 AsO 2 H) 2 (hqn) 2 ](NO 3 ) (3), where hqn is 8-hydroxyquinoline. The Fe 12 core of 1 is a type never previously encountered in Fe III carboxylate chemistry, consisting of two Fe 6 units each of which comprises two {Fe 3 (μ 3 -O 2- )} units bridged by three Me 2 AsO 2 - groups and linked into an Fe 12 loop structure by two anti-anti η 1 :η 1 :μ Me 2 AsO 2 - groups, a bridging mode extremely rare with carboxylates. 2 also consists of two Fe 6 units, differing in their ligation from those in 1, and this time linked together into a linear structure by a central {Na 2 (NO 3 ) 2 } bridging unit. 3 is a linear Fe 3 complex with no monoatomic bridges between Fe III ions, a very rare situation in Fe III chemistry with any ligands, and unprecedented in Fe carboxylate chemistry. The distinct differences observed in arsinate vs carboxylate ligation modes are rationalized largely based on the greater basicity of the former vs the latter. Variable-temperature dc and ac magnetic susceptibility data reveal all Fe 2 pairwise interactions to be antiferromagnetic. For 1 and 2, the different J ij couplings were estimated by use of a magnetostructural correlation for high nuclearity Fe III -oxo clusters and by density functional theory calculations using broken symmetry methods, allowing identification of their relative spin vector alignments and thus rationalization of their S = 0 ground states. The J ij values were then used as input values to give excellent fits of the experimental χM T vs T data. For 3, the fits of the experimental χM T vs T data to the Van Vleck equation or with PHI gave a very weak J 12 = -0.8(1) cm -1 (H = –2JŠ i ·Š j convention) between adjacent Fe III ions, and an S = 5/2 ground state. Furthermore, these initial Fe III arsinate complexes also provide structural parameters that help validate literature assignments of arsinate binding modes to iron oxide/hydroxide minerals as part of environmental concerns of using arsenic-containing herbicides in agriculture.

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

NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems

Global optimization constitutes an important and fundamental problem in theoretical studies in many chemical fields, such as catalysis, materials or separations problems. In this paper, a novel algorithm has been developed for the global optimization of large systems including neat and ligated clusters in gas phase, and supported clusters in periodic boundary conditions. The method is based on an updated artificial bee colony (ABC) algorithm method, that allows for adaptive-learning during the search process. The new algorithm is tested against four classes of systems of diverse chemical nature: gas phase Au_55, ligated Au_8^(2+), Au_8 supported on graphene oxide and defected rutile, and a large cluster assembly ?[Co?_6 Te_8 (PEt_3 )_6][C_60 ]_n, with sizes ranging between 1 to 3 nm and containing up to 1300 atoms. Reliable global minima (GMs) are obtained for all cases, either confirming published data or reporting new lower energy structures. The algorithm and interface to other codes in the form of an independent program, Northwest Potential Energy Search Engine (NWPEsSe), is freely available and it provides a powerful and efficient approach for global optimization of nanosized cluster systems. The work described in this publication was performed at Pacific Northwest National Laboratory (PNNL), which is operated by Battelle for the United States Department of Energy (DOE) under Contract DE-AC05-76RL0180. J. Z. and V.-A. G. acknowledge support from DOE, Office of Science, Office of Basic Energy Sci-ences, Chemical, Geological and Biological Sciences Division and computing resources from PNNL’s Research Computing Facility and the National Energy Research Scientific Computing Center.

Zhang, Jun↗
DOE OSTI2025

Neptunium Pyridine Dipyrrolide Complexes

Two pyridine dipyrrolide neptunium(IV) complexes, ( Mes PDP Ph )NpCl 2 (THF) and Np( Mes PDP Ph ) 2 , where ( Mes PDP Ph ) 2– is the doubly deprotonated form of 2,6-bis(5-(2,4,6-trimethylphenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine, have been prepared. Characterization of the complexes has been performed through a combination of solid- and solution-state methods, including single-crystal X-ray diffraction and electronic absorption and nuclear magnetic resonance spectroscopies. Collectively, these data confirm the formation of the mono- and bis-ligated species. Electrochemistry of a series of bis-ligated actinide complexes, An( Mes PDP Ph ) 2 (An = Th, U, Np), is presented.

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

An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4

Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. Finally, by identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tuning the Lifetimes of Photoinduced Deligation in a Metal–Organic Framework via Linker Functionalization

Recently photoinduced dynamic ligation in a metal–organic frameworks (MOFs) was reported, where a long-lived charge-transfer excited state (ca. 30 μs) featuring partial dissociation between the carboxylate linker and metal-based node was probed by time-resolved infrared (TRIR) spectroscopy. The study offers a new mechanistic perspective to evaluate the potential contribution from the excited state molecular configuration to the performance of MOF photocatalysts. In this work, by employing MIL-101(Fe) as the study platform, we have further explored the influence of intramolecular interactions on the stability of relevant excited states and demonstrated the effective tuning of their lifetimes through the incorporation of different functional groups into the system. The correlations between the varied excited state lifetimes and coordination configurations with specific functional groups (−NH 2 or −NO 2 ) was inferred from the analyses of infrared spectroscopic data and theoretical calculations, revealing the essential role of the intramolecular interactions (i.e., between the added functional groups and the carboxylate group) in the modulation of system energetics. Overall, the work presents a pathway to tune the excited state dynamics and expands the knowledge regarding the photoinduced dynamic ligation in carboxylate-based MOFs.

excited states↗
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↗
DOE OSTI2024

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electronic relaxation dynamics in [Au 25 (SR) 18 ] -1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) thiolate-protected nanoclusters

Here we investigate the excited electron dynamics in [Au 25 (SR) 18 ] -1 (R = CH3, C 2 H 5 , C 3 H 7 , MPA, PET) [MPA = mercaptopropanoic acid, PET = phenylethylthiol] nanoparticles to understand how different ligands affect the excited state dynamics in this system. The population dynamics of the core and higher excited states lying in the energy range 0.00–2.20 eV are studied using a surface hopping method with decoherence correction in a real-time DFT approach. All of the ligated clusters follow a similar trend in decay for the core states (S 1 –S 6 ). The observed time constants are on the picosecond time scale (2–19 ps), which agrees with the experimental time scale, and this study confirms that the time constants observed experimentally could originate from core-to-core transitions and not from core-to-semiring transitions. In the presence of higher excited states, R = H, CH 3 , C 2 H 5 , C 3 H 7 , and PET demonstrate similar relaxations trends whereas R = MPA shows slightly different relaxation of the core states due to a smaller gap between the LUMO+1 and LUMO+2 gap in its electronic structure. The S 1 (HOMO → LUMO) state gives the slowest decay in all ligated clusters, while S 7 has a relatively long decay. Furthermore, separate electron and hole relaxations were performed on the [Au 25 (SCH 3 ) 18 ] -1 nanocluster to understand how independent electron and hole relaxations contribute to the overall relaxation dynamics.

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

Elucidating the mechanism of photochemical CO 2 reduction to CO using a cyanide-bridged di-manganese complex

The complex, [{[Mn(bpy)(CO) 3 ] 2 }(μ-CN)] + (Mn 2 CN + ), has previously been shown to photochemically reduce CO 2 to CO. The detailed mechanism behind its reactivity was not elucidated. In this work, the photoevolution of this reaction is studied in acetonitrile (MeCN) using IR and UV-vis spectroscopy. Samples were excited into the Mn I → π* bpy metal-to-ligand charge transfer (MLCT) absorption band triggering CO loss, and rapid MeCN solvent ligation at the open coordination site. It is concluded that this process occurs selectively at the Mn axial ligation site that is trans to the C-end of the bridging cyanide. Upon further photolysis, the metal–metal bonded dimeric species, [(CO) 3 (bpy)Mn–Mn(bpy)(CO) 3 ] (Mn–Mn) is observed to form under anaerobic conditions. The presence of this dimeric species coincides with the observation of CO production. When oxygen is present, CO 2 photoreduction does not occur, which is attributed to the inability of Mn 2 CN + to convert to the metal–metal bonded dimer. Photolysis experiments, where the Mn–Mn dimer is formed photochemically under argon first and then exposed to CO 2 , reveal that it is the radical species, [Mn(bpy)(CO) 3 ˙] (Mn˙), that interacts with the CO 2 . Since the presence of Mn–Mn and light is required for CO production, [Mn(bpy)(CO) 3 ˙] is proposed to be a photochemical reagent for the transformation of CO 2 to CO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A potential role for RNA aminoacylation prior to its role in peptide synthesis

Coded ribosomal peptide synthesis could not have evolved unless its sequence and amino acid–specific aminoacylated tRNA substrates already existed. We therefore wondered whether aminoacylated RNAs might have served some primordial function prior to their role in protein synthesis. Here, we show that specific RNA sequences can be nonenzymatically aminoacylated and ligated to produce amino acid–bridged stem-loop RNAs. We used deep sequencing to identify RNAs that undergo highly efficient glycine aminoacylation followed by loop-closing ligation. The crystal structure of one such glycine-bridged RNA hairpin reveals a compact internally stabilized structure with the same eponymous T-loop architecture that is found in many noncoding RNAs, including the modern tRNA. We demonstrate that the T-loop-assisted amino acid bridging of RNA oligonucleotides enables the rapid template-free assembly of a chimeric version of an aminoacyl-RNA synthetase ribozyme. We suggest that the primordial assembly of amino acid–bridged chimeric ribozymes provides a direct and facile route for the covalent incorporation of amino acids into RNA. A greater functionality of covalently incorporated amino acids could contribute to enhanced ribozyme catalysis, providing a driving force for the evolution of sequence and amino acid–specific aminoacyl-RNA synthetase ribozymes in the RNA World. The synthesis of specifically aminoacylated RNAs, an unlikely prospect for nonenzymatic reactions but a likely one for ribozymes, could have set the stage for the subsequent evolution of coded protein synthesis.

Science & Technology - Other Topics↗
DOE OSTI2020

Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri

ABSTRACT In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.

Microbiology↗
DOE OSTI2025

Use of Split‐Intein Proteins to Design a Small Molecule Biosensor in Plants

Understanding how plants perceive their environment is fundamental to advancing agricultural productivity and sustainability. Many biological small molecules, including those involved in microbial recognition, act rapidly at the plant cell surface, but the absence of tools to visualise these dynamics has limited our ability to dissect plant–microbe communication. To address this gap, we sought to create a genetically encoded biosensor that couples ligand-induced protein dimerization with the production of a fluorescent reporter. Inteins are peptide regions that excise themselves from precursor proteins and ligate the flanking chains (exteins). When each half of a split intein is fused to one of two dimerizing proteins, ligand binding brings them into proximity, inducing intein splicing and ligation of flanking extein sequences (Kang et al. 2022). Similar to previous studies, we split the yeast vacuolar ATPase subunit 1 (VMA1) intein, creating a protein biosensor that produces eGFP upon protein dimerization after ligand binding (Figure 1A) (Mootz et al. 2003). Specifically, eGFP halves (i.e., non-functional N- and C-terminal GFP fragments) were fused to the intein halves, resulting in two fusion proteins: N-terminal GFP::N-terminal intein and C-terminal intein::C-terminal GFP (Figure 1A).

Boone, Brandon A. [Oak Ridge National Laboratory (↗
DOE OSTI2020

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗
DOE OSTI2021

Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide

RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)–GMP, RNA 3'-phosphate, and RNA 3 'pp 5 'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. In this work, we report a 2.7 Å crystal structure of Pyrococcus horikoshii RtcB in complex with a 6-mer 5'-OH DNA oligonucleotide HO A 1 pT 2 pG 3 pT 4 pC 5 pC 6 , which reveals enzymic contacts of Asn202 to the terminal 5'-OH nucleophile; Arg238 to the A1pT2 and T2pG3 phosphates; Arg190 and Gln194 to the T 2 pG 3 phosphate; and an Arg190 π-cation interaction with the G 3 nucleobase. The structural insights affirm functional studies of E. coli RtcB that implicated the conserved counterpart of Arg238 in engagement of the 5'-OH strand for ligation. The essential active site Cys98 that coordinates two manganese ions is oxidized to cysteine sulfonic acid in our structure, raising the prospect that RtcB activity might be sensitive to modulation during oxidative stress.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

In vitro selection of optimal DNA substrates for T4 RNA ligase

We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 RNA ligase. We find that the ensemble of selected sequences ligated about 10 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly, the majority of the selected sequences approximated a well-defined consensus sequence.

Harada, Kazuo↗
NASA NTRS1993

Isolation of new ribozymes from a large pool of random sequences

An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules. These ribozymes ligate two RNA molecules that are aligned on a template by catalyzing the attack of a 3'-hydroxyl on an adjacent 5'-triphosphate - a reaction similar to that employed by the familiar protein enzymes that synthesize RNA. The corresponding uncatalyzed reaction also yields a 3',5'-phosphodiester bond. In vitro evolution of the population of new ribozymes led to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate.

Bartel, David P.↗
NASA NTRS1999

Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

Kauffman, Stuart↗