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177Lu-PSMA-617 is a promising radiotheranostic agent for metastatic castration-resistant prostate cancer (mCRPC) patients that is composed of prostate-specific membrane antigen (PSMA) conjugated with 177Lu. PSMA-INER-56 is a molecule with PSMA-617 targeting activity and an albumin-binding motif and extends the blood retention time. PSMA-INER-56 is radiolabeled with indium-111 (111In) as a diagnostic agent and with lutetium-177 (177Lu) as a therapeutic agent. This study determines the efficacy of molecular targeted imaging and the preliminary therapeutic effect of 111In/177Lu-PSMA-INER-56 in PSMA expressing mice that bear a prostate tumor mice. The stability of 111In-PSMA-INER-56 and 177Lu-PSMA-INER-56 is evaluated in normal saline and human serum. Head-to-head comparisons between 177Lu-PSMA-INER-56 and 177Lu-PSMA-617 use NanoSPECT/CT molecular imaging to determine the distribution, targeting and anti-tumor efficacy in LNCaP tumor-bearing mice. The radiochemical purity of 111In-PSMA-INER-56 or 177Lu-PSMA-INER-56 is 99.09 ± 0.38 and 98.87 ± 0.73%, respectively. The in vitro stability for both radio-labeled peptides is more than 95% up to 96 h. The greatest uptake of 111In-PSMA-INER-56 or 177Lu-PSMA-INER-56 in the tumor occurs at 24 h. The uptake is 43.78 ± 6.55 and 22.08 ± 6.63%ID/g, respectively. The 177Lu-PSMA-INER-56 more effectively inhibits tumor growth (96.0%) than 177Lu-PSMA-617 (54.7%) 44 days post injection (p.i). PSMA-INER-56 that is labeled with 111In or 177Lu is demonstrated to be a potential radiotheranostic pair for PSMA-positive tumors. 177Lu-PSMA-INER-56 also exhibits better targeting than 177Lu-PSMA-617.

We investigate the gas-phase photochemistry of the enolone tautomer of acetylacetone (pentane-2,4-dione) following S2(ππ*) ← S0 excitation at λ = 266 and 248 nm, using three complementary time-resolved spectroscopic methods. Contrary to earlier reports, which claimed to study one-photon excitation of acetylacetone and found OH and CH3 as the only important gas-phase products, we detect 15 unique primary photoproducts and demonstrate that five of them, including OH and CH3, arise solely by multiphoton excitation. We assign the one-photon products to six photochemical channels and show that the most significant pathway is phototautomerization to the diketone form, which is likely an intermediate in several of the other product channels. Furthermore, we measure the equilibrium constant of the tautomerization of the enolone to diketone on S0 from 320 to 600 K and extract Δ H = 4.1 ± 0.3 kcal·mol-1 and Δ S = 6.8 ± 0.5 cal·mol-1·K-1 using a van't Hoff analysis. We correct the C-OH bond dissociation energy in acetylacetone, previously determined as 90 kcal·mol-1 by theory and experiment, to a new value of 121.7 kcal·mol-1. Our experiments and electronic structure calculations provide evidence that some of the product channels, including phototautomerization, occur on S0, while others likely occur on excited triplet surfaces. Although the large oscillator strength of the S2 ← S0 transition results from the (ππ*) excitation of the C═C-C═O backbone, similar to conjugated polyenes, the participation of triplets in the dissociation pathways of acetylacetone appears to have more in common with ketone photochemistry.

Three new monoterpenoid indole alkaloids, kopsiaofficines A–D (1–3), were isolated from the 95% EtOH extract of the aerial parts of Kopsia officinalis. Their structures were established on the basi...

The Arg–Gly–Asp (RGD) peptide shows a high affinity for αvβ3 integrin, which is overexpressed in new tumor blood vessels and many types of tumor cells. The radiolabeled RGD peptide has been studied for cancer imaging and radionuclide therapy. We have developed a long-term tumor-targeting peptide DOTA-EB-cRGDfK, which combines a DOTA chelator, a truncated Evans blue dye (EB), a modified linker, and cRGDfK peptide. The aim of this study was to evaluate the potential of indium-111(111In) radiolabeled DOTA-EB-cRGDfK in αvβ3 integrin-expressing tumors. The human glioblastoma cell line U-87 MG was used to determine the in vitro binding affinity of the radiolabeled peptide. The in vivo distribution of radiolabeled peptides in U-87 MG xenografts was investigated by biodistribution, nanoSPECT/CT, pharmacokinetic and excretion studies. The in vitro competition assay showed that 111In-DOTA-EB-cRGDfK had a significant binding affinity to U-87 MG cancer cells (IC50 = 71.7 nM). NanoSPECT/CT imaging showed 111In-DOTA-EB-cRGDfK has higher tumor uptake than control peptides (111In-DOTA-cRGDfK and 111In-DOTA-EB), and there is still a clear signal until 72 h after injection. The biodistribution results showed significant tumor accumulation (27.1 ± 2.7% ID/g) and the tumor to non-tumor ratio was 22.85 at 24 h after injection. In addition, the pharmacokinetics results indicated that the 111In-DOTA-EB-cRGDfK peptide has a long-term half-life (T1/2λz = 77.3 h) and that the calculated absorbed dose was safe for humans. We demonstrated that radiolabeled DOTA-EB-cRGDfK may be a promising agent for glioblastoma tumor imaging and has the potential as a theranostic radiopharmaceutical.

Selected vibronic bands of the B ← X laser-induced fluorescence (LIF) spectra of jet-cooled 2-pentoxy and 2-hexoxy, including the origin and CO-stretch bands, have been measured with rotational resolution and analyzed using (1) an effective Hamiltonian that comprises a rotational part and a spin-rotation (SR) part (the "isolated-states model") and (2) a recently developed Hamiltonian in which the nearly degenerate A and X states are treated together (the "coupled-states model") (see Liu, J., J. Chem. Phys. 2018, 148, 124112). The observed rotational and fine structures of the strongest vibronic bands have first been simulated using a genetic algorithm with the isolated-states model. The parameters for the simulation include rotational constants for both the X and B states, which can be calculated from the electronic structure theory, as well as the electronic SR constants of the X state and the transition dipole moments (TDMs), both of which are predicted based on their transferability in an "orbital-fixed coordinate system" using iso-propoxy as the reference molecule. Quantum chemistry calculations suggest that the lowest two electronic (X and A) states of secondary alkoxy radicals have small energy separations on the order of 100 cm-1 (see Part I of this series: J. Phys. Chem. A 2021, DOI: 10.1021/acs.jpca.0c10662). The electron configurations of these two nearly degenerate states have been determined by comparing the experimentally determined rotational constants and the TDMs to the ones predicted for the X and A states. The experimental LIF spectra were also simulated with the coupled-states model, in which the effective spin-orbit (SO) constants (aζed) and the SO-free separation between the A and the X states (ΔE0) have been determined. Molecular constants derived from fitting the rotational and fine structures of the experimental LIF spectra enabled unambiguous assignment of the observed vibronic bands to specific conformers of 2-pentoxy and 2-hexoxy as reported in Part I.

The stringent response, regulated by the bifunctional (p)ppGpp synthetase/hydrolase Rel in mycobacteria, is critical for long-term survival of the drug-tolerant dormant state of Mycobacterium tuberculosis. During amino acid starvation, MtRel senses a drop in amino acid concentration and synthesizes the messengers pppGpp and ppGpp, collectively called (p)ppGpp. Here, we investigate the role of the regulatory 'Aspartokinase, Chorismate mutase and TyrA' (ACT) domain in MtRel. Using NMR spectroscopy approaches, we report the high-resolution structure of dimeric MtRel ACT which selectively binds to valine out of all other branched-chain amino acids tested. A set of MtRel ACT mutants were generated to identify the residues required for maintaining the head-to-tail dimer. Through NMR titrations, we determined the crucial residues for binding of valine and show structural rearrangement of the MtRel ACT dimer in the presence of valine. This study suggests the direct involvement of amino acids in (p)ppGpp accumulation mediated by MtRel independent to interactions with stalled ribosomes. Database Structural data are available in the PDB database under the accession number 6LXG. Ministry of Education (MOE) We would like to thank the Singapore Ministry ofEducation Academic Research Fund Tier 1 (Rg137/15)for the funding to GG. BS thanks the Nanyang Tech-nological University, Singapore, for awarding her aPhD Scholarship during her studies.

Chemical proteomics methods have been used as effective tools to identify novel protein targets for small molecules. These methods have great potential to be applied as environmental toxicants to figure out their mode of action. However, these assays usually generate dozens of possible targets, making it challenging to validate the most important one. In this study, we have integrated the cellular thermal shift assay (CETSA), quantitative proteomics, metabolomics, computer-assisted docking, and target validation methods to uncover the protein targets of monoethylhexyl phthalate (MEHP). Using the mass spectrometry implementation of CETSA (MS-CETSA), we have identified 74 possible protein targets of MEHP. The Gene Ontology (GO) enrichment integration was further conducted for the target proteins, the cellular dysregulated proteins, and the metabolites, showing that cell cycle dysregulation could be one primary change due to the MEHP-induced toxicity. Flow cytometry analysis confirmed that hepatocytes were arrested at the G1 stage due to the treatment with MEHP. Subsequently, the potential protein targets were ranked by their binding energy calculated from the computer-assisted docking with MEHP. In summary, we have demonstrated the development of interactomics workflow to simplify the redundant information from multiomics data and identified novel cell cycle regulatory protein targets (CPEB4, ANAPC5, and SPOUT1) for MEHP. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Ministry of Health (MOH) Nanyang Technological University National Environmental Agency (NEA) National Research Foundation (NRF) This work is supported by the Singapore Ministry of Education Academic Research Fund Tier 1 (04MNP000567C120), the NTU-Harvard SusNano (M4082370.030), the National Environment Agency-Singapore (04SBS000714N025), and the Singapore Ministry of Health’s National Medical Research Council under its Clinician-Scientist Individual Research Grant (CS-IRG) (MOH-000141) and the Open Fund-Individual Research Grant (OFIRG/0076/2018) to M.F. and A-STAR core fundings and NRF-SiS grant by National Research Foundation to R.M.S.

[Image: see text] We describe a cysteine-rich, membrane-penetrating, joint-targeting, and remarkably stable peptide, EgK5, that modulates voltage-gated K(V)1.3 potassium channels in T lymphocytes by a distinctive mechanism. EgK5 enters plasma membranes and binds to K(V)1.3, causing current run-down by a phosphatidylinositol 4,5-bisphosphate-dependent mechanism. EgK5 exhibits selectivity for K(V)1.3 over other channels, receptors, transporters, and enzymes. EgK5 suppresses antigen-triggered proliferation of effector memory T cells, a subset enriched among pathogenic autoreactive T cells in autoimmune disease. PET-CT imaging with (18)F-labeled EgK5 shows accumulation of the peptide in large and small joints of rodents. In keeping with its arthrotropism, EgK5 treats disease in a rat model of rheumatoid arthritis. It was also effective in treating disease in a rat model of atopic dermatitis. No signs of toxicity are observed at 10–100 times the in vivo dose. EgK5 shows promise for clinical development as a therapeutic for autoimmune diseases.

Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) contains an N-terminal RNA helicase with both nucleotide triphosphatase and RNA triphosphatase activities, and a C-terminal cysteine protease that is responsible for polyprotein processing. Both N-terminal RNA helicase and C-terminal cysteine protease are connected through a flexible linker. Although the structure of the C-terminal cysteine protease has been solved, the structure and the conformational arrangement of full-length nsP2 remains elusive. Here, we determined the crystal structure of the helicase part of the CHIKV nsP2 (nsP2h) bound to the conserved 3′-end of the genomic RNA and the nucleotide analogue ADP-AlF4. The structure of this ternary complex revealed the molecular basis for viral RNA recognition and ATP hydrolysis by the nsP2h. Unique hydrophobic protein–RNA interactions play essential roles in viral RNA replication. We also determined the solution structure of full-length nsP2 using small-angle X-ray scattering (SAXS). The solution architecture of the nsP2 was modeled using the available high-resolution structures and program CORAL (complexes with random loops). The CORAL model revealed that nsP2 is partially unfolded and the N-terminal protease domain is arranged near the N-terminal domain of the helicase domain. These findings expand our knowledge of CHIKV and related alphaviruses and might also have broad implications for antiviral and vaccine developments against pathogenic alphaviruses.

Flavivirus is a genus of the Flaviviridae family which includes significant emerging and re-emerging human disease-causing arboviruses such as dengue and Zika viruses. Flaviviral non-structural protein 3 (NS3) protease-helicase plays essential roles in viral replication and is an attractive antiviral target. A construct which connects the cytoplasmic cofactor region of NS2B and NS3 protease with an artificial glycine-rich flexible linker has been widely used for structural, biochemical and drug-screening studies. The effect of this linker on the dynamics and enzymatic activity of the protease has been studied by several biochemical and NMR methods but the findings remained inconclusive. Here, we designed and carried out a comparative study of constructs of NS2B cofactor joined to the full length DENV4 NS3 in three different ways, namely bNS2B47NS3 (bivalent), eNS2B47NS3(enzymatically cleavable) and gNS2B47NS3 (glycine-rich linker). We report the crystal structures of linked and unlinked NS2B47-NS3 constructs in their free state and in complex with bovine pancreatic trypsin inhibitor (BPTI). These structures demonstrate that the NS2B cofactor predominantly adopts a closed conformation in complex with full-length NS3. The glycine-rich linker between NS2B and NS3 may promote the open conformation which interferes with protease activity. This negative impact on the enzyme structure and function is restricted to the protease activity as the ATPase activity is not affected in vitro. Ministry of Education (MOE) Nanyang Technological University National Research Foundation (NRF) This work was supported by (1) the start-up grant to DL lab from Lee Kong Chian School of Medicine, Nanyang Technological University, (2) Ministry of Education grant MOE2016-T2-2-097 to DL lab, (3) National Medical Research Council grant NMRC/CBRG/0103/2016 to SV lab, (4) National Research Foundation grant NRF2016NRFCRP001-063. Ms. Wint Wint Phoo was supported by Nanyang Research Scholarship, Nanyang Technological University.

Formation of the key general radical chain carriers, ˙OH and HO2˙, during pulsed-photolytic ˙Cl-initiated oxidation of tetrahydropyran and cyclohexane are measured with time-resolved infrared absorption in a temperature-controlled Herriott multipass cell in the temperature range of 500–750 K at 20 Torr. The experiments show two distinct timescales for HO2˙ and ˙OH formation in the oxidation of both fuels. Analysis of the timescales reveals striking differences in behavior between the two fuels. In both cyclohexane and tetrahydropyran oxidation, a faster timescale is strongly related to the “well-skipping” (˙R + O2 → alkene + HO2˙ or cyclic ether + ˙OH) mechanism and is expected to have, at most, a weak temperature dependence. Indeed, the fast HO2˙ formation timescale is nearly temperature independent both for cyclohexyl + O2 and for tetrahydropyranyl + O2 below 700 K. A slower HO2˙ formation timescale in cyclohexane oxidation is shown to be linked to the sequential ˙R + O2 → ROO˙ → alkene + HO2˙ pathway, and displays a strong temperature dependence mainly from the final step (with energy barrier ∼32.5 kcal mol−1). In contrast, the slower HO2˙ formation timescale in tetrahydropyran oxidation is surprisingly temperature insensitive across all measured temperatures. Although the ˙OH formation timescales in tetrahydropyran oxidation show a temperature dependence similar to the cyclohexane oxidation, the temperature dependence of ˙OH yield is opposite in both cases. This significant difference of HO2˙ formation kinetics and ˙OH formation yield for the tetrahydropyran oxidation can arise from contributions related to ring-opening pathways in the tetrahydropyranyl + O2 system that compete with the typical ˙R + O2 reaction scheme. This comparison of two similar fuels demonstrates the consequences of differing chemical mechanisms on ˙OH and HO2˙ formation and shows that they can be highlighted by analysis of the eigenvalues of a system of simplified kinetic equations for the alkylperoxy-centered ˙R + O2 reaction pathways. We suggest that such analysis can be more generally applied to complex or poorly known oxidation systems.

Asparaginyl endopeptidases (AEPs) are cysteine proteases which break Asx (Asn/Asp)–Xaa bonds in acidic conditions. Despite sharing a conserved overall structure with AEPs, certain plant enzymes such as butelase 1 act as a peptide asparaginyl ligase (PAL) and catalyze Asx–Xaa bond formation in near-neutral conditions. PALs also serve as macrocyclases in the biosynthesis of cyclic peptides. Here, we address the question of how a PAL can function as a ligase rather than a protease. Based on sequence homology of butelase 1, we identified AEPs and PALs from the cyclic peptide-producing plants Viola yedoensis ( Vy ) and Viola canadensis ( Vc ) of the Violaceae family. Using a crystal structure of a PAL obtained at 2.4-Å resolution coupled to mutagenesis studies, we discovered ligase-activity determinants flanking the S1 site, namely LAD1 and LAD2 located around the S2 and S1′ sites, respectively, which modulate ligase activity by controlling the accessibility of water or amine nucleophile to the S -ester intermediate. Recombinantly expressed Vy PAL1–3, predicted to be PALs, were confirmed to be ligases by functional studies. In addition, mutagenesis studies on Vy PAL1–3, Vy AEP1, and Vc AEP supported our prediction that LAD1 and LAD2 are important for ligase activity. In particular, mutagenesis targeting LAD2 selectively enhanced the ligase activity of Vy PAL3 and converted the protease Vc AEP into a ligase. The definition of structural determinants required for ligation activity of the asparaginyl ligases presented here will facilitate genomic identification of PALs and engineering of AEPs into PALs.

Free fatty acid receptor G protein-coupled receptor 120 (GPR120) is highly expressed in macrophages and was reported to inhibit lipopolysaccharide (LPS)-stimulated cytokine expression. Under inflammation, macrophages exhibit striking functional changes, but changes in GPR120 expression and signaling are not known. In this study, the effects of LPS treatment on macrophage GPR120 expression and activation were investigated. The results showed that LPS inhibited GPR120 expression in mouse macrophage cell line Ana-1 cells. Moreover, LPS treatment inhibited GPR120 expression in mouse alveolar macrophages both in vitro and in vivo. The inhibitory effect of LPS on GPR120 expression was blocked by Toll-like receptor 4 (TLR4) inhibitor TAK242 and p38 mitogen-activated protein kinase inhibitor LY222820, but not by ERK1/2 inhibitor U0126 and c-Jun N-terminal kinase inhibitor SP600125. LPS-induced inhibition of GPR120 expression was not attenuated by GPR120 agonists TUG891 and GW9508. TUG891 inhibited the phagocytosis of alveolar macrophages, and LPS treatment counteracted the effects of TUG891 on phagocytosis. These results indicate that pretreatment with LPS inhibits GPR120 expression and activation in macrophages. It is suggested that LPS-induced inhibition of GPR120 expression is a reaction enhancing the LPS-induced pro-inflammatory response of macrophages.

Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3′-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF 4 . Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general.

Summary Here we report a molecular docking-based approach to identify small molecules that can target the β-catenin (β-cat)-TCF4 protein-protein interaction (PPI), a key effector complex for nuclear Wnt signaling activity. Specifically, we developed and optimized a computational model of β-cat using publicly available β-cat protein crystal structures, and existing β-cat-TCF4 interaction inhibitors as the training set. Using our computational model to an in silico screen predicted 27 compounds as good binders to β-cat, of which 3 were identified to be effective against a Wnt-responsive luciferase reporter. In vitro functional validation experiments revealed GB1874 as an inhibitor of the Wnt pathway that targets the β-cat-TCF4 PPI. GB1874 also affected the proliferation and stemness of Wnt-addicted colorectal cancer (CRC) cells in vitro. Encouragingly, GB1874 inhibited the growth of CRC tumor xenografts in vivo, thus demonstrating its potential for further development into therapeutics against Wnt-associated cancer indications., Graphical abstract, Highlights • A computational docking model for β-catenin was developed and optimized. • The model was trained using protein crystal structures and known inhibitor compounds. • Compound GB1874 was identified by in silico screening and functionally validated. • GB1874 inhibited colon cancer growth in vitro and in vivo by blocking Wnt activity., Pharmacology; Biochemistry; Structural biology; Cancer; Omics

Oxidation thermodynamics of silicon carbide (SiC)ceramic was studied by means of HSC Chemistry code, and the weight change, morphology and phase of oxidation products were analyzed by thermogravimetric analysis(TG), scanning electron microscopy(SEM ) and X-ray diffraction (XRD). The results showed that SiC ceramic could be oxidized to silicon dioxide(SiO2) with release of small molecular gases under oxidizing atmosphere at 800°C, and the formed SiO2 film with appropriate fluidity and low oxygen diffusion coefficient could prevent the spread of oxygen with the oxidation temperature increasing up to 1200°C, which favored the anti-oxidation of SiC ceramic matrix composite.

The objective of this study was to evaluate radiolabeled DOTA-SP90 as a radiotracer for breast cancer. The in vitro competition assay showed that radiolabeled DOTA-SP90 had significant binding affinity to BT-483 cancer cells. Biodistribution, nanoSPECT/CT and nanoPET/CT imaging results indicated that radiolabeled DOTA-SP90 can accumulate in tumors. In addition, radiolabeled DOTA-SP90 peptides can also detect metastatic tumors. Therefore, radiolabeled SP90 peptide may provide the potential capability as diagnostic agent for breast cancer patients.

Methanol is a benchmark for understanding tropospheric oxidation, but is underpredicted by up to 100% in atmospheric models. Recent work has suggested this discrepancy can be reconciled by the rapid reaction of hydroxyl and methylperoxy radicals with a methanol branching fraction of 30%. However, for fractions below 15%, methanol underprediction is exacerbated. Theoretical investigations of this reaction are challenging because of intersystem crossing between singlet and triplet surfaces – ∼45% of reaction products are obtained via intersystem crossing of a pre-product complex – which demands experimental determinations of product branching. Here we report direct measurements of methanol from this reaction. A branching fraction below 15% is established, consequently highlighting a large gap in the understanding of global methanol sources. These results support the recent high-level theoretical work and substantially reduce its uncertainties., The reaction of hydroxyl and methylperoxy radicals has recently been suggested as the source of missing methanol in the remote troposphere. Here, the authors present direct experimental measurements demonstrating the reaction leads to further underprediction of modelled methanol.

The reactions of Criegee intermediates with NO2 have been proposed as a potentially significant source of the important nighttime oxidant NO3, particularly in urban environments where concentrations of ozone, alkenes and NOx are high. However, previous efforts to characterize the yield of NO3 from these reactions have been inconclusive, with many studies failing to detect NO3. In the present work, the reactions of formaldehyde oxide (CH2OO) and acetaldehyde oxide (CH3CHOO) with NO2 are revisited to further explore the product formation over a pressure range of 4–40 Torr. NO3 is not observed; however, temporally resolved and [NO2]-dependent signal is observed at the mass of the Criegee–NO2 adduct for both formaldehyde- and acetaldehyde-oxide systems, and the structure of this adduct is explored through ab initio calculations. The atmospheric implications of the title reaction are investigated through global modelling.

Equilibrium compositions of chemical vapor deposition progress for silicon carbide (CVD-SiC) coatings with MTS/H2 mixture system were calculated by means of HSC Chemistry5.0 code, and influences of the reaction temperature (T), the system pressure (P) and the composition of raw materials (molar ratio of H2 to SiCH3Cl3, β) were investigated. Thermodynamic analysis showed that the value of nC /nSiC in reaction product decreased to a minimum and then increased with the increase of the reaction temperature between 700-1600°C, which meant an optimal reaction temperature existed theoretically for CVD-SiC coatings with highest purity. Furthermore, CVD-SiC coatings with high purity were obtained by experiments under the reaction pressure of 10kPa, H2/SiCH3Cl3 value of 10 and reacton temperature of 1100°C, which was in accordance with the theoretical prediction.

SiC continuous fiber reinforced SiC ceramic matrix composites (SiCf/SiC CMCs) and SiC fiber reinforced SiC micro ceramic matrix composites (SiCf/SiC micro-CMCs) were prepared through polymer impregnation pyrolysis (PIP) progress, then the structures, mechanical properties and forming mechanisms of SiCf/SiC CMCs were investigated. Results showed that volume shrinkage of SiC matrix occurred, and pyrolysates with bamboo-like layered structure were attached to the surface of SiC multifilament gradually. Furthermore, the mechanical properties of SiCf/SiC micro-CMCs were consistent with SiCf/SiC CMCs, so the PIP process parameters for the preparation of SiCf/SiC CMC might be optimized primarily through SiCf/SiC micro-CMCs, which could enhance the design and preparation efficiency of SiCf/SiC CMCs obviously.Key word: polymer impregnation pyrolysis progress, micro ceramic matrix composites, forming mechanism

The pyrolysis kinetic behaviors and reaction mechanism of polycarbosilane (PCS) were characterized by means of XRD, SEM and on-line TG-DSC-FTIR-MS coupling technique, which showed that the pyrolysis process accorded with the F2 integral model (300-600°C), and the values of apparent activation energy (Ea) and pre-exponential factor (A) were 56.10KJ/mol and 10.84, respectively. During the pyrolysis process, PCS was converted into amorphous inorganic solid from organic polymer with breakage and rearrangement of chemical bonds, then to well-defined crystal structure of good thermal stability. Furthermore, the weight loss occurred mainly among 300°C and 800°C with CH4, (CH3)4Si,(CH3)3SiH,(CH3)2SiH2and other silane gases releasing from pyrolysis product leading to the conversion from organic polymers to inorganic ceramic. The pyrolysis product was converted into β-SiC crystal completely at 1400°C, and the crystallization of α-SiC phase occurred after 1550°C which might influence the stability of SiC matrix. Key words:polycarbosilane, organic precursor, pyrolysis kinetic behavior

Reactive oxygen species (ROS) induce different cellular stress responses but can also mediate cellular signaling. Augmented levels of ROS are associated with aging, cancer as well as various metabolic and neurological disorders. ROS can also affect the efficacy and adverse effects of drugs. Although proteins are key mediators of most ROS effects, direct studies of ROS-modulated-protein function in the cellular context are very challenging. Therefore the understanding of specific roles of different proteins in cellular ROS responses is still relatively rudimentary. In the present work we show that Mass Spectrometry-Cellular Thermal Shift Assay (MS-CETSA) can directly monitor ROS and redox modulations of protein structure at the proteome level. By altering ROS levels in cultured human hepatocellular carcinoma cell lysates and intact cells, we detected CETSA responses in many proteins known to be redox sensitive, and also revealed novel candidate ROS sensitive proteins. Studies in intact cells treated with hydrogen peroxide and sulfasalazine, a ROS modulating drug, identified not only proteins that are directly modified, but also proteins reporting on downstream cellular effects. Comprehensive changes are seen on rate-limiting proteins regulating key cellular processes, including known redox control systems, protein degradation, epigenetic control and protein translational processes. Interestingly, concerted shifts on ATP-binding proteins revealed redox-induced modulation of ATP levels, which likely control many cellular processes. Collectively, these studies establish CETSA as a novel method for cellular studies of redox modulations of proteins, which implicated in a wide range of processes and for the discovery of CETSA-based biomarkers reporting on the efficacy as well as adverse effects of drugs., Graphical abstract Image 1, Highlights • Redox-mediated protein modulations can be monitored by MS-CETSA. • CETSA signals reflect disulfide reorganization, covalent adduction, redox-sensitive metal level changes, and complex formation. • In-cell redox modulation by SSA, H2O2 or oligomycin affects cellular ATP levels. • In-cell CETSA identifies rate-limiting proteins controlling redox downstream effects.

The pyrolysis dynamic process of ZrB2 organic precursor,soluble in benzene homologues with polycarbosilane, was characterized by means of on-line TG-DSC-FTIR-MS coupling technique. The conversion mechanism of ZrB2 ceramic was investigated based on EDS, SEM and XRD. The results show that methylamine, methane, acetone and propene were given off before heat treatment at 1000°C, and the pyrolysis product of ZrB2 precursor existed in the form of ZrO2, B2O3 and amorphous carbon. ZrB2 crystals are obtained completely by the carbothermal reduction process with the release of carbon dioxide at 1500°C. Key words:ZrB2 organic precursor, pyrolysis kinetic behavior, carbothermal reduction process.

The pyrolysis ceramic dynamic process of ZrC ceramic precursor was characterized by means of on-line TG-DSC-FTIR-MS coupling technique, and the conversion mechanism of ZrC ceramic was investigated based on XRD, SEM, TEM and XRF. ZrC ceramic could be obtained at 1400°C lower than theoretic temperature when Zirconium element is reduced by carbon from ZrO2. The results showed that ZrC ceramic precursor presented storage stability and excellent solubility in toluene. Ethanol, carbon dioxide, acetone and tetrahydrofuran (THF) were given off before heat treatment at 1100°C, and the pyrolysis product held in the form of ZrO2 and amorphous carbon. ZrC crystals were gradually formed when heated up to 1200°C and obtained completely at 1400°C. This ZrC ceramic precursor provides promising candidate for oxidation resistance and ablation resistance ZrC-SiC ceramic matrix composites.

SiC fiber reinforced SiC matrix (SiCf-SiC) composites with and without pyrolytic carbon interphase were prepared by polymer impregnation pyrolysis (PIP) progress. The effect of pyrolytic carbon interphase on the fracture behavior and mechanical properties of SiCf/SiC composites was studied. The results show that pyrolytic carbon interphase weakened the bonding between the matrix and the fibers. The mechanical properties of SiCf-SiC composites with carbon coating were improved effectively via fiber debonding and pulling-out from matrix under external loads. The flexural strength and fracture toughness of the above composites reached up to 498.52MPa and 24.09MPa•m1/2, respectively.

The β -substituted halogen and hydroxy alkoxy radicals are important intermediates in the atmospheric chemistry of alkenes while hydroxy substituted alkoxy radicals are key intermediates in the combustion of alcohols. The FCH 2 CH 2 O radical is an example of these radicals. Jet-cooled excitation spectra of the B ∼ - X ∼ transition of FCH 2 CH 2 O were obtained using laser induced fluorescence and were assigned to two different conformers of FCH 2 CH 2 O with G(±60°) and T(180°) orientations of the OCCF dihedral angle. Rotational and vibronic analyses were performed to obtain rotational constants for both the X ∼ and B ∼ states and origin and vibrational frequencies of the B ∼ state.

Chikungunya virus (CHIKV) is an important arboviral infectious agent in tropical and subtropical regions, often causing persistent and debilitating disease. The viral enzyme non-structural protein 4 (nsP4), as RNA-dependent RNA polymerase (RdRP), catalyzes the formation of negative-sense, genomic and subgenomic viral RNAs. Here we report a truncated nsP4 construct that is soluble, stable and purified recombinantly from Escherichia coli. Sequence analyses and homology modelling indicate that all necessary RdRP elements are included. Hydrogen/deuterium exchange with mass spectrometry was used to analyze solvent accessibility and flexibility of subdomains. Fluorophore-conjugated RNA ligands were designed and screened by using fluorescence anisotropy to select a suitable substrate for RdRP assays. Assay trials revealed that nsP4 core domain is conditionally active upon choice of detergent species, and carries out both primed extension and terminal adenylyltransferase activities. The polymerization assay can be further developed to screen for antiviral compounds in vitro. MOE (Min. of Education, S’pore) Accepted version

Alkyl nitrites have been used previously to produce alkoxy radicals, which are important intermediates in the oxidation of alkanes in atmospheric and combustion processes. Substituted alkoxy radicals, particulary hydroxyalkoxy radicals, are also important intermediates in the atmospheric oxidation of alkenes and combustion of alcohols. In order to produce substituted alkoxy radicals we have photolyzed at 351 nm substituted alkyl nitrites, XCH(2)CH(2)ONO (X = F, Cl, Br, OH). Using laser-induced fluorescence only in the case of X = F do we observe the spectrum of substituted alkoxy radical, XCH(2)CH(2)O; but we always observe the electronic transitions of formaldehyde, HCHO, and vinoxy radical, CH(2)CHO. HCHO can be formed by the dissociation of XCH(2)CH(2)O in its ground state as the barrier to C-C bond dissociation is less than the photon energy remaining after O-NO bond breakage. However, the barrier along the reaction path directly leading from XCH(2)CH(2)O to CH(2)CHO + HX is much higher than the available energy remaining after O-NO bond breakage. A roaming mechanism, involving a frustrated dissociation of X followed by HX extraction, might explain the apparent paradox. Under the conditions of our observations vinoxy retains considerable vibrational excitation but the observed rotational temperatures of both HCHO and CH(2)CHO are ≲7 K.

The nucleotide messenger cyclic di-GMP (c-di-GMP) plays a central role in the regulation of motility, virulence, and biofilm formation in many pathogenic bacteria. EAL domain-containing phosphodiesterases are the major signaling proteins responsible for the degradation of c-di-GMP and maintenance of its cellular level. We determined the crystal structure of a single mutant (R286W) of the response regulator RocR fromPseudomonas aeruginosato show that RocR exhibits a highly unusual tetrameric structure arranged around a single dyad, with the four subunits adopting two distinctly different conformations. Subunits A and B adopt a conformation with the REC domain located above the c-di-GMP binding pocket, whereas subunits C and D adopt an open conformation with the REC domain swung to the side of the EAL domain. Remarkably, the access to the substrate-binding pockets of the EAL domains of the open subunits C and D are blocked intransby the REC domains of subunits A and B, indicating that only two of the four active sites are engaged in the degradation of c-di-GMP. In conjunction with biochemical and biophysical data, we propose that the structural changes within the REC domains triggered by the phosphorylation are transmitted to the EAL domain active sites through a pathway that traverses the dimerization interfaces composed of a conserved regulatory loop and the neighboring motifs. This exquisite mechanism reinforces the crucial role of the regulatory loop and suggests that similar regulatory mechanisms may be operational in many EAL domain proteins, considering the preservation of the dimerization interface and the spatial arrangement of the regulatory domains.

Changes in actual efficiency of PS II photochemistry, non-photochemical quenching (NPQ), content of xanthophylls and kinetics of de-epoxidation were studied in ABA-fed and non-ABA-fed leaves of rice and cabbage under NaCl stress. Salt stress induced more progressive decrease in actual efficiency of PS II photochemistry (ФPS II), higher reduction state of PS II, and a small significant increase in NPQ in NaCl-sensitive rice plants as compared with NaCl-tolerant cabbage plants, whereas exogenously supplied ABA alleviated the decrease in actual efficiency of PS II photochemistry (ФPS II), induced a lower reduction state of PS II, and caused higher capacity of NPQ in ABA-fed plants than in non-ABA-fed plants. As a result, there were higher activities of photosynthetic electron transport, higher capacity of energy dissipation, and lower cumulation of excess light in cabbage than in rice plants, and in ABA-fed leaves than in non-ABA-fed leaves. The effect of ABA was more efficient in cabbage than in rice plants. Addition of exogenous ABA resulted in enhancement of the size of the xanthophyll cycle pool, promotion of de-epoxidation of the xanthophyll cycle components, and a rise in the level of NPQ by altering the kinetics of de-epoxidation of the xanthophyll cycle. Protection from photodamage appears to be achieved by coordinated contributions by exogenous ABA and xanthophyll cycle-mediated NPQ. This variety of photoprotective mechanisms may be essential for conferring photodamage tolerance under NaCl stress.

The A˜(2)E(″)←X˜(2)A2 (') spectrum of NO3 radical from 7550 cm(-1) to 9750 cm(-1) has been recorded and analyzed. Our spectrum differs from previously recorded spectra of this transition due to jet-cooling, which narrows the rotational contours and eliminates spectral interference from hot bands. Assignments of numerous vibronic features can be made based on both band contour and position including the previously unassigned 30 (1) band and several associated combination bands. We have analyzed our spectrum first with an independent anharmonic oscillator model and then by a quadratic Jahn-Teller vibronic coupling model. The fit achieved with the quadratic Jahn-Teller model is excellent, but the potential energy surface obtained with the fitted parameters is in only qualitative agreement with one obtained from ab initio calculations.

Fluorescence excitation spectra for transition A 1Au–X 1Ag of trans-glyoxal in a supersonic jet were recorded with laser excitation in a wavelength region near 395 nm. With resolution 0.04 cm−1, most lines in these spectra are resolved and are assigned rotationally; of six bands assigned, three have c-type rotational structure, and another three have types a/b hybrid, a and b. Fluorescence decays with quantum beats, resulting from coherent excitation of S1 and T1 states, are observed for most rotational levels in this region. In spectra transformed to the frequency domain for these decays, the widths are larger than those obtained at low excitation energy. The widths from nonzero frequency lines, reflecting mostly the triplet character, indicate that the triplet state is dissociating. Fluorescence spectra of fragment HCO confirm that the dissociation channel correlated to the triplet surface of glyoxal involves formation of radical products. From an abrupt decrease of lifetime of the triplet state and on...

The goal of this study was to relate conformational changes in the N-terminal domain of chicken troponin I (TnI) to Ca2+ activation of the actin–myosin interaction. The two cysteine residues in this region (Cys48 and Cys64) were labeled with two sulfhydryl-reactive pyrene-containing fluorophores [N-(1-pyrene)maleimide, and N-(1-pyrene)iodoacetamide]. The labeled TnI showed a typical fluorescence spectrum: two sharp peaks of monomer fluorescence and a broad peak of excimer fluorescence arising from the formation of an excited dimer (excimer). Results obtained show that forming a binary complex of labeled TnI with skeletal TnC (sTnC) in the absence of Ca2+ decreases the excimer fluorescence, indicating a separation of the two residues. This reduction in excimer fluorescence does not occur when labeled TnI is complexed with cardiac TnC (cTnC). The latter causes only partial activation of the Ca2+-dependent myofibrillar ATPase. The binding of Ca2+ to the two N-terminal sites of sTnC causes a significant decrease in excimer fluorescence and an increase in monomer fluorescence in complexes of labeled TnI with skeletal TnC or TnC/TnT, while Ca2+ binding to site II of cTnC only causes an increase in monomer fluorescence but no change in excimer fluorescence. Thus a conformational change in the N-terminal region of TnI may be necessary for full activation of muscle contraction.

The NS2B-NS3 viral protease is an attractive drug target against Zika virus (ZIKV) due to its importance in viral replication and maturation. Here we report the crystal structure of protease in complex with a dipeptide inhibitor, Acyl-KR-aldehyde (compound 1). The aldehyde moiety forms a covalent bond with the catalytic Ser135 of NS3. The Arg and Lys residues in the inhibitor occupy the S1 and S2 sites of the protease, respectively. Nuclear magnetic resonance studies demonstrate that the complex is in the closed conformation in solution. The chemical environment of residues surrounding the active site is sensitive to the bound inhibitor as demonstrated by the comparison with two other non-covalent dipeptides, Acyl-K-Agmatine (compound 2) and Acyl-KR-COOH (compound 3). Removing the aldehyde moiety in 1 converts the binding mode from a slow to a fast exchange regime. The structural dynamics information obtained in this study will guide future drug discovery against ZIKV and other flaviviruses.

Cell-surface proteins are central for the interaction of cells with their surroundings and are also associated with numerous diseases. These molecules are exposed to mechanical forces, but the exact relation between force and the functions and pathologies associated with cell-surface proteins is unclear. An important cell-surface protein is CD4, the primary receptor of HIV-1. Here we show that mechanical force activates conformational and chemical changes on CD4 that may be important during viral attachment. We have used single-molecule force spectroscopy and analysis on HIV-1 infectivity to demonstrate that the mechanical extension of CD4 occurs in a time-dependent manner and correlates with HIV-1 infectivity. We show that Ibalizumab, a monoclonal antibody that blocks HIV-1, prevents the mechanical extension of CD4 domains 1 and 2. Furthermore, we demonstrate that thiol/disulfide exchange in CD4 requires force for exposure of cryptic disulfide bonds. This mechanical perspective provides unprecedented information that can change our understanding on how viruses interact with their hosts.

Bacteria can adapt to different biotic and abiotic environments by changing their life style, switching between sessile or motile, free-living or community-bound, virulent or dormant states. Each bacterium also faces the challenges of maintaining a protective barrier while growing, replicating and responding to environmental changes. Governing these processes are enzymes involved in signalling and cell-wall biogenesis, which are the subjects of this thesis. DOCTOR OF PHILOSOPHY (SBS)

Radiolabeled annexin V (ANV) has been widely used for imaging cell apoptosis. Recently, a novel ANV-Kunitz-type protease inhibitor fusion protein, ANV-6L15, was found to be a promising probe for improved apoptosis detection based on its higher affinity to phosphatidylserine (PS) compared to native ANV. The present paper investigates the feasibility of apoptosis detection using radioiodinated ANV-6L15. Native ANV and ANV-6L15 were labeled with iodine-123 and iodine-125 using Iodogen method. The binding between the radioiodinated proteins and erythrocyte ghosts or chemical-induced apoptotic cells was examined. ANV-6L15 can be radioiodinated with high yield (40%−60%) and excellent radiochemical purity (>95%).123I-ANV-6L15 exhibited a higher binding ratio to erythrocyte ghosts and apoptotic cells compared to123I-ANV. The biodistribution of123I-ANV-6L15 in mice was also characterized.123I-ANV-6L15 was rapidly cleared from the blood. High uptake in the liver and the kidneys may limit the evaluation of apoptosis in abdominal regions. Our data suggest that radiolabled ANV-6L15 may be a better scintigraphic tracer than native ANV for apoptosis detection.

The dynamics of photodissociation of glyoxal (HOC-COH) near the dissociation threshold on the triplet manifold are studied through measurement of distributions of nascent fragment HCO in various internal states. Three rotational levels 1(01) (*), 4(13) (*), and 3(21) (*)+3(22) (*) of vibrational state U (excitation wavelength approximately 394.4 nm, origin at 25,331.865 cm(-1)) of glyoxal in state A (1)A(u) and two other vibrational states at excitation wavelengths 390.33 and 382.65 nm are selected to produce fragment HCO. By means of fluorescence in the transition B (2)A(')-X (2)A(') of HCO, we determined the relative populations of internal states of that fragment. Rotational states of product HCO up to N=26 and K=2 are populated, and bimodal distributions of these rotational states are observed for the photolysis wavelengths used in this work. The high rotational part of the distribution with average energy near values calculated on the basis of the statistical model-phase-space theory is assigned to arise from glyoxal on its S(0) surface, and the low rotational part from the T(1) surface with an exit barrier. After photolysis near the threshold region on the triplet surface, HCO arising from the T(1) state appears to be a major component of products because these rotational levels 1(01) (*), 4(13) (*), and 3(2) (*) of U state selected are gateway states with an enhanced rate of intersystem crossing.

Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) reduces UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP+ in two crystal forms to resolutions of 2.2 and 2.1 Å, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP+ stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N-acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival. Published version

The jet-cooled Ã-X̃ near IR origin band spectra of the G(1)G(2)G(3) conformer of four β-hydroxyethylperoxy isotopologues, β-HEP (HOCH(2)CH(2)OO), β-DHEP (DOCH(2)CH(2)OO), β-HEP-d(4) (HOCD(2)CD(2)OO), and β-DHEP-d(4) (DOCD(2)CD(2)OO), have been recorded by a cavity ringdown spectrometer with a laser source linewidth of ~70 MHz. The spectra of all four isotopologues have been analyzed and successfully simulated with an evolutionary algorithm, confirming the cyclic structure of the molecule responsible for the observed origin band. The analysis also provides experimental à and X̃ state rotational constants and the orientation of the transition dipole moment in the inertial axis system; these quantities are compared to results from electronic structure calculations. The observed, broad linewidth (Δν2 GHz) is attributed to a shortened lifetime of the à state associated with dynamics along the reaction path for hydrogen transfer from the OH to OO group.

Rotationally resolved laser induced fluorescence and stimulated emission pumping Ã(2)A(1)-X̃(2)E spectra, along with pure rotational spectra in the 153-263 GHz region within the E(3/2) component of the ground state in asymmetrically deuterated methoxy radicals CH(2)DO and CHD(2)O have been observed. The combined data set allows for the direct measurement with high precision of the energy separation between the E(1/2) and E(3/2) components of the ground state and the energy separation between the parity stacks in the E(3/2) component of the ground state. The experimentally observed frequencies in both isotopologues are fit to an effective rotational Hamiltonian accounting for rotational and spin-rotational effects arising in a near-prolate asymmetric top molecule with dynamic Jahn-Teller distortion. Isotopic dependencies for the molecular parameters have been successfully implemented to aid the analysis of these very complex spectra. The analysis of the first and second order contributions to the effective values of molecular parameters has been extended to elucidate the physical significance of resulting molecular parameters. Comparisons of measured parameters, e.g., spin-orbit coupling, rotational and spin-rotation constants, are made among the 5 methoxy isotopologues for which data is now available. Comparisons of experimental results, including the derived geometric structure at both the C(3v) conical intersection and at the Jahn-Teller distorted minima, are made with quantum chemistry calculations.

New experimental data have been obtained for the methoxy radical by observing at high-resolution laser-induced fluorescence (LIF) and stimulated emission pumping (SEP) transitions between the X (2)E and lowest excited A (2)A(1) state. The SEP transitions were from the A state (pumped from the X (2)E(3/2) spin-orbit component) to the X (2)E(1/2) spin-orbit component. These data for the first time directly connect with high precision the spin-orbit components of the X (2)E ground state of CH(3)O. Surprisingly these new SEP observations are inconsistent with predictions of the X state structure based on long-standing analyses primarily based on the microwave spectra of ground state CH(3)O. It is found that all the experimental data can be understood consistently when the previously accepted value of the spin-orbit coupling constant is adjusted and the reflection parity assignments in the X state are reversed. The latter action changes the sign of a number of reflection-parity-dependent parameters in the X state. The ramifications of the changes and the physical interpretation of the resulting parameters are discussed in some detail.