Characterization of structure of peptidyl-tRNA hydrolase from Enterococcus faecium and its inhibition by a pyrrolinone compound.

In bacteria, peptidyl-tRNA hydrolase (Pth, E.C. 3.1.1.29) is a ubiquitous and essential enzyme for preventing the accumulation of peptidyl-tRNA and sequestration of tRNA. Pth is an esterase that cleaves the ester bond between peptide and tRNA. Here, we present the crystal structure of Pth from Enterococcus faecium (EfPth) at a resolution of 1.92 Å. The two molecules in the asymmetric unit differ in the orientation of sidechain of N66, a conserved residue of the catalytic site. Enzymatic hydrolysis of substrate α-N-BODIPY-lysyl-tRNALys (BLT) by EfPth was characterized by Michaelis-Menten parameters KM 163.5 nM and Vmax 1.9 nM/s. Compounds having pyrrolinone scaffold were tested for inhibition of Pth and one compound, 1040-C, was found to have IC50 of 180 nM. Antimicrobial activity profiling was done for 1040-C. It exhibited equipotent activity against drug-susceptible and resistant S. aureus (MRSA and VRSA) and Enterococcus (VSE and VRE) with MICs 2-8 µg/mL. 1040-C synergized with gentamicin and the combination was effective against the gentamicin resistant S. aureus strain NRS-119. 1040-C was found to reduce biofilm mass of S. aureus to an extent similar to Vancomycin. In a murine model of infection, 1040-C was able to reduce bacterial load to an extent comparable to Vancomycin.

Membrane-targeting, ultrashort lipopeptide acts as an antibiotic adjuvant and sensitizes MDR gram-negative pathogens toward narrow-spectrum antibiotics.

Globally, infections due to multi-drug resistant (MDR) Gram-negative bacterial (GNB) pathogens are on the rise, negatively impacting morbidity and mortality, necessitating urgent treatment alternatives. Herein, we report a detailed bio-evaluation of an ultrashort, cationic lipopeptide 'SVAP9I' that demonstrated potent antibiotic activity and acted as an adjuvant to potentiate existing antibiotic classes towards GNBs. Newly synthesized lipopeptides were screened against ESKAPE pathogens and cytotoxicity assays were performed to evaluate the selectivity index (SI). SVAP9I exhibited broad-spectrum antibacterial activity against critical MDR-GNB pathogens including members of Enterobacteriaceae (MIC 4-8 mg/L), with a favorable CC50 value of ≥100 mg/L and no detectable resistance even after 50th serial passage. It demonstrated fast concentration-dependent bactericidal action as determined via time-kill analysis and also retained full potency against polymyxin B-resistant E. coli, indicating distinct mode of action. SVAP9I targeted E. coli's outer and inner membranes by binding to LPS and phospholipids such as cardiolipin and phosphatidylglycerol. Membrane damage resulted in ROS generation, depleted intracellular ATP concentration and a concomitant increase in extracellular ATP. Checkerboard assays showed SVAP9I's synergism with narrow-spectrum antibiotics like vancomycin, fusidic acid and rifampicin, potentiating their efficacy against MDR-GNB pathogens, including carbapenem-resistant Acinetobacter baumannii (CRAB), a WHO critical priority pathogen. In a murine neutropenic thigh infection model, SVAP9I and rifampicin synergized to express excellent antibacterial efficacy against MDR-CRAB outcompeting polymyxin B. Taken together, SVAP9I's distinct membrane-targeting broad-spectrum action, lack of resistance and strong in vitro andin vivopotency in synergism with narrow spectrum antibiotics like rifampicin suggests its potential as a novel antibiotic adjuvant for the treatment of serious MDR-GNB infections.

Beyond HbA1c: Identifying Gaps in Glycemic Control Among Children and Young People with Type 1 Diabetes Using Continuous Glucose Monitoring.

OBJECTIVES: To describe continuous glucose monitoring (CGM) derived glycemic variables, and study their association with HbA1c and socio-economic factors in young people with Type 1 diabetes mellitus (T1DM). METHODS: Ninety-two participants [age 15.7 ± 5.0 y (mean ± SD), HbA1c 8.0 ± 1.5% (mean ± SD)] wore a professional CGM sensor for 14 d. RESULTS: Median (IQR) time in range (TIR) was 41 (18)%. Participants spent 41 ± 20% of their day in hyperglycemia (>180 mg/dl), and 14 (13)% in hypoglycemia (<70 mg/dl). High glycemic variability (percent CV >36%) was seen in 92% participants. Older age at diagnosis was associated with higher TIR (ß = 0.267, p = 0.01), lower time above range (TAR) (ß = -0.352, p <0.001), but higher time below range (TBR) (ß = 0.274, p = 0.006). The use of NPH vs. glargine basal insulin was associated with higher TBR (ß = -0.262, p = 0.009) but lower TAR (ß = 0.202, p = 0.041). HbA1c showed negative correlation with TIR (r = -0.449, p <0.001) and TBR (r = -0.466, p <0.001) and positive correlation with TAR (r = 0.580, p <0.001) and mean glucose (r = 0.589, p <0.001). CONCLUSIONS: These data demonstrate wide gaps between the recommended vs. real world glycemic variables in patients with T1DM in this region on multiple daily insulin injections. CGM identifies glycemic variability and complements HbA1c in improving glycemic control.

Structural and biophysical characterization of PadR family protein Rv1176c of Mycobacterium tuberculosis H37Rv.

Rv1176c of Mycobacterium tuberculosis H37Rv belongs to the PadR-s1 subfamily of the PadR family of protein. Rv1176c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 39.4 °C. The crystal structure of Rv1176c was determined at a resolution of 2.94 Å, with two monomers in the asymmetric unit. Each monomer has a characteristic N-terminal winged-helix-turn-helix DNA-binding domain. Rv1176c C-terminal is a coiled-coil dimerization domain formed of α-helices α5 to α7. In the Rv1176c dimer, there is domain-swapping of the C-terminal domain in comparison to other PadR homologs. In the dimer, there is a long inter-subunit tunnel in which different ligands can bind. Rv1176c was found to bind to the promoter region of its own gene with high specificity. M. smegmatis MC2 155 genome lacks homolog of Rv1176c. Therefore, it was used as a surrogate to characterize the functional role of Rv1176c. Expression of Rv1176c in M. smegmatis MC2 155 cells imparted enhanced tolerance towards oxidative stress. Rv1176c expressing M. smegmatis MC2 155 cells exhibited enhanced intracellular survival in J774A.1 murine macrophage cells. Overall, our studies demonstrate Rv1176c to be a PadR-s1 subfamily transcription factor that can moderate the effect of oxidative stress.

Qualification of a LC-HRMS platform method for biosimilar development using NISTmab as a model.

Biosimilars are a cost-effective alternative to biopharmaceuticals, necessitating rigorous analytical methods for consistency and compliance. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is a versatile tool for assessing key attributes, encompassing molecular mass, primary structure, and post-translational modifications (PTMs). Adhering to ICH Q2R1, we validated an LC-HRMS based peptide mapping method using NISTmab as a reference. The method validation parameters, covering system suitability, specificity, accuracy, precision, robustness, and carryover, were comprehensively assessed. The method effectively differentiated the NISTmab from similar counterparts as well as from artificially introduced spiked conditions. Notably, the accuracy of mass error for NISTmab specific complementarity determining region peptides was within a maximum of 2.42 parts per million (ppm) from theoretical and the highest percent relative standard deviation (%RSD) observed for precision was 0.000219 %. It demonstrates precision in sequence coverage and PTM detection, with a visual inspection of total ion chromatogram approach for variability assessment. The method maintains robustness when subjected to diverse storage conditions, encompassing variations in column temperature and mobile phase composition. Negligible carryover was noted during the carryover analysis. In summary, this method serves as a versatile platform for multiple biosimilar development by effectively characterizing and identifying monoclonal antibodies, ultimately ensuring product quality.

Basic carbohydrate counting and glycemia in young people with type 1 diabetes in India: A randomized controlled trial.

OBJECTIVES: The aim of this study was to evaluate the effect on glycemic control and acceptability of basic carbohydrate counting (BCC) in children and young adults with type 1 diabetes (T1DM). METHODS: Ninety-two children and young adults (6-25 y of age) with T1DM were randomized to receive either routine nutrition education (RNE), which addressed food groups, glycemic index, and effects of food and exercise on glycemia, or learn BCC with personalized portion size education. A continuous glucose monitoring study and glycosylated hemoglobin (HbA1c) were performed at baseline and after 12 wk. The primary outcome was a change in time-in-range from baseline through 12 wk. A questionnaire on the acceptability of BCC was administered. RESULTS: At 12 wk, there was no significant difference in change in time-in-range between the two groups (BCC group: 1.2 ± 12.2; RNE group: 1.9 ± 12.3; P = 0.786). No significant changes were observed in the percentage of time that blood glucose was >180 or >250 mg/dL; <70 or <54 mg/dL; glycemic variability, percentage of nights with hypoglycemia and HbA1c. In subgroup analysis, there was a significant decrease in HbA1c in the BCC group among participants with higher maternal education (-0.5 versus 0.2, P = 0.042). The total score on the acceptability questionnaire was higher in the BCC group (P = 0.022). CONCLUSION: Among children and young adults in our region with T1DM, BCC provided flexibility in food choices and perception of greater ease of insulin adjustment. Although BCC was equivalent to RNE in terms of glycemic control, larger studies may reveal benefit in outcomes in certain subgroups.

Highly efficient functionalized MOF-LIC-1 for extraction of U(VI) and Th(IV) from aqueous solution: experimental and theoretical studies.

A set of four new functionalized MOFs, namely MOF-LIC-DPPC, MOF-LIC-GA, MOF-LIC-PCA and MOF-LIC-SA, were synthesized via the post-synthetic modification (PSM) strategy using MOF-LIC-1 for efficient extraction of U(VI) and Th(IV) from an aqueous medium. FTIR, powder XRD, TGA and SEM-EDX were employed for characterization of the functionalized MOFs. Sorption studies for U(VI) and Th(IV) were performed by monitoring the pH and contact time. Interestingly, the modified MOF-LIC-SA displayed rapid (∼5 min) and efficient extraction towards U(VI) and Th(IV) from an aqueous medium and modified MOF-LIC-DPPC displayed enhanced thermal stability (600 °C) compared with the parent MOF-LIC-1 (450 °C). These studies revealed that the grafted functionalities on MOF-LIC-1 possess enhanced sorption efficiency towards U(VI) and Th(IV) as well as thermal stability. MOF-LIC-SA exhibited the highest sorption capacity towards U(VI) and Th(IV), viz. 298 mg g-1 (pH 6) and 149 mg g-1 (pH 6), respectively. Leaching, recyclability, and radiation stability studies were also performed using MOF-LIC-1 MOFs. Additionally, we investigated the nature of U(VI) interactions on MOFs by applying density functional theory (DFT). PSM MOFs with various functionalities display high selectivity and efficient extraction of U(VI) and Th(IV) over a wide pH range (2-9) and also exhibit easy recovery of metal ions from MOFs. These studies reveal that U(VI) and Th(IV) can be extracted from aqueous streams in a pH range from 6 to 8 and potential applications of these MOFs include recovery of U(VI) and Th(IV) from mine water, sea water, etc. The studies reported in the present work also have extensive potential applications for environmental concerns as well as in the nuclear industry.

Effect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders.

Actin, an ATPase superfamily protein, regulates some vital biological functions like cell locomotion, cytokinesis, synaptic plasticity and cell signaling in higher eukaryotes, and is dependent on the dynamics of actin polymerization process. Impaired regulation of actin polymerization has been implicated in the formation and deposition of rod-like paracrystalline structures called as Hirano bodies in neuronal cells of patients suffering from Alzheimer's disease, Pick's disease, Guam amyotrophic lateral sclerosis and parkinsonism-dementia complex. Aggregation of actin forming amorphous deposition in the brain cells is also associated with chronic alcoholism and aging of the neurons. In the current article, we propose the breaking of the highly amorphous and dysregulated actin aggregates using generic compounds like tetracycline, oxytetracycline, doxycycline and minocycline which are used as antibiotics against tuberculosis and infection caused due to various Gram-negative bacteria. We have investigated the effect and affinity of binding of these four compounds to that of actin aggregates using 90° light scattering, size exclusion chromatography, dynamic light scattering, circular dichroism, scanning electron microscopy, transmission electron microscopy imaging and kinetic analysis. The isothermal calorimetric measurements showed that the binding constant for the cycline family molecules used in this study range from 9.8 E4 M-1 to 1.3 E4 M-1. To understand the in vivo effect, we also studied the effect of these drugs on Saccharomyces cerevisiae Δend3 mutant cells. Our data suggest that these generic compounds can plausibly be used for the treatment of various neurodegenerative diseases occurring due to Hirano body formation in brain cells.Communicated by Ramaswamy H. Sarma.

Post synthetically modified IRMOF-3 for efficient recovery and selective sensing of U(vi) from aqueous medium.

A simple and efficient route to develop various novel functionalized MOF materials for rapid and excellent recovery of U(vi) from aqueous medium, along with selective sensing has been demonstrated in the present study. In this connection, a set of four distinct post synthetically modified (PSM) iso-reticular metal organic frameworks were synthesized from IRMOF-3 namely, IRMOF-PC (2-pyridine carboxaldehyde), IRMOF-GA (glutaric anhydride), IRMOF-SMA (sulfamic acid), and IRMOF-DPC (diphenylphosphonic chloride) for the recovery and sensing of U(vi) from aqueous medium. The MOFs were characterized by Fourier transform infrared spectroscopy (FTIR), powder XRD, BET surface area analysis, thermogravimetric analysis (TGA), NMR (13C, 1H and 31P), Scanning Electron Microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX). Among all MOFs, post synthetically modified IRMOF-SMA showed enhanced thermal stability of about 420 °C. The MOFs were investigated for U(vi) sorption studies using a batch technique. All the MOFs exhibit excellent sorption capacity towards U(vi) (>90%) and maximum uptake was observed at pH 6. Sorption capacity of MOFs have the following order; IRMOF-3-DPC (300 mg U g-1) > IRMOF-SMA (292 mg U g-1) > IRMOF-PC (289 mg U g-1) > IRMOF-GA (280 mg U g-1) > IRMOF-3 (273 mg U g-1). IRMOF-DPC shows rapid sorption of uranium within 5 min with excellent uptake of U(vi) (>99%). The desorption of U(vi) was examined with different eluents and 0.01 M HNO3 was found to be most effective. The fluorescence sensing studies of U(vi) via IRMOF-3 and its PSM MOFs revealed high sensitivity and selectivity towards U(vi) over other competing rare earth metal ions (La3+, Ce4+, Sm3+, Nd3+, Gd3+, and Eu3+), wherein IRMOF-GA displayed an impressive detection limit of 0.36 mg L-1 for U(vi).

Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae.

Klebsiella pneumoniae is a member of the ESKAPE panel of pathogens that are top priority to tackle AMR. Bacterial peptidyl tRNA hydrolase (Pth), an essential, ubiquitous enzyme, hydrolyzes the peptidyl-tRNAs that accumulate in the cytoplasm because of premature termination of translation. Pth cleaves the ester bond between 2' or 3' hydroxyl of the ribose in the tRNA and C-terminal carboxylate of the peptide, thereby making free tRNA available for repeated cycles of protein synthesis and preventing cell death by alleviating tRNA starvation. Pth structures have been determined in peptide-bound or peptide-free states. In peptide-bound state, highly conserved residues F67, N69 and N115 adopt a conformation that is conducive to their interaction with peptide moiety of the substrate. While, in peptide-free state, these residues move away from the catalytic center, perhaps, in order to facilitate release of hydrolysed peptide. Here, we present a novel X-ray crystal structure of Pth from Klebsiella pneumoniae (KpPth), at 1.89 Å resolution, in which out of the two molecules in the asymmetric unit, one reflects the peptide-bound while the other reflects peptide-free conformation of the conserved catalytic site residues. Each molecule of the protein has canonical structure with seven stranded ß-sheet structure surrounded by six α-helices. MD simulations indicate that both the forms converge over 500 ns simulation to structures with wider opening of the crevice at peptide-binding end. In solution, KpPth is monomeric and its 2D-HSQC spectrum displays a single set of well dispersed peaks. Further, KpPth was demonstrated to be enzymatically active on BODIPY-Lys-tRNALys3.

Ofloxacin as a Disruptor of Actin Aggresome "Hirano Bodies": A Potential Repurposed Drug for the Treatment of Neurodegenerative Diseases.

There is a growing number of aging populations that are more prone to the prevalence of neuropathological disorders. Two major diseases that show a late onset of the symptoms include Alzheimer's disorder (AD) and Parkinson's disorder (PD), which are causing an unexpected social and economic impact on the families. A large number of researches in the last decade have focused upon the role of amyloid precursor protein, Aß-plaque, and intraneuronal neurofibrillary tangles (tau-proteins). However, there is very few understanding of actin-associated paracrystalline structures formed in the hippocampus region of the brain and are called Hirano bodies. These actin-rich inclusion bodies are known to modulate the synaptic plasticity and employ conspicuous effects on long-term potentiation and paired-pulse paradigms. Since the currently known drugs have very little effect in controlling the progression of these diseases, there is a need to develop therapeutic agents, which can have improved efficacy and bioavailability, and can transport across the blood-brain barrier. Moreover, finding novel targets involving compound screening is both laborious and is an expensive process in itself followed by equally tedious Food and Drug Administration (FDA) approval exercise. Finding alternative functions to the already existing FDA-approved molecules for reversing the progression of age-related proteinopathies is of utmost importance. In the current study, we decipher the role of a broad-spectrum general antibiotic (Ofloxacin) on actin polymerization dynamics using various biophysical techniques like right-angle light scattering, dynamic light scattering, circular dichroism spectrometry, isothermal titration calorimetry, scanning electron microscopy, etc. We have also performed in silico docking studies to deduce a plausible mechanism of the drug binding to the actin. We report that actin gets disrupted upon binding to Ofloxacin in a concentration-dependent manner. We have inferred that Ofloxacin, when attached to a drug delivery system, can act as a good candidate for the treatment of neuropathological diseases.

Resonance assignments and secondary structure prediction of secretory protein Rv0603 from Mycobacterium tuberculosis H37Rv.

We report the NMR resonance assignments of N-terminal signal sequence deleted secretory protein Rv0603 (∆1-28-Rv0603) from Mycobacterium tuberculosis H37Rv. ∆1-28-Rv0603 displayed good peak yield and signal dispersion in 2D [15N-1H] HSQC spectrum, which prompted us to proceed for resonance assignments on this construct. Standard triple-resonance experiments for resonance assignments were recorded on [U-15N]-∆Rv0603 and [U-15N, 13C]-∆Rv0603 samples. We obtained 97% of backbone 1HN, 98% of 13Cα, 98% of 1Hα, 96% of 13C´, 100% of 13Cß, 100% of 1Hß and 98% of side-chain 1H chemical shifts. This protein does not show any sequence similarity to any other protein of known structure. Determination of its solution structure would facilitate understanding of its biological function.

Assorted functionality-appended UiO-66-NH2 for highly efficient uranium(vi) sorption at acidic/neutral/basic pH.

A series of functionalized metal organic frameworks (MOFs) were synthesized by the post-synthetic modification (PSM) of Zr(iv)-containing UiO-66-NH2 MOFs using covalent grafting with various functional groups utilizing pendant -NH2 moieties. The tethering of amide (with/without pendant carboxylic acid), iminopyridine, phoshinic amide and sulphur-containing functionalities produced a library of eight different UiO-66-NH2 derivatives. The functionalized MOFs were characterized by FT-IR spectroscopy, NMR, PXRD, TGA, SEM-EDX and BET surface area analysis. Uranyl ion extraction with the functionalized MOFs was investigated in acidic/neutral/basic conditions (pH 1 to 9). This work presents a comprehensive study of different functionalized MOFs to investigate the effects of various analytical parameters, including pH, contact time, and desorption process. The MOFs as solid phase extractants (SPEs) provide a direct comparison of the sorption efficiencies of different functional groups on a common solid support. A phosphorous-functionalized material, UiO-66-PO-Ph, with enhanced thermal stability (∼500 °C) exhibits the best sorption capacity (∼96%) in an acidic medium (pH 3). The parent MOF UiO-66-NH2 (92%) and iminopyridine-functionalized UiO-66-IMP (90%) showed excellent sorption in neutral conditions (pH 7). Amide-containing MOFs UiO-66-AM1 (40%), UiO-66-AMMal (31%) and UiO-66-AMGlu (70%), sulfur-based MOFs UiO-66-SMA (65%) and UiO-66-SSA (27%), and phosphorous-functionalized UiO-66-PO-OPh (50%) displayed maximum sorption in basic conditions (pH 8). The kinetics studies revealed rapid uranium sorption in about 2 h due to the effective binding of uranyl ions with the anchored functional groups of MOFs; quantitative elution of uranyl ions from the MOF framework was carried out with 0.1/0.01 M HNO3. The MOFs also exhibit moderate recyclability for uranium sorption and can be regenerated by an acidic solution. The functionalized MOFs alter the stability in acidic/basic media; thus, UiO-66-NH2 is a versatile MOF material employed as an SPE for the extraction of radionuclides from aqueous media. This work also provides a platform for the development of new functionalized MOF materials for the efficient sorption of uranium as well as moderate recyclability for its removal, and the potential applications include the removal of uranium from aqueous waste streams.

Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress.

The availability of complete genome sequence of Mycobacterium tuberculosis has provided an important tool to understand the mycobacterial biology with respect to host-pathogen interaction, which is an unmet need of the hour owing to continuous increasing drug resistance. Hypothetical proteins are often an overlooked pool though half the genome encodes for such proteins of unknown function that could potentially play vital roles in mycobacterial biology. In this context, we report the structural and functional characterization of the hypothetical protein Rv3272. Sequence analysis classifies Rv3272 as a Family III CoA transferase with the classical two domain structure and conserved Aspartate residue (D175). The crystal structure of the wild type protein (2.2 Å) demonstrated the associated inter-locked dimer while that of the D175A mutant co-crystallized with octanoyl-CoA demonstrated relative movement between the two domains. Isothermal titration calorimetry studies indicate that Rv3272 binds to fatty acyl-CoAs of varying carbon chain lengths, with palmitoyl-CoA (C16:0) exhibiting maximum affinity. To determine the functional relevance of Rv3272 in mycobacterial biology, we ectopically expressed Rv3272 in M. smegmatis and assessed that its expression encodes significant alteration in cell surface with marked differences in triacylglycerol accumulation. Additionally, Rv3272 expression protects mycobacteria from acidic, oxidative and antibiotic stress under in vitro conditions. Taken together, these studies indicate a significant role for Rv3272 in host-pathogen interaction.

Molecular interaction between human SUMO-I and histone like DNA binding protein of Helicobacter pylori (Hup) investigated by NMR and other biophysical tools.

The proteins secreted by bacteria contribute to immune mediated gastric inflammation and epithelial damage; thus aid bacterial invasion in host tissue, and may also interact with host proteins, conspirating a mechanism against host-immune system. The Histone-like DNA binding protein is one of the most abundant nucleoid-associated proteins in Helicobacter pylori (H. pylori). The protein -referred here as Hup- is also secreted in vitro by H. pylori, thus it may have its role in disease pathogenesis. This is possible only if Hup interact with some human proteins including Small-Ubiquitin-like-Modifier (SUMO) proteins. Studies have established that SUMO-proteins participate in various innate-immune pathways and thus promote an efficient immune response to combat pathogenic infections. Sequence analysis revealed the presence of two SUMO interacting motifs (SIMs) and several positively charged lysine residues on the protein surface of Hup. Additionally, SUMO-proteins epitomize negatively charged surface which confers them the ability to bind to DNA/RNA binding proteins. Based on the presence of SIMs as well as charge complementarity between the proteins, it is legitimate to consider that Hup protein would bind to SUMO-proteins. The present study has been undertaken to establish this interaction for the first time using NMR in combination with ITC and other biophysical techniques.

Structural and Biophysical Characterization of Rab5a from Leishmania Donovani.

Leishmania donovani possess two isoforms of Rab5 (Rab5a and Rab5b), which are involved in fluid phase and receptor-mediated endocytosis, respectively. We have characterized the solution structure and dynamics of a stabilized truncated LdRab5a mutant. For the purpose of NMR structure determination, protein stability was enhanced by systematically introducing various deletions and mutations. Deletion of hypervariable C-terminal and the 20 residues LdRab5a specific insert slightly enhanced the stability, which was further improved by C107S mutation. The final construct, truncated LdRab5a with C107S mutation, was found to be stable for longer durations at higher concentration, with an increase in melting temperature by 10°C. Solution structure of truncated LdRab5a shows the characteristic GTPase fold having nucleotide and effector binding sites. Orientation of switch I and switch II regions match well with that of guanosine 5'-(ß, γ-imido)triphosphate (GppNHp)-bound human Rab5a, indicating that the truncated LdRab5a attains the canonical GTP bound state. However, the backbone dynamics of the P-loop, switch I, and switch II regions were slower than that observed for guanosine 5'-(ß, γ-imido)triphosphate (GMPPNP)-bound H-Ras. This dynamic profile may further complement the residue-specific complementarity in determining the specificity of interaction with the effectors. In parallel, biophysical investigations revealed the urea induced unfolding of truncated LdRab5a to be a four-state process that involved two intermediates, I1 and I2. The maximal 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (Bis-ANS) binding was observed for I2 state, which was inferred to have molten globule like characteristics. Overall, the strategy presented would have significant impact for studying other Rab and small GTPase proteins by NMR spectroscopy.

Structural and functional characterization of the transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv.

Rv3488 of Mycobacterium tuberculosis H37Rv has been assigned to the phenolic acid decarboxylase repressor (PadR) family of transcriptional regulators that play key roles in multidrug resistance and virulence of prokaryotes. The binding of cadmium, zinc, and several other metals to Rv3488 was discovered and characterized by isothermal titration calorimetery to be an exothermic process. Crystal structures of apo-Rv3488 and Rv3488 in complex with cadmium or zinc ions were determined by X-ray crystallography. The structure of Rv3488 revealed a dimeric protein with N-terminal winged-helix-turn-helix DNA-binding domains composed of helices α1, α2, α3, and strands ß1 and ß2, with the dimerization interface being formed of helices α4 and α1. The overall fold of Rv3488 was similar to PadR-s2 and metal sensor transcriptional regulators. In the crystal structure of Rv3488-Cd complex, two octahedrally coordinated Cd2+ ions were present, one for each subunit. The same sites were occupied by zinc ions in the structure of Rv3488-Zn, with two additional zinc ions complexed in one monomer. EMSA studies showed specific binding of Rv3488 with its own 30-bp promoter DNA. The functional role of Rv3488 was characterized by expressing the rv3488 gene under the control of hsp60 promoter in Mycobacterium smegmatis Expression of Rv3488 increased the intracellular survival of recombinant M. smegmatis in murine macrophage cell line J774A.1 and also augmented its tolerance to Cd2+ ions. Overall, the studies show that Rv3488 may have transcription regulation and metal-detoxifying functions and its expression in M. smegmatis increases intracellular survival, perhaps by counteracting toxic metal stress.

Multistimuli-Responsive Hydrolytically Stable "Smart" Mercury(II) Coordination Polymer.

A new one-dimensional double chain photoluminescent Hg(II) coordination polymer (CP), {[Hg(L)2]·(ClO4)2} n (1), was synthesized using a benzimidazole-appended tripodal tridentate ligand, 1,3,5-tris(benzimidazolylmethyl)benzene (L). The dynamic and flexible framework of 1 allows it to be entitled as first Hg(II)-based CP belonging to the rare category of CPs that exhibit multistimuli-responsive photoluminescence sensing properties and called as "smart" material. The sensitivity of this material via luminescence quenching method showing "turn off" behavior to a range of stimuli, including anions, solvents, and nitroaromatic compounds (NACs), offers more fine-grained control over its properties. 1 can easily adjust its channel dimensions to encapsulate different guest anions forming complete/partial anion-exchanged materials 1A-1B/1C-1E using NO3-, BF4-, OTf-, OTs-, and PF6- anions, respectively. Reversible (1A and 1B) and irreversible (1C-1E) anion exchange behaviors were observed for the complete and partial anion-exchanged products, respectively. The noteworthy feature of the anion-exchanged compounds is their anion-triggered luminescent behavior depending on different properties of anions.The excellent emission in water and high hydrolytic stability of 1 allows its use for rapid and efficient fluorescence-based detections of NACs in aquatic system. The uncoordinated pendant benzimidazole moiety in 1 serves as Lewis basic recognition site for trinitrophenol (TNP) detection, and along with electron- and energy-transfer mechanisms, 1 forms a luminescent probe for detection of TNP with low detection limits (0.55 ppm), exhibiting excellent photostability and recyclability. 1 also represents the first reported Hg(II)-based sensory CP material that can discriminate nitrophenol and nitroaniline isomers through fluorescence sensing.

Solution structure and dynamics of glia maturation factor from Caenorhabditis elegans.

BACKGROUND: The GMF class of the ADF-H domain family proteins regulate actin dynamics by binding to the Arp2/3 complex and F-actin through their Site-1 and Site-2, respectively. CeGMF of C. elegans is analogous to GMFγ of human and mouse and is 138 amino acids in length. METHODS: We have characterized the solution structure and dynamics of CeGMF by solution NMR spectroscopy and its thermal stability by DSC. RESULTS: The solution structure of CeGMF shows canonical ADF-H fold with two additional ß-strands in the ß4-ß5 loop region. The Site-1 of CeGMF is well formed and residues of all three regions of Site-1 show dynamic flexibility. However, the ß4-ß5 loop of Site-2 is less inclined towards the C-terminal, as the latter is truncated by four residues in comparison to GMF isoforms of human and mouse. Regions of Site-2 show motions on ns-ps timescale, but dynamic flexibility of ß4-ß5 loop is low in comparison to corresponding F-loop region of ADF/cofilin UNC-60B. A general difference in packing of α3 and α1 between GMF and ADF/cofilins was noticed. Additionally, thermal stability of CeGMF was significantly higher than its ADF/cofilin homologs. CONCLUSION: We have presented the first solution structure of GMF from C. elegans, which highlights the structural differences between the Site-2 of CeGMF and mammalian GMF isoforms. Further, we have seen the differences in structure, dynamics, and thermal stability of GMF and ADF/cofilin. GENERAL SIGNIFICANCE: This study provides a useful insight to structural and dynamics factors that define the specificity of GMF towards Arp2/3 complex.

Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase.

BACKGROUND: Bacterial peptidyl-tRNA hydrolase (Pth) is an essential enzyme that alleviates tRNA starvation by recycling prematurely dissociated peptidyl-tRNAs. The specificity of Pth for N-blocked-aminoacyl-tRNA has been proposed to be contingent upon conserved residue N14 forming a hydrogen bond with the carbonyl of the first peptide bond in the substrate. M71 is involved in forming a conserved hydrogen bond with N14. Other interactions facilitating this recognition are not known. METHODS: The structure, dynamics, and stability of the M71A mutant of Pth from Vibrio cholerae (VcPth) were characterized by X-ray crystallography, NMR spectroscopy, MD simulations and DSC. RESULTS: Crystal structure of M71A mutant was determined. In the structure, the dimer interface is formed by the insertion of six C-terminal residues of one molecule into the active site of another molecule. The side-chain amide of N14 was hydrogen bonded to the carbonyl of the last peptide bond formed between residues A196 and E197, and also to A71. The CSP profile of mutation was similar to that observed for the N14D mutant. M71A mutation lowered the thermal stability of the protein. CONCLUSION: Our results indicate that the interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. Overall, these interactions of M71 are important for the activity, stability, and compactness of the protein. SIGNIFICANCE: The work presented provides original and new structural and dynamics information that significantly enhances our understanding of the network of interactions that govern this enzyme's activity and selectivity.