Obtaining high yield recombinant Enterococcus faecium nicotinate nucleotide adenylyltransferase for X-ray crystallography and biophysical studies

Nicotinate nucleotide adenylyltransferase (NNAT) has been a significant research focus on druggable targets, given its indispensability in the biosynthesis of NAD+, which is crucial to the survival of bacterial pathogens. However, no information is available on the structure-function of Enterococcus faecium NNAT (EfNNAT). This study established the expression and purification protocol for obtaining a high-yield recombinant EfNNAT using the E. coli expression system and a single-step IMAC purification method. Approximately 101 mg of EfNNAT was obtained per 7.8 g of wet E. coli cells, estimated to be over 98 % pure. We further characterized the biophysical structure and determined the three-dimensional structure of the EfNNAT. Biophysical studies revealed a dimeric protein with a higher α-helical composition. The highly stable protein crystalizes in multiple conditions, yielding high-quality crystals diffracting between 1.78 and 2.80 Å. Two high-resolution crystal structures of EfNNAT in its native and adenine-bound forms were determined at 1.90 Å and 1.82 Å, respectively. The X-ray structures of the EfNNAT revealed the presence of phosphate and sulfate ions occupying and interacting with conserved amino acid residues within the putative substrate binding site, hence providing insight into the probable substrate preference of EfNNAT and, consequently, why EfNNAT may not prefer β-nicotinamide mononucleotide as a substrate. With the accessibility to high-resolution structures of EfNNAT, further structural evaluation and drug-based screening can be achieved. Hence, we anticipate that this study will provide the basis for the discovery of structure-based inhibitors against this enzyme.

Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir

Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.

Non-active site mutations in the HIV protease: Diminished drug binding affinity is achieved through modulating the hydrophobic sliding mechanism

The global HIV/AIDS epidemic still currently affects approximately 38 million individuals globally. The protease enzyme of the human immunodeficiency virus is a major drug target in antiviral therapy, however, under the influence of reverse transcriptase and in the context of drug pressure, the rapid PR mutation rate contributes significantly to clinical failure. The set of cooperative non-active site mutations, I13V/I62V/V77I, have been associated with reduced inhibitor susceptibility and are the focus of the current study. When compared to the wild-type protease the mutant protease exhibited decreased binding affinities towards ATV and DRV by 64- and 12-fold, respectively, and decreased the overall favourable Gibbs free energy for ATV, DRV, RTV and SQV. Moreover, these mutations decreased the thermal stability of the protease when in complex with ATV and DRV by approximately 6.4 and 4.2 °C, respectively. The crystal structure of the mutant protease revealed that the location of these mutations and their effect on the hydrophobic sliding mechanism may be crucial in their role in resistance.

Effects of Pb assisted cation chemistry on the superconductivity of BSCCO thin films

Thin films of Bi-based superconductors, highly c-axis oriented, were deposited on single crystalline substrates of SrTiO3, LaAlO3, and MgO using a pulsed laser deposition technique with a Bi-2223 target of nominal composition Bi1.75Pb0.25Sr2Ca2Cu3O10±δ prepared by the solid state reaction method. The effect of different deposition parameters on the evolution of the requisite properties in the thin films has been studied. These films have been characterized by X-ray diffraction to investigate their structural properties, scanning electron microscopy to understand the effect of ex situ annealing on the grain growth, and DC resistivity measurements to quantify their superconducting critical temperature. Furthermore, the chemical states of the constituent elements Bi, Pb, Sr, Ca, Cu and O were confirmed using X-ray photoelectron spectroscopy. This information has helped in deciphering the empirical stoichiometry of the films on each of the chosen substrates. We have also been able to comment on the influence made by the choice of the substrates on the mechanism of evolution of superconductivity based on the interplay of the cation chemistry between the substituent and the constituent elements. Thin films with superior superconducting properties were obtained on SrTiO3 substrates with 58% of Bi-2223 phase fraction yielding a superconducting transition temperature (TC,offset) of 107 K. Magnetotransport studies were performed on these films to quantify their superconducting upper critical field and to comprehend the pinning mechanism.

Molecular basis of inhibition of Schistosoma japonicum glutathione transferase by ellagic acid: Insights into biophysical and structural studies

Schistosoma japonicum glutathione transferase (Sj26GST), an enzyme central to detoxification of electrophilic compounds in the parasite, is upregulated in response to drug treatment. Therefore, Sj26GST may serve as a potential therapeutic target for the treatment of schistosomiasis. Herewith, we describe the structural basis of inhibition of Sj26GST by ellagic acid (EA). Using 1-chloro-2,4-dinitrobenzene and reduced glutathione (GSH) as Sj26GST substrates, EA was shown to inhibit Sj26GST activity by 66 % with an IC₅₀ of 2.4 μM. Fluorescence spectroscopy showed that EA altered the polarity of the environment of intrinsic tryptophan and that EA decreased (in a dose-dependent manner) the interaction between Sj26GST and 8-Anilino-1-naphthalenesulfonate (ANS), which is a known GST H-site ligand. Thermodynamic studies indicated that the interaction between Sj26GST and EA is spontaneous (ΔG = -29.88 ± 0.07 kJ/mol), enthalpically-driven (ΔH = -9.48 ± 0.42 kJ/mol) with a favourable entropic change (ΔS = 20.40 ± 0.08 kJ/mol/K), and with a stoichiometry of four EA molecules bound per Sj26GST dimer. The 1.53 Å-resolution Sj26GST crystal structure (P 21 21 21 space group) complexed with GSH and EA shows that EA binds primarily at the dimer interface, stabilised largely by Van der Waal forces and H-bonding. Besides, EA bound near the H-site and less than 3.5 Å from the ε-NH₂ of the γ-glutamyl moiety of GSH, in each subunit.

A model compound for pyridinechalcone-based multistate systems. Ring opening-closure as the slowest kinetic step of the multistate

Amino-substituted pyridinechalcones configure multistate systems where a new type of flavylium derivative with potential biological activity are present.

Unexpected production of singlet oxygen by sub-micron cerium oxide particles and enhanced photocatalytic activity against methyl orange

Photodegradation of methyl orange (MO) by hydrothermally grown cerium oxide (CeO₂) particles has been studied. Unexpected production of singlet oxygen is reported..

Synthesis and crystal structures of 2-methyl-4-aryl-5-oxo-5H-indeno [1,2-b] pyridine carboxylate derivatives

Background

Hantzsch 1,4-dihydropyridines (Hantzsch1,4-DHP) have been extensively utilized as the analogs of nicotinamide adenine dinucleotide (NADH) coenzyme to study the mechanism and various redox processes. During the redox processes 1,4-DHP systems undergo transformation into the corresponding pyridine derivatives through oxidation. Consequently, the interest in this aromatization reaction, investigation of a wide range of 1, 4-DHPs continues to attract the attention of researchers. Herein, we report the preparation of pyridine derivatives and the crystal structures determined by X-ray crystallographic methods.

Results

The crystal structures and conformational studies of two organic compounds, namely ethyl 2-methyl-4-phenyl-5-oxo-5H-indeno [1,2-b] pyridine-3-carboxylate (I) and ethyl 2-methyl-4-(4 chlorophenyl)-5-oxo-5H-indeno [1,2-b] pyridine-3-carboxylate (II) are reported. The terminal ethyl group of the compound I is disordered over two positions with the refined occupancies of 0.645 & 0.355 and C8 one dimensional zig-zag chain running along 101 direction through C-H…O type of intermolecular interactions. In the compound II, C-H…O interactions connect the molecules to form an R2 2 (16) dimer running along 011 direction.

Conclusion

The crystal structures ethyl 2-methyl-4-phenyl-5-oxo-5H-indeno [1,2-b] pyridine-3-carboxylate and ethyl 2-methyl-4-(4 chlorophenyl)-5-oxo-5H-indeno [1,2-b] pyridine-3-carboxylate have been investigated in detail. The terminal ethyl group of compound I is disordered. In compound II, the substitution of Cl atom in the phenyl ring alters the configuration of carboxylate group with respect to the pyridine indane ring.

Crystallization and preliminary X-ray analysis of a novel type of lipolytic hydrolase from Bacillus licheniformis

With increasing demand in biotechnological applications, the identification and characterization of novel lipolytic enzymes are of great importance. The crystallization and preliminary X-ray crystallographic study of a novel type of hydrolase from Bacillus licheniformis (BL28) are described here. Recombinant BL28 protein containing a C-terminal His tag was overproduced in Escherichia coli and purified to homogeneity. BL28 was crystallized using 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30%(w/v) PEG 4000 as a crystallizing solution. X-ray diffraction data were collected to a resolution of 1.67 Å with an Rmerge of 5.8%. The BL28 crystals belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 57.89, c = 167.25 Å. A molecular-replacement solution was obtained and structure refinement of BL28 is in progress.

Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa

The peptidases in clan MH are known as cocatalytic zinc peptidases that have two zinc ions in the active site, but their metal preference has not been rigorously investigated. In this study, the molecular basis for metal preference is provided from the structural and biochemical analyses. Kinetic studies of Pseudomonas aeruginosa aspartyl aminopeptidase (PaAP) which belongs to peptidase family M18 in clan MH revealed that its peptidase activity is dependent on Co(2+) rather than Zn(2+): the kcat (s(-1)) values of PaAP were 0.006, 5.10 and 0.43 in no-metal, Co(2+), and Zn(2+)conditions, respectively. Consistently, addition of low concentrations of Co(2+) to PaAP previously saturated with Zn(2+) greatly enhanced the enzymatic activity, suggesting that Co(2+)may be the physiologically relevant cocatalytic metal ion of PaAP. The crystal structures of PaAP complexes with Co(2+) or Zn(2+) commonly showed two metal ions in the active site coordinated with three conserved residues and a bicarbonate ion in a tetragonal geometry. However, Co(2+)- and Zn(2+)-bound structures showed no noticeable alterations relevant to differential effects of metal species, except the relative orientation of Glu-265, a general base in the active site. The characterization of mutant PaAP revealed that the first metal binding site is primarily responsible for metal preference. Similar to PaAP, Streptococcus pneumonia glutamyl aminopeptidase (SpGP), belonging to aminopeptidase family M42 in clan MH, also showed requirement for Co(2+) for maximum activity. These results proposed that clan MH peptidases might be a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase.

Crystallization and preliminary X-ray analysis of a highly stable novel SGNH hydrolase (Est24) from Sinorhizobium meliloti

The SGNH hydrolase family includes enzymes that catalyze the hydrolysis of a broad range of substrates. Here, the crystallization and preliminary X-ray crystallographic studies of a novel SGNH hydrolase (Est24) from Sinorhizobium meliloti were performed. Recombinant Est24 protein containing an N-terminal His tag was expressed in Escherichia coli and purified to homogeneity. Est24 was then crystallized using a solution consisting of 0.2 M ammonium phosphate pH 4.6, 20% polyethylene glycol 3350. X-ray diffraction data were collected to a resolution of 1.45 Å with an R(merge) of 9.4%. The Est24 crystals belonged to space group C2, with unit-cell parameters a = 129.09, b = 88.63, c = 86.15 Å, α = 90.00, β = 114.30, γ = 90.00°. A molecular-replacement solution was obtained using the crystal structure of Mycobacterium smegmatis arylesterase as a template and structure refinement of Est24 is in progress.

Intra-renal angiotensin II/AT1 receptor, oxidative stress, inflammation, and progressive injury in renal mass reduction

Significant reduction of renal mass triggers a chain of events that result in glomerular hypertension/hyperfiltration, proteinuria, glomerulosclerosis, tubulointerstitial injury, and end-stage renal disease. These events are mediated by a constellation of hemodynamic, oxidative, and inflammatory reactions that are, in part, driven by local AT1 receptor (AT1r) activation by angiotensin II (Ang II). Here we explored the effects of 5/6 nephrectomy with and without AT1r blockade (losartan for 8 weeks) on AT1r and AT2r and Ang II-positive cell count, pathways involved in oxidative stress and inflammation [NAD(P)H oxidase, nuclear factor kappaB (NFkappaB), 12-lipooxygenase, cyclooxygenase (COX)-1, COX-2, monocyte chemoattractant protein (MCP)-1, plasminogen activator inhibitor (PAI)-1, renal T cell, and macrophage infiltration] as well as renal function and structure. The untreated group exhibited hypertension, deterioration of renal function and structure, reduced or unchanged plasma renin activity, aldosterone concentration, marked up-regulations of AT1r (250%), Ang II-expressing cell count (>20-fold), NAD(P)H oxidase subunits (gp91(phox,) p22(phox), and P47(phox); 20-40%), COX-2 (250%), 12-lipooxygenase (100%), MCP-1 (400%), and PAI-1 (>20-fold), activation of NFkappaB, and interstitial infiltrations of T cells and macrophages in the remnant kidneys. AT1r blockade attenuated the biochemical and histological abnormalities, prevented hypertension, and decelerated deterioration of renal function and structure. Thus, the study demonstrated a link between up-regulation of Ang II/AT1r system and oxidative stress, inflammation, hypertension, and progression of renal disease in rats with renal mass reduction.

DNA sequence and analysis of human chromosome 9

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Comparison of different culture media and storage temperatures for the long-term preservation of Streptococcus pneumoniae in the tropics

OBJECTIVE

The preservation of Streptococcus pneumoniae by standard freezing methods for subsequent tests--such as serotyping and antibiotic susceptibility--is not possible or is difficult in many developing countries because of the high cost of equipment, inadequate equipment maintenance, and irregular power supply. We evaluated alternative low-cost methods, by comparing different culture media and storage temperatures.

METHODS

Clinical isolates of five capsular types (1, 5, 7, 19, and 23) of S. pneumoniae were preserved in rabbit blood, sheep blood, skimmed milk, or glycerol-chocolate broth, and stored at -20 degrees C or -70 degrees C. The cultures were also preserved by lyophilization or sand desiccation, followed by storage at room temperature and 4 degrees C. The viability of the preserved cultures was determined by making serial colony counts on day 0 and after 1 week, 4 weeks, 4 months and 16 months. The viability of cultures preserved by sand desiccation and storage at 4 degrees C was also determined every 6 months for up to 68 months.

FINDINGS

Irrespective of the media used, cultures maintained at -20 degrees C became nonviable by the fourth month, while those maintained at -70 degrees C were still viable at 16 months. Cultures preserved by lyophilization or sand desiccation lost their viability by the fourth month when maintained at local room temperature (30-42 degrees C), but remained viable when stored at 4 degrees C for up to 68 months.

CONCLUSIONS

Our results confirm that freezing at -70 degrees C, or lyophilization and storage at 4 degrees C are the ideal methods for the preservation of S. pneumoniae. In laboratories where lyophilization is not feasible, sand desiccation and storage at 4 degrees C offers an alternative low-cost method for the long-term preservation of S. pneumoniae.

Bacteremia due to beta haemolytic streptococci

The Beta haemloytic streptococci (BHS) are well recognised human pathogens causing a variety of infections, including septicemia. It is important to ensure their isolation from clinical specimens by using optimum media. Moreover, since the different groups have different pathogenic potential, it is equally important to routinely serogroup them; this is emphasized here. Since, BHS are uniformly will greatly decrease morbidity and mortality due to BHS infection.

The spectrum of antimicrobial resistance among methicillin resistant Staphylococcus aureus (MRSA) in a tertiary care centre in India

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen globally, including India. Staph. aureus strains isolated from pus or blood of patients during January 1993 to November 1994 were tested for antimicrobial susceptibility using Kirby-Bauer disc diffusion technique. Among 1382 isolates of Staph. aureus, 332 (24%) were MRSA. Among the latter, 97 per cent were resistant to trimethoprim-sulphamethoxazole; 85.5 per cent to gentamicin and 45 per cent to amikacin. While over 90 per cent were resistant to norfloxacin and ciprofloxacin, only 53 per cent were resistant to ofloxacin. Fifty seven per cent were susceptible to rifampicin and 87 per cent to netilmicin. All tested strains were susceptible to vancomycin. Therefore, when antimicrobials other than vancomycin are considered for therapy, their choice requires the results of in vitro susceptibility testing of every isolate of MRSA.

Long-term preservation of streptococci

Strains of 12 T types of group A streptococci preserved by sand desiccation and stored at 4 degrees to 10 degrees C were regularly sub-cultured to check their viability. For this, streptococci coated onto sand particles mixed with sterile sheep blood were inoculated into Todd-Hewitt broth with added blood and incubated for 24 to 48 h. Checking for viability every six months showed that group A streptococci could be preserved by this method for 21 yr. Our study shows that sand desiccation is a convenient and cheap method for the long-term preservation of streptococci in laboratories where other methods of preservation are not feasible on a regular basis.

False resistance of salmonellae to trimethoprim-sulphamethoxazole in disc diffusion method

Apparent resistance to trimethoprim-sulphamethoxazole (TMP-SMZ) in disc diffusion method was found in 14 strains of Salmonella typhi and 2 strains of S. paratyphi A grown on Mueller Hinton agar (MHA) of one manufacturer. On MHA from another manufacturer and on diagnostic sensitivity test agar (DSTA), these 16 strains were sensitive to TMP-SMZ. The minimum inhibitory concentration of trimethoprim (TMP) assayed by agar dilution method, on DSTA medium for these 16 strains was in the range of 0.01 to 0.04 micrograms/ml. Thus, the apparent resistance was a spurious result due to the unsatisfactory quality of the batch of MHA of the first manufacturer. Presumably the medium contained thymine or its derivatives which act as antagonists to TMP and sulphonamide drugs.

Control of poliomyelitis by pulse immunisation in Vellore, India

In a simple study into the control of polio in the Third World a town was divided into 16 zones and pulses or oral polio vaccine given at one station in each zone, after extensive publicity about the campaign. Some 62% of children received three doses of the vaccine and the incidence of polio fell dramatically over the study period. It is suggested that this method is applicable to similar communities because it is cheap, effective, and able to be extended to unimmunised communities when resources allow.