Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis

Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide‐range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of protein classification are based on the canonical paradigm that attributes proteins’ function to their three‐dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in C_α atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes.     

Application of artificial intelligence technique for modelling elastic properties of 2D nanoscale material

A novel computational approach is proposed to investigate the shear modulus of graphene nanostructures. In this approach, the factors that affect the shear modulus of graphene structures are analysed using an integrated artificial intelligence (AI) cluster comprising molecular dynamics (MD) and gene expression programming. The MD-based-AI approach has the ability to formulate the explicit relationship of shear modulus graphene nanostructure with respect to aspect ratio, temperature, number of atomic planes and vacancy defects. In addition, the shear modulus of graphene predicted using an integrated MD-based-AI model is in good agreement with that of experimental results obtained from the literature. The sensitivity and parametric analysis were further conducted to find out specific influence and variation of each of the input system parameters on the shear modulus of two graphene structures. It was found that the number of defects has the most dominating influence on the shear modulus of graphene nanostructure.     

Induction of systemic acquired resistance in Zea mays L. by Aspergillus flavus and A. parasiticus derived elicitors

Host defence mechanisms can be elicited by using different elicitors produced from the pathogen/host. In this study, an effort has been made to study the effect of two fungal elicitors derived from Aspergillus flavus and A. parasiticus on induction of various defence-related enzymes in maize (Zea mays L.). Foliar application was done on 20-days-old maize plant with 10% A. flavus fungal culture filtrate (AFFCF) and A. parasiticus fungal culture filtrate (APFCF) as elicitors to trigger systemic acquired resistance (SAR). As a response of SAR, an increase in activities of phenylalanine ammonia lyase (PAL), peroxidase (POX), β-1,3-glucanase, nitrate reductase (NR) and nitrite reductase (NiR), total proteins were found highest on 4th day after treatment (DAT), whereas total carbohydrate and total chlorophyll on 2nd and 6th DAT, respectively, in comparison with the control plants. The SDS PAGE analysis revealed the induction of PR proteins, namely Chitinase (25, 29?kDa) and β-1,3-glucanase (33?kDa), in treated plants in comparison with untreated control plants. The treated plants showed enhanced growth and development as well as increase in yield. About 100% survival rate was found in maize seeds treated with AFFCF and APFCF and grown on respective fungal infested soil than control. The enhanced activities of defence enzymes and elevated protein, carbohydrate, chlorophyll content in treated maize plants suggest the induction of SAR against A. flavus and A. parasiticus by using the same fungal elicitors.     

Tannic acid protects against experimental acute lung injury through downregulation of TLR4 and MAPK

Acute lung injury (ALI) and its severe form acute respiratory distress syndrome (ARDS) remain a major cause of morbidity and mortality in critically ill patients, and no specific therapies are still available to control the mortality rate. Thus, we explored the preventive and therapeutic effects of tannic acid (TA), a natural polyphenol in the context of ALI. We used in vivo and in vitro models, respectively, using lipopolysaccharide (LPS) to induce ALI in mice and exposing J774 and BEAS-2B cells to LPS. In both preventive and therapeutic approaches, TA attenuated LPS-induced histopathological alterations, lipid peroxidation, lung permeability, infiltration of inflammatory cells, and the expression of proinflammatory mediators. In addition, in-vitro study showed that TA treatment could reduce the expression of proinflammatory mediators. Further studies revealed that TA-dampened inflammatory responses by downregulating the LPS-induced toll-like receptor 4 (TLR4) expression and inhibiting extracellular-signal-regulated kinase (ERK)1/2 and p38 mitogen-activated protein kinase (MAPK) activation. Furthermore, cells treated with the inhibitors of ERK1/2 (PD98059) and p38 (SB203580) mitigated the expression of cytokines induced by LPS, thus suggesting that ERK1/2 and p38 activity are required for the inflammatory response. In conclusion, TA could attenuate LPS-induced inflammation and may be a potential therapeutic agent for ALI-associated inflammation in clinical settings.     

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion‐corrected density functional theory study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence‐directed features, such as small roll values for the purine–pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near‐zero slide to be most favorable for the purine–pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar–phosphate backbone with C3′‐endo sugars and this demands C1′–C1′ distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1′–C1′ distance from the mean value, to the recent DFT‐D functionals, specifically ωB97X‐D appears to predict reliable energy contour for AU/AU step. Such distance‐based penalty improves energy contours for the other purine–pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107–120, 2014.     

In silico study of binding motifs in squalene synthase enzyme of secondary metabolic pathway solanaceae family

Solanaceae is an important family with several plants of medicinal importance. These medicinal plants have distinctive pathways for secondary metabolite biosynthesis. In most of the plants, two important compounds, dimethylallyl diphosphate and isopentenyl diphosphate, synthesize isoprenoid or terpenoids. Squalene synthase (SQS) is a key enzyme of the biosynthesis of isoprenoid (farnesyl pyrophosphate (FPP) → squalene). Withania somnifera (ashwagandha), an important medicinal plant of family solanaceae produces withanolides. Withanolides are secondary metabolites synthesized through isoprenoid pathway. In this study, 13 SQS protein sequences from the plants of solanacae family and Arabidopsis thaliana were analyzed. The conserved domains in corresponding sequences were searched. The multiple sequence alignment of conserved domains revealed the important motifs and identified the residue substitution in each motif. Our result further indicated that residue substitution in motifs might not lead to functional variation, although it may affect the binding affinity of Mg⁺⁺, FPP and NAD(P)H. In addition, the homology modelling of SQS enzyme of W. somnifera was done for the prediction of three-dimensional structure. Molecular docking study of considered substrates with WsSQS was performed and the docked structure were analyzed further. The docked structures showed binding affinity for motif 2 of WsSQS. Our analysis revealed that 29 residues of motif 2 might be important for catalytic/functional activity of SQS enzyme of W. somnifera. This study may provide an understanding of metabolic pathways responsible for the production of secondary metabolites. The motifs may play a key role in regulating the pathway towards enhanced production of metabolites.     

Syphilis and Its Correlates among Heterosexual Males Attending Sexually Transmitted Infection Clinics – Observation from a Multicity Cohort in Jiangsu Province,China

Objectives

To estimate the prevalence of HIV and syphilis, incidence of syphilis and to identify the correlates of syphilis infection among heterosexual male attendees of sexually transmitted infection (STI) clinics (MSC).

Methods

A cohort study of one-year duration was conducted in Yangzhou and Changzhou cities in Jiangsu province of China. The baseline survey commenced in June 2009, recruited 1225 consenting adult MSCs (609 in Yangzhou and 617 in Changzhou) through STI-clinic based convenience sampling.

Results

Baseline HIV and syphilis prevalence were 0.49% and 17.29% respectively. Syphilis incidence rate was 7.22 per 100 person-years (6.53 in Yangzhou and 7.76 in Changzhou) during the 6-month follow-up with retention fractions of 27.38% and 35.15% for Yangzhou and Changzhou respectively. Majority of the participants were middle-aged, high school educated, married, living with partners and non-migrants. Very few subjects reported recent and consistent condom-use with regular partners. Although considerable number of MSCs reported recent sexual exposure with female sex workers (FSW) and non-FSW casual partners, the proportion of reported condom use was very low during those exposures. In multivariate analyses higher age, having recent sex with FSWs and being HIV-positive were associated with higher syphilis sero-positivity while higher education was protective. In bivariate analyses, being married, divorced/widowed, official residency of the study cities and non-use of condom with regular partners predicted higher risk.

Conclusions

Considering the potential bridging role of MSCs between high and low-risk populations, effective intervention strategies among them targeting the correlates of syphilis infection are urgently called for in Jiangsu province of China.     

Exposure to Pornographic Videos and Its Effect on HIV-Related Sexual Risk Behaviours among Male Migrant Workers in Southern India

Objective

Research on pornography and its association with HIV-related sexual behaviours is limited in India. This study aims to examine the prevalence and correlates of viewing pornographic videos and examine its associations with HIV-related sexual risk behaviours among male migrant workers in India.

Methods

Data were drawn from a cross-sectional survey conducted in 2007–08 across 21 districts in four states of India. Respondents included 11,219 male migrants aged 18 years or older, who had migrated to at least two places in the past two years for work. Bivariate and multivariate methods were used to examine the association between viewing pornography and HIV-related sexual risk behaviours.

Results

Two-fifths (40%) of the migrants had viewed pornographic videos in one month prior to the survey. Migrants aged 25–29 years, literate, unmarried and away from native village for more than five years were more likely to view pornography than their counterparts. Migrants who viewed pornographic videos were more likely to engage in paid (Adjusted odds ratio [AOR]: 4.2, 95% confidence interval [CI]: 3.7–4.8) and unpaid sex (AOR: 4.2, 95% CI: 3.7–4.7), report inconsistent condom use in paid sex (AOR: 2.3, 95% CI: 1.7–3.0) and experience STI-like symptoms (AOR: 1.7, 95% CI: 1.5–1.8) than their counterparts.

Conclusions

The findings regarding migrants'' exposure to pornography and its linkage with high HIV risk behaviour suggest that the HIV prevention programmes for migrants need to be more innovative to communicate on the negative-effects of viewing pornography. More importantly, programmes need to find alternative ways to engage migrants in infotainment activities during their leisure time in an effort to reduce their exposure to pornographic videos as well as risky sexual behaviours.     

Alterations in follicular fluid estradiol, progesterone and insulin concentrations during ovarian acyclicity in water buffalo (Bubalus bubalis)

Ovarian acyclicity is one of the most important causes of infertility in water buffalo. Recent studies have indicated alterations in the composition of follicular fluid during the condition. The aim of this study was to determine the changes in follicular fluid concentrations of estradiol, progesterone and insulin during ovarian acyclicity in water buffalo. Ovaries were collected from 50 acyclic and 95 cyclic (control) buffaloes and follicular fluid was aspirated from small (5.0-6.9 mm), medium (7.0-9.9 mm) and large (≥10.0 mm) sized follicles. Estradiol concentration was lower (P<0.0001) in acyclic (1.4 ± 0.09 ng/ml) than in cyclic (3.3 ± 0.18 ng/ml) buffaloes. Regardless of the ovarian cyclic status, there was an increase (P<0.01) in estradiol concentration with the increase in follicle size; the mean concentrations were 2.4 ± 0.16 ng/ml, 2.8 ± 0.29 ng/ml and 3.5 ± 0.41 ng/ml in small, medium and large follicles, respectively. A higher (P<0.001) progesterone concentration was recorded in acyclic (24.3 ± 2.61 ng/ml) compared to the cyclic (7.6 ± 0.79 ng/ml) group. Furthermore, acyclic buffaloes had a lower (P<0.05) concentration of insulin in the follicular fluid than that of cyclic buffaloes (15.2 ± 1.55 μIU/ml versus 25.9 ± 2.78 μIU/ml, respectively). In conclusion, acyclic buffaloes have lower concentrations of estradiol and insulin concurrent with higher concentrations of progesterone in the follicular fluid. These hormonal changes in the follicular microenvironment are possibly a manifestation of the disturbances in the normal follicular development leading to anovulation and anestrus in acyclic buffaloes.