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71.
Vaideeswaran Sivasakthi Parimelzaghan Anitha Kalavathi Murugan Kumar Susmita Bag Padmanaban Senthilvel Pandian Lavanya Rayapadi Swetha Anand Anbarasu Sudha Ramaiah 《Bioinformation》2013,9(8):432-439
Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we have
analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π
interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that
these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the
aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π
interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins. 相似文献
72.
Alar, a Pyridoxal 5′-phosphate (PLP)-dependent bacterial enzyme is responsible for the racemisation of L-alanine into D-alanine which is essential for the peptidoglycan biosynthesis in both Gram-positive and Gram-negative bacteria. In the present study, we performed induced fit docking, binding free energy calculation and molecular dynamics simulation to elucidate the Alar inhibition potential of 1,2,4-thiadiazolidine-3,5-dione-based inhibitor 1. The inhibitor binds to the hydrophobic groove of Alar and the binding was found to be stable throughout 20-ns MD simulation. Induced fit docking result showed that Lys42, Tyr46, Tyr175 and Tyr364 residues are primarily responsible for the stabilisation of inhibitor–protein complex. Further, high negative van der Waals binding free energy value of –38.88 kcal/mol, indicated it as the main driving force for the inhibitor binding. Based on the information obtained from this study, we designed few molecules as potent Alar inhibitor. In order to gain structural insight and to validate the stability of complex, we performed 20-ns MD simulation of the designed molecule D1. Results obtained from this study can be used for the design of M. tuberculosis Alar potent inhibitors lacking affinity for the co-factor PLP. 相似文献
73.
Gurleen K. Samra Irakli Intskirveli Anitha P. Govind Christopher Liang Ronit Lazar William N. Green Raju Metherate Jogeshwar Mukherjee 《Bioorganic & medicinal chemistry letters》2018,28(3):371-377
Nicotinic acetylcholine α4β21 receptors (nAChRs) are implicated in various neurodegenerative diseases and smoking addiction. Imaging of brain high-affinity α4β21 nAChRs at the cellular and subcellular levels would greatly enhance our understanding of their functional role. Since better resolution could be achieved with fluorescent probes, using our previously developed positron emission tomography (PET) imaging agent [18F]nifrolidine, we report here design, synthesis and evaluation of two fluorescent probes, nifrodansyl and nifrofam for imaging α4β21 nAChRs. The nifrodansyl and nifrofam exhibited nanomolar affinities for the α4β21 nAChRs in [3H]cytisine-radiolabeled rat brain slices. Nifrofam labeling was observed in α4β21 nAChR-expressing HEK cells and was upregulated by nicotine exposure. Nifrofam co-labeled cell-surface α4β21 nAChRs, labeled with antibodies specific for a β2 subunit extracellular epitope indicating that nifrofam labels α4β21 nAChR high-affinity binding sites. Mouse brain slices exhibited discrete binding of nifrofam in the auditory cortex showing promise for examining cellular distribution of α4β21 nAChRs in brain regions. 相似文献
74.
75.
Anitha Moorthy Amita Gupta Ramesh Bhosale Srikanth Tripathy Jayagowri Sastry Smita Kulkarni Madhuri Thakar Renu Bharadwaj Anju Kagal Arvind V. Bhore Sandesh Patil Vandana Kulkarni Varadharajan Venkataramani Usha Balasubramaniam Nishi Suryavanshi Carrie Ziemniak Nikhil Gupte Robert Bollinger Deborah Persaud for the India SWEN Study Team 《PloS one》2009,4(1)
Background
Daily nevirapine (NVP) prophylaxis to HIV-exposed infants significantly reduces breast-milk HIV transmission. We assessed NVP-resistance in Indian infants enrolled in the “six-week extended-dose nevirapine” (SWEN) trial who received single-dose NVP (SD-NVP) or SWEN for prevention of breast-milk HIV transmission but who also acquired subtype C HIV infection during the first year of life.Methods/Findings
Standard population sequencing and cloning for viral subpopulations present at ≥5% frequency were used to determine HIV genotypes from 94% of the 79 infected Indian infants studied. Timing of infection was defined based on when an infant''s blood sample first tested positive for HIV DNA. SWEN-exposed infants diagnosed with HIV by six weeks of age had a significantly higher prevalence of NVP-resistance than those who received SD-NVP, by both standard population sequencing (92% of 12 vs. 38% of 29; p = 0.002) and low frequency clonal analysis (92% of 12 vs. 59% of 29; p = 0.06). Likelihood of infection with NVP-resistant HIV through breast-milk among infants infected after age six weeks was substantial, but prevalence of NVP-resistance did not differ among SWEN or SD-NVP exposed infants by standard population sequencing (15% of 13 vs. 15% of 20; p = 1.00) and clonal analysis (31% of 13 vs. 40% of 20; p = 0.72). Types of NVP-resistance mutations and patterns of persistence at one year of age were similar between the two groups. NVP-resistance mutations did differ by timing of HIV infection; the Y181C variant was predominant among infants diagnosed in the first six weeks of life, compared to Y188C/H during late breast-milk transmission.Conclusions/Significance
Use of SWEN to prevent breast-milk HIV transmission carries a high likelihood of resistance if infection occurs in the first six weeks of life. Moreover, there was a continued risk of transmission of NVP-resistant HIV through breastfeeding during the first year of life, but did not differ between SD-NVP and SWEN groups. As with SD-NVP, the value of preventing HIV infection in a large number of infants should be considered alongside the high risk of resistance associated with extended NVP prophylaxis.Trial Registration
ClinicalTrials.gov NCT00061321相似文献76.
Chien-Hui Ma Aashiq H. Kachroo Anna Macieszak Tzu-Yang Chen Piotr Guga Makkuni Jayaram 《PloS one》2009,4(9)
Background
Reactions of vaccinia topoisomerase and the tyrosine site-specific recombinase Flp with methylphosphonate (MeP) substituted DNA substrates, have provided important insights into the electrostatic features of the strand cleavage and strand joining steps catalyzed by them. A conserved arginine residue in the catalytic pentad, Arg-223 in topoisomerase and Arg-308 in Flp, is not essential for stabilizing the MeP transition state. Topoisomerase or its R223A variant promotes cleavage of the MeP bond by the active site nucleophile Tyr-274, followed by the rapid hydrolysis of the MeP-tyrosyl intermediate. Flp(R308A), but not wild type Flp, mediates direct hydrolysis of the activated MeP bond. These findings are consistent with a potential role for phosphate electrostatics and active site electrostatics in protecting DNA relaxation and site-specific recombination, respectively, against abortive hydrolysis.Methodology/Principal Findings
We have examined the effects of DNA containing MeP substitution in the Flp related Cre recombination system. Neutralizing the negative charge at the scissile position does not render the tyrosyl intermediate formed by Cre susceptible to rapid hydrolysis. Furthermore, combining the active site R292A mutation in Cre (equivalent to the R223A and R308A mutations in topoisomerase and Flp, respectively) with MeP substitution does not lead to direct hydrolysis of the scissile MeP bond in DNA. Whereas Cre follows the topoisomerase paradigm during the strand cleavage step, it follows the Flp paradigm during the strand joining step.Conclusions/Significance
Collectively, the Cre, Flp and topoisomerase results highlight the contribution of conserved electrostatic complementarity between substrate and active site towards transition state stabilization during site-specific recombination and DNA relaxation. They have potential implications for how transesterification reactions in nucleic acids are protected against undesirable abortive side reactions. Such protective mechanisms are significant, given the very real threat of hydrolytic genome damage or disruption of RNA processing due to the cellular abundance and nucleophilicity of water. 相似文献77.
Xu C Sin S McDonough JM Udupa JK Guez A Arens R Wootton DM 《Journal of biomechanics》2006,39(11):2043-2054
Computational fluid dynamic (CFD) analysis was used to model the effect of airway geometry on internal pressure in the upper airway of three children with obstructive sleep apnea syndrome (OSAS), and three controls. Model geometry was reconstructed from magnetic resonance images obtained during quiet tidal breathing, meshed with an unstructured grid, and solved at normative peak resting flow. The unsteady Reynolds-averaged Navier-Stokes equations were solved with steady flow boundary conditions in inspiration and expiration, using a two-equation low-Reynolds number turbulence model. Model results were validated using an in-vitro scale model, unsteady flow simulation, and reported nasal resistance measurements in children. Pharynx pressure drop strongly correlated to airway area restriction. Inspiratory pressure drop was primarily proportional to the square of flow, consistent with pressure losses due to convective acceleration caused by area restriction. On inspiration, in OSAS pressure drop occurred primarily between the choanae and the region where the adenoids overlap the tonsils (overlap region) due to airway narrowing, rather than in the nasal passages; in controls the majority of pressure drop was in the nasal passages. On expiration, in OSAS the majority of pressure drop occurred between the oropharynx (posterior to the tongue) and overlap region, and local minimum pressure in the overlap region was near atmospheric due to pressure recovery in the anterior nasopharynx. The results suggest that pharyngeal airway shape in children with OSAS significantly affects internal pressure distribution compared to nasal resistance. The model may also help explain regional dynamic airway narrowing during expiration. 相似文献
78.
Folding of naturally occurring proteins has eluded a universal molecular level explanation till date. Rather, there is an abundance of diverse views on dominant factors governing protein folding. Through rigorous analyses of several thousand crystal structures, we observe that backbones of folded proteins display some remarkable invariant features. Folded proteins are characterized by spatially well-defined, distance dependent, and universal, neighborhoods of amino acids which defy any of the conventionally prevalent views. These findings present a compelling case for a newer view of protein folding which takes into account solvent mediated and amino acid shape and size assisted optimization of the tertiary structure of the polypeptide chain to make a functional protein. 相似文献
79.
Kozlowski JA Zhou G Tagat JR Lin SI McCombie SW Ruperto VB Duffy RA McQuade RA Crosby G Taylor LA Billard W Binch H Lachowicz JE 《Bioorganic & medicinal chemistry letters》2002,12(5):791-794
A novel series of 2-(R)-methyl-substituted piperazines (e.g., 2) is described. They are potent M(2) selective ligands that have >100-fold selectivity versus the M(1) receptor. In the rat microdialysis assay, compound 14 showed significantly enchanced levels of acetylcholine after oral administration. 相似文献
80.
A. Anitha N. DeepaK.P. Chennazhi Vinoth-Kumar LakshmananR. Jayakumar 《Biochimica et Biophysica Acta (BBA)/General Subjects》2014