calculating steric effects from 2d molecular structures of related molecules

... to obtain crystal structures of active PR with peptide substrates Two strategies have been used to analyze the structures of the transition state(s) We have analyzed structures of active PR with ... Sciences, Of ce of Science, under Contract No W-31-109-Eng-38 Use of the National Synchrotron Light Source was supported by the US Department of Energy, Division of Materials Sciences and Division of ... subunit of the dimer These residues were located on the PR surface and were either very flexible or interacted with symmetry related molecules The presence of alternate conformations of side chains...

Ngày tải lên: 30/03/2014, 20:20

... 6929-6936 Collier, R J (1967) Effect of diphtheria toxin on protein synthesis: inactivation of one of the transfer factors J Mol Biol 25, 83-98 Cooper, J A (1987) Effects of cytochalasin and phalloidin ... Popoff, M R., Milward, F W., Bancillon, B., and Boquet, P (1989) Purification of the Clostridium spiroforme binary toxin and activity of the toxin on HEp-2 cells Infect Immun 57, 2462-2469 Popoff, ... Nucleotide sequence of Clostridium difficile toxin B gene Nucleic Acids Res 18, 4004 Barth, H., Preiss, J C., Hofmann, F., and Aktories, K (1998) Characterization of the catalytic site of the ADP-ribosyltransferase...

Ngày tải lên: 16/09/2015, 15:54

... the stabilization of the nicotinamide mononucleotide (NMN) ring moiety of NAD (upon binding of NAD to Ia) through electrical charge-charge interaction of positively charged atoms from Arginine residues ... cleavage of NAD by H-bond formation of the nicotinamide carboxyamide and the amide (NO1) and carbonyl group of Arg296 with the NN7 if nicotinamide followed by spontaneous withdrawal of electron from ... cleavage of the N-glycoside bond; the stabilization of the resulting oxocarbenium cation via charge-charge chelation of the positive NC1 of ADP-ribose by negative carboxylate group of Glu380...

Ngày tải lên: 16/09/2015, 15:54

... sets of genome that have hybridized The process has led to the identification of several virulence genes and characterization of variant forms of cdt whose detection was reported at about 6% of ... eluates, respectively M, high molecular weight protein ladder D, Lane contained cellular extract from pQE-30 of induced SK1203 Lane had CDTa and CDTb expressed from pDA576 of SK1216 in 10% SDS-PAGE ... of actin Arg177 to increase its nucleophilicity for attach of the C1’ of the oxocarbenium ion upon the binding of actin to VIP2NAD complex (Fig 3.11)(Han, Craig et al 1999) The conservation of...

Ngày tải lên: 16/09/2015, 15:54

... Images were reprinted from Brian W Hurley and Cuong C Nguyen, “The spectrum of pseudomembranous enterocolitis and antibioticassociated diarrhea (2002)” discontinuance of use of offending antibiotic ... glucosylation of G-proteins (Fig 1.3) Site-directed modification of toxin B histidine residue of the nucleotide-binding site to glutamine resulted in 90% loss of toxic activity (Aktories and Just 1995; Hofmann, ... through primary 15 induction of the release of proinflammatory cytokine by myeloid cells prior to biomolecular disruption Expectedly however, similar cellular effects of toxin A was observable on...

Ngày tải lên: 16/09/2015, 15:54

... and actin isoform ratio 95 4.2.3 Effects of cdt with actin modifying agents 98 4.2.4 Changes in expression of signal proteins 99 4.2.5 Stimulation of stress -related proteins ... outcomes of PMC 1.2 Morphological views of PMC 1.3 Genetic map of C difficile PaLoc 1.4 Mode of action of toxin A and toxin B 12 1.5 Genetic map of C ... accessory role of CDT toxin in pathogenesis Unison mRNA expression of cdtA and cdtB was suggestive of bicistronic conformation of the cdt operon, supported by regulatory elements found upstream of cdtA...

Ngày tải lên: 16/09/2015, 15:54

... positions of the Ca of Ala156 in HYDJs and the Ca of Met156 in HYDBp located in the SGL3, which leads to the increased size of the substrate binding pocket of HYDJs The side chain of Ala156 is ... understanding of the roles of each of these residues will enable manipulation of these SGLs by rational design or molecular evolution methods to obtain the desired catalytic activity Overexpression of heterologous ... For preparation of the ligands, all structures were converted from isomeric SMILES (Simplified Molecular Input Line Entry System) to 3D structures using CORINA [46] Partial charges of the ligands...

Ngày tải lên: 18/02/2014, 08:20

... a half-life of 273 at 80 °C and even 28 at 100 °C In addition, NFX is active at pH The crystal structures of CTX and NFX allowed us to make detailed comparison of 12 xylanases, five from thermophilic ... reliable comparison of the enzyme structures in relation to their thermostability than earlier studies and helps us to understand the molecular basis of the thermostability of these industrially ... STAMP software [28] was applied The secondary structures were assigned with the DSSP software [29] The solvent accessible surface areas of xylanases were ˚ calculated with the NACCESS software...

Ngày tải lên: 20/02/2014, 23:20

... importance of the integrity of the alveolar epithelium in the pathogenesis of parenchymal fibrosis Opportunities to approach lung disease pathogenesis from the vantage point of a primary molecular ... Department of Internal Medicine, University of Cincinnati School of Medicine and Cincinnati VA Medical Center, Cincinnati, OH, USA Bruce C Trapnell, MD Department of Pediatrics and Department of Internal ... gained from the study of PAP about the role of GM-CSF in the lung has sparked interest in the use of anti GM-CSF approaches to control both pulmonary and extrapulmonary inflammation in a variety of...

Ngày tải lên: 05/03/2014, 23:20

... The results of MS of recombinant b-fructofuranosidase are close to the theoretical value of the molecular mass A peak of molecular ion at m ⁄ z = 58 879 Da was observed on the MALDITOF mass spectrum ... hydrodynamic radius ˚ ˚ of 16.78 A, average radius of 34.02 A and ratio of the shortest to the longest axis of 0.628 Kinetic parameters of b-fructofuranosidase The activity of b-fructofuranosidase was ... expression and purification of recombinant b-fructofuranosidase The high-resolution structure of b-fructofuranosidase from B longum is the first one for an enzyme of the GH32 family from nonsporulating...

Ngày tải lên: 06/03/2014, 00:21

... roles of Asn266 and Tyr370 in comparison with the structures of typical enzymes in the penicillin-recognizing family of serine-reactive hydrolases Results and Discussion Cumulative effects of amino ... available: Fig S1 Stereoview of the catalytic cleft of Hyb-24DN Fig S2 Stereoviews of surface structure of Ald-bound and unbound Hyb-24DNY Fig S3 Stereoview of the catalytic cleft of Hyb24DNY and class ... Although the mutation had negative effects on kcat (30% of that of Hyb24), the kcat ⁄ Km value of Hyb-24DNY (1.58 s)1Æmm)1) was four-fold to five-fold that of Hyb-24DN (0.34 s)1Æmm)1) and wild-type...

Ngày tải lên: 07/03/2014, 00:20

... blue G-250 Lane 1, lg of factor X; lane 2, 0.3 lg of factor X; lane 3, lg of factor IX; lane 4, lg of prothrombin; lane 5, lg of protein C; lane 6, lg of protein S; lane 7, lg of Gla-domainless factor ... permethylation of carbohydrates Carbohydr Res 131, 209–217 40 Yu SY, Wu S & Khoo KH (2006) Distinctive characteristics of MALDI-Q/TOF and TOF/TOF tandem mass spectrometry for sequencing of permethylated ... all of the Fuc residues may be attached to the terminal sequences As shown by MALDI-TOF/TOF MS/MS analyses of representative Fuc-containing major N-glycans (Fig 7), the trimannosyl core structures...

Ngày tải lên: 07/03/2014, 06:20

... occurred after h of Yield of CD8 (% of starch) A 40 30 20 10 0 5 10 15 20 25 Yield of CD8 (% of starch) B 40 30 20 reaction with the CLIP CGTase from A11 The differences in the time course of CD8 formation ... ratios of the CD8-imprinted CLIP CGTases suggests that the molecular imprinting had a pronounced effect on the structure of the active site of the enzymes Imprinting of the CGTases with CD of different ... the yield of CD8 increased four-fold with the CLIP CGTase from A11, and three-fold with the CLIP CGTase from BM, after 24 h of reaction The amount of CD8 produced by the CLIP CGTase from BM slowly...

Ngày tải lên: 07/03/2014, 10:20

... fluids of V volvacea only during the latter stages of primary growth In order to better understand these effects at the molecular level, we have now Fig RT-PCR analysis of total RNA isolated from ... sequence of native protein was N-ALSSHTLTLTNGFASPD Cloning of full-length cDNA of lac1 The cDNA contained a predicted ORF of 1557 bp encoding 519 amino acids (Fig 1) The amino acid sequence from ... analysis of transcription patterns of lac1 induced by different concentrations of copper Total RNA was isolated from V volvacea, V14, grown in defined medium with various concentrations of copper...

Ngày tải lên: 07/03/2014, 15:20

... loss of hydrogen bond and weak stacking and also (b) entropic and enthalpic contribution resulting from the nature of interaction of water in the vicinity of mismatch [16] However, lack of structural ... hybrid deviates from that of DNA duplex [11], comparison of the MD structure of parallel PNAÆDNA [36] with the B DNA indicates some amount of similarity especially with respect to lack of X-displacement ... program for visualization of structure and dynamics of biomolecules and STO – A program for computing stochastic paths In Modeling of Biomolecular Structure 4069 Effect of A .C mismatch in PNAÆDNA...

Ngày tải lên: 07/03/2014, 21:20

... part of the protein had apparently lost its cofactor Indeed, during the purification of especially NoxA-1, it was observed that the yellow colour of the enzyme fractions gradually disappeared From ... NoxC from A fulgidus M, Calibration proteins The molecular mass of the calibration proteins is indicated (kDa) Addition of EDTA to the assay mixture did not cause a decrease in activity of NoxA-1 ... program DNASTAR Expression of the NADH oxidase genes in E coli Ten millilitres of Luria–Bertani medium with 50 lgÆmL)1 kanamycin was inoculated (1%) from overnight cultures of E coli BL21(DE3) containing...

Ngày tải lên: 08/03/2014, 02:21

... Lowenergy structures of the b-amino acids that best fit are shown in Fig They all correspond to gauche(+) values of the h angle The methyl group of b2-HAla occupies a position close to that of CH2b of ... following questions Which structures of b-amino acids overlap the canonical structures of a-amino acids? Subsequently, is it possible to substitute one a-amino acid in the sequence of a linear peptide ... antagonist structures [21–23] By molecular mechanics calculations the conformers of Ac-HGly-NHMe, Ac-b2-HAla-NHMe and Ac-b3-HAlaNHMe have been generated and compared to the canonical structures of the...

Ngày tải lên: 08/03/2014, 08:20

... amplication of the fragment from )949 to +33 (5Â-CCGGAGCTCGAGCCGCTAAAGA ể FEBS 2002 Functional analysis of Xenopus MGP gene promoter (Eur J Biochem 269) 1949 GGAAAC-3Â) for amplication of the region from ... coding sequence (Fig 2) Analysis of the phase of each of the xMGP introns located within the coding region revealed that introns and are of phase I while intron is of phase II [29] The same phases ... region, one copy of a double stranded oligonucleotide spanning the region from )70 to )36 was fused upstream of pTATALUC Evaluation of reporter activity following transfection of A6 cells revealed...

Ngày tải lên: 08/03/2014, 10:20

... the Ki is in the order of 800 mm Comparison of the available RpiB structures suggests that allosteric changes not occur purely as a result of phosphate binding This type of behaviour has been ... using the 806 software sod [33], which was placed at the position of the molecular replacement solution From this starting point, the software arp ⁄ warp [34] was used to auto-build 99% of the structure, ... the stated conclusions apply, regardless of which molecules were used in the comparisons For the structures in the P42212 space group, the two molecules of the asymmetric unit form a homodimer...

Ngày tải lên: 15/03/2014, 00:20

... survival of ticks, for which the blood-meal from the host is the only source of energy Elucidation of the function of HlSCP1 in the hard tick may contribute a better understanding of the physiology of ... having a molecular mass of 53 kDa and a pI of 7.5 (Fig 2A), corresponding to the predicted size of the putative protein calculated from the HlSCP1 amino acid sequence To detect the localization of ... with a hexahistidine tag of kDa by SDS ⁄ PAGE (Fig 5, lane 3) The molecular mass of rHlSCP1 protein is  51 kDa, similar to the mass predicted from the amino acid sequence of HlSCP1 excluding the...

Ngày tải lên: 16/03/2014, 10:20