Dynamics of chemical

Present study aims to investigate the seasonal variations of physico-chemical properties and associated weed flora at Dalpatsagar reservoir.

9p chauchaungayxua11 23-03-2021 9 2   Download

This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist.

10p system191 01-06-2013 37 4   Download

Department of Nutritional Science, Faculty of Health and Welfare Science, Okayama Prefectural University, Soja, Japan; 2Division of Biological Science, Institute of Scientific and Industrial Research, Osaka University, Japan; 3Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Japan The function of the translation products of six different cDNAs for Acetabularia V-ATPase proteolipid subunit (AACEVAPD1 to AACEVAPD6 ) was examined using a Saccharomyces cerevisiae VMA3-deficient strain that lacked its own gene for one of the proteolipid subunits of V-AT...

8p system191 01-06-2013 40 5   Download

Gomesin is the first peptide isolated from spider exhibiting antimicrobial activities. This highly cationic peptide is composed of 18 amino-acid residues including four cysteines forming two disulfide linkages. The solution structure of gomesin has been determined using proton two-dimensional NMR (2D-NMR) and restrained molecular dynamics calculations. The global fold of gomesin consists in a wellresolved two-stranded antiparallel b sheet connected by a noncanonical b turn.

9p research12 01-06-2013 38 3   Download

Two-dimensional NMR and molecular dynamics simula-tions have been used to determine the three-dimensional structures of two hairpin DNA structures: d-CTAGAG GATCCUTTTGGATCCT (abbreviated as U1-hairpin) and d-CTAGAGGATCCTTUTGGATCCT (abbreviated as U3-hairpin). The 1 H resonances of both of these hairpin structures have been assigned almost completely.

9p research12 23-04-2013 21 3   Download

DNA ligases are the enzymes responsible for the repair of single-strandedanddouble-strandednicks indsDNA.DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNAhas yet to be solved.DNA ligases share common structural elementswith DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase–dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase....

7p tumor12 22-04-2013 40 2   Download

Amathematicalmodel hasbeendevelopedtostudy theeffect of external tryptophan on the trp operon. The model accounts for the effect of feedback repression by tryptophan through the Hill equation. We demonstrate that the trp operonmaintains an intracellular steady-state concentration in a fivefold range irrespective of extracellular conditions. Dynamic behavior of thetrp operon corresponding to varying levels of extracellular tryptophan illustrates the adaptive nature of regulation.

8p fptmusic 16-04-2013 49 4   Download

The low affinity of peptide nucleic acid (PNA) to hybridize with DNA in the presence of a mismatch endows PNA with a high degree of discriminat-ory capacity that has been exploited in therapeutics for the selective inhibi-tion of the expression of point-mutated genes. To obtain a structural basis for this intriguing property, molecular dynamics simulations are carried out on PNAÆDNA duplexes formed at the Ki-ras proto-oncogene, compri-sing the point-mutated (GAT), and the corresponding wild-type (GGT) codon 12. ...

16p fptmusic 11-04-2013 52 2   Download

Many organelle enzymes coded for by nuclear genes have N-terminal sequences, which directs them into the organelle (precursor) and are removed upon import (mature). The experiments described below charac-terize the differences between the precursor and mature forms of water-melon glyoxysomal malate dehydrogenase. Using recombinant protein methods, the precursor (p-gMDH) and mature (gMDH) forms were puri-fied to homogeneity using Ni 2+ –NTA affinity chromatography.

0p awards 05-04-2013 48 1   Download

The NMR solution structures of NTX-1 (PDB code 1W6B and BMRB 6288), a long neurotoxin isolated from the venom ofNaja naja oxiana, and the molecular dynamics simulation of these structures are reported. Calculations are based on 1114NOEs, 19 hydrogen bonds, 19 dihedral angle restraints and secondary chemical shifts derived from 1 Hto 13 C HSQC spectrum. Similar to other long neurotoxins, the three-finger like structure shows a double and a triple strandedb-sheet aswell as some flexible regions, particularly at the tip of loop II and the C-terminal tail....

0p awards 05-04-2013 46 2   Download

High-quality quantitative data generated under standardized conditions is critical for understanding dynamic cellular processes. We report strategies for error reduction, and algorithms for automated data processing and for establishing the widely used techniques of immunoprecipitation and immu-noblotting as highly precise methods for the quantification of protein levels and modifications.

12p dell39 27-03-2013 53 3   Download

Although the chemical nature of the catalytic mechanism of the serine pro-tease a-chymotrypsin (a-CT) is largely understood, the influence of the enzyme’s structural dynamics on its catalysis remains uncertain. Here we investigate whether a-CT’s structural dynamics directly influence the kinet-ics of enzyme catalysis.

17p inspiron33 23-03-2013 31 3   Download

The complexity of full-scale metabolic models is a major obstacle for their effective use in computational systems biology. The aim of model reduction is to circumvent this problem by eliminating parts of a model that are unimportant for the properties of interest.

16p inspiron33 23-03-2013 31 2   Download

The ergodic hypothesis, which assumes the independence of each cell of the ensemble from all the others, is a necessary prerequisite to attach single cell based explanations to the grand averages taken from population data. This was the prevailing view about the interpretation of cellular biology experi-ments that typically are performed on colonies of billions of cells.

9p galaxyss3 19-03-2013 36 2   Download

The molecular mechanism of cGMP-dependent protein kinase activation by its allosteric regulator cyclic-3¢,5¢-guanosine monophosphate (cGMP) has been intensely studied. However, the structural as well as thermo-dynamic changes upon binding of cGMP to type I cGMP-dependent protein kinase are not fully understood.

13p galaxyss3 19-03-2013 36 4   Download

Aberrant regulation of protein kinases impairs normal cellular functioning and may lead to disease. The protein kinase involved in the regulation of the dynamics of the actin cytoskeleton, Rho-kinase (ROCK), phosphory-lates various substrates (e.g. myosin light chain, myosin phosphatase), caus-ing the formation of actin fibers and tension inside cells.

17p galaxyss3 07-03-2013 37 6   Download

The nuage is a unique organelle in animal germ cells that is known as an electron-dense amorphous structure in the perinuclear region. Although the nuage is essential for primordial germ cell (PGC) determination and devel-opment, its roles and functions are poorly understood.

9p media19 05-03-2013 41 2   Download

Detailed understanding of the dynamics of living systems requires a means to monitor, in real time, changes in the levels of key components in response to specific stimuli. Applications involving cultured cells, tissue slices and implantation in living systems are discussed.

10p media19 04-03-2013 19 1   Download

The eukaryotic class 1 polypeptide chain release factor is a three-domain protein involved in the termination of translation, the final stage of poly-peptide biosynthesis. In attempts to understand the roles of the mid-dle domain of the eukaryotic class 1 polypeptide chain release factor in the transduction of the termination signal from the small to the large ribo-somal subunit and in peptidyl-tRNA hydrolysis, its high-resolution NMR structure has been obtained.

15p media19 04-03-2013 44 3   Download

In many laboratories, the requirement of microtubule-associated proteins (MAPs) and the stabilization of microtubules for the elongation of neurites has been intensively investigated, with controversial results being obtained. We have observed that the neurite microtubules of Cath.a-differentiated (CAD) cells, a mouse brain derived cell, are highly dynamic structures, and so we analyzed several aspects of the cytoskeleton to investigate the molecu-lar causes of this phenomenon.

14p vinaphone15 25-02-2013 40 4   Download