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The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of the enzyme. Molecular dynamics simulations of the simple ligand, tetramethylammonium, crossing this bottleneck region are conducted using umbrella potential sampling and activated flux techniques. The low potential of mean force obtained is consistent with the fast reaction rate of acetylcholinesterase observed experimentally. From the results of the activated dynamics simulations, local conformational fluctuations of the gorge residues and larger scale collective motions of the protein are found to correlate highly with the ligand crossing. 相似文献
22.
Comparing the shapes of regression functions 总被引:1,自引:0,他引:1
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GW Patton R Stephens IA Sidorov X Xiao RA Lempicki DS Dimitrov RH Shoemaker G Tudor 《BMC bioinformatics》2006,7(1):81
Background
Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes. 相似文献26.
RH Behrens Z Bisoffi A Björkman J Gascon C Hatz T Jelinek F Legros N Mühlberger P Voltersvik 《Malaria journal》2006,5(1):1-4
Background
Thick blood films are routinely used to diagnose Plasmodium falciparum malaria. Here, they were used to diagnose volunteers exposed to experimental malaria challenge.Methods
The frequency with which blood films were positive at given parasite densities measured by PCR were analysed. The poisson distribution was used to calculate the theoretical likelihood of diagnosis. Further in vitro studies used serial dilutions to prepare thick films from malaria cultures at known parasitaemia.Results
Even in expert hands, thick blood films were considerably less sensitive than might have been expected from the parasite numbers measured by quantitative PCR. In vitro work showed that thick films prepared from malaria cultures at known parasitaemia consistently underestimated parasite densities.Conclusion
It appears large numbers of parasites are lost during staining. This limits their sensitivity, and leads to erroneous estimates of parasite density. 相似文献27.
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Lauren RH Krumpe Kathryn M Schumacher James B McMahon Lee Makowski Toshiyuki Mori 《BMC biotechnology》2007,7(1):65
Background
Amino acid sequence diversity is introduced into a phage-displayed peptide library by randomizing library oligonucleotide DNA. We recently evaluated the diversity of peptide libraries displayed on T7 lytic phage and M13 filamentous phage and showed that T7 phage can display a more diverse amino acid sequence repertoire due to differing processes of viral morphogenesis. 相似文献29.
Henchman RH McCammon JA 《Protein science : a publication of the Protein Society》2002,11(9):2080-2090
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Djian P; Phillips M; Easley K; Huang E; Simon M; Rice RH; Green H 《Molecular biology and evolution》1993,10(6):1136-1149
The involucrin genes of the mouse (Mus musculus) and the rat (Rattus
norvegicus) have been cloned and sequenced. The coding region of each gene
contains, at site P, a segment of repeats homologous to that of other
nonanthropoid mammals. In contrast to the repeats of species belonging to
different mammalian orders, many individual repeats of the mouse and the
rat can be matched. Both before and after the divergence of the two
species, these repeats have been the site of systematic alterations in
nucleotide sequence. One of the alterations is the correction of
nucleotides of one repeat by those of another. Corrected nucleotides may be
closely linked to flanking nucleotides that are uncorrected; the systematic
correction process therefore appears to be due to gene conversion. There is
a stretch of 18 reiterated CAGs in the segment of repeats of the Mus gene;
most of these reiterations were introduced recently, supporting the idea
that the gene was generated originally from poly CAG. An antiserum to a
synthetic peptide encoded by the segment of repeats of the Mus gene reveals
differentiation- specific expression of the gene in the epidermis.
相似文献