排序方式: 共有45条查询结果,搜索用时 625 毫秒
11.
Yuan Y Chung HS Leimkuhler C Walsh CT Kahne D Walker S 《Journal of the American Chemical Society》2005,127(41):14128-14129
EryCIII is a desosaminyltransferase that converts an inactive macrolide precursor to a biologically active antibiotic. It may have potential for the synthesis of unnatural macrolides with useful biological activities. However, it has been difficult to reconstitute the activity of EryCIII in vitro. We report here that purified, inactive EryCIII can be converted to an active catalyst by the addition of another protein encoded in the same gene cluster, EryCII. The EryCII-treated protein retains activity even when EryCII is removed. We also show that AknT, an activator protein from an unrelated gene cluster, is capable of activating EryCIII. Although the mechanism of activation is not yet understood, we have concluded from these experiments that these antibiotic Gtf activator proteins do not function to deliver substrates to EryCIII and do not exert their effects by forming stable complexes with the Gtf during the glycosyltransfer reaction. We report that activated EryCIII is capable of utilizing an alternative sugar donor, so these results lay the groundwork for the production of novel macrolides. 相似文献
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Leimkuhler C Chen L Barrett D Panzone G Sun B Falcone B Oberthür M Donadio S Walker S Kahne D 《Journal of the American Chemical Society》2005,127(10):3250-3251
The glycopeptide antibiotics prevent maturation of the bacterial cell wall by binding to the terminal d-alanyl-d-alanine moiety of peptidoglycan precursors, thereby inhibiting the enzymes involved in the final stages of peptidoglycan synthesis. However, there are significant differences in the biological activity of particular glycopeptide derivatives that are not related to their affinity for d-Ala-d-Ala. We compare the ability of vancomycin and a set of clinically relevant glycopeptides to inhibit Staphylococcus aureus PBP2 (penicillin binding protein), the major transglycosylase in a clinically relevant pathogen, S. aureus. We report experiments suggesting that activity differences between glycopeptides against this organism reflect a combination of substrate binding and secondary interactions with key enzymes involved in peptidoglycan synthesis. 相似文献
13.
Beta-2-Deoxy sugar nucleotides are substrates used by a variety of glycosyltransferases (Gtfs). We have developed a chemical route to synthesize beta-2-deoxy sugar phosphates that starts from alpha-glycosyl chlorides. Our approach reliably provides access to a range of NDP beta-2-deoxy sugars essential for studying glycosyltransferases involved in the synthesis of biologically active natural products. 相似文献
14.
A broad array of canonical sampling methods are available for molecular simulation based on stochastic-dynamical perturbation
of Newtonian dynamics, including Langevin dynamics, Stochastic Velo- city Rescaling, and methods that combine Nosé-Hoover
dynamics with stochastic perturbation. In this article we discuss several stochastic-dynamical thermostats in the setting
of simulating systems with holonomic constraints. The approaches described are easily implemented and facilitate the recovery
of correct canonical averages with minimal disturbance of the underlying dynamics. For the purpose of illustrating our results,
we examine the numerical application of these methods to a simple atomic chain, where a Fixman term is required to correct
the thermodynamic ensemble. 相似文献
15.
Molecular dynamics typically incorporates a stochastic-dynamical device, a “thermostat,” in order to drive the system to the
Gibbs (canonical) distribution at a prescribed temperature. When molecular dynamics is used to compute time-dependent properties,
such as autocorrelation functions or diffusion constants, at a given temperature, there is a conflict between the need for
the thermostat to perturb the time evolution of the system as little as possible and the need to establish equilibrium rapidly.
In this article we define a quantity called the “efficiency” of a thermostat which relates the perturbation introduced by
the thermostat to the rate of convergence of average kinetic energy to its equilibrium value. We show how to estimate this
quantity analytically, carrying out the analysis for several thermostats, including the Nosé-Hoover-Langevin thermostat due
to Samoletov et al. (J. Stat. Phys. 128:1321–1336, 2007) and a generalization of the “stochastic velocity rescaling” method suggested by Bussi et al. (J. Chem. Phys. 126:014101,
2007). We find efficiency improvements (proportional to the number of degrees of freedom) for the new schemes compared to Langevin
Dynamics. Numerical experiments are presented which precisely confirm our theoretical estimates. 相似文献
16.
We discuss a dynamical technique for sampling the canonical measure in molecular dynamics. We present a method that generalizes
a recently proposed scheme (Samoletov et al., J. Stat. Phys. 128:1321–1336, 2007), and which controls temperature by use of a device similar to that of Nosé dynamics, but adds random noise to improve ergodicity.
In contrast to Langevin dynamics, where noise is added directly to each physical degree of freedom, the new scheme relies
on an indirect coupling to a single Brownian particle. For a model with harmonic potentials, we show under a mild non-resonance
assumption that we can recover the canonical distribution. In spite of its stochastic nature, experiments suggest that it
introduces a relatively weak perturbative effect on the physical dynamics, as measured by perturbation of temporal autocorrelation
functions. The kinetic energy is well controlled even in the early stages of a simulation. 相似文献
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A systematic investigation of the synthetic utility of glycopeptide glycosyltransferases 总被引:2,自引:0,他引:2
Oberthür M Leimkuhler C Kruger RG Lu W Walsh CT Kahne D 《Journal of the American Chemical Society》2005,127(30):10747-10752
Glycosyltransferases involved in the biosynthesis of bacterial secondary metabolites may be useful for the generation of sugar-modified analogues of bioactive natural products. Some glycosyltransferases have relaxed substrate specificity, and it has been assumed that promiscuity is a feature of the class. As part of a program to explore the synthetic utility of these enzymes, we have analyzed the substrate selectivity of glycosyltransferases that attach similar 2-deoxy-L-sugars to glycopeptide aglycons of the vancomycin-type, using purified enzymes and chemically synthesized TDP beta-2-deoxy-L-sugar analogues. We show that while some of these glycopeptide glycosyltransferases are promiscuous, others tolerate only minor modifications in the substrates they will handle. For example, the glycosyltransferases GtfC and GtfD, which transfer 4-epi-L-vancosamine and L-vancosamine to C-2 of the glucose unit of vancomycin pseudoaglycon and chloroorienticin B, respectively, show moderately relaxed donor substrate specificities for the glycosylation of their natural aglycons. In contrast, GtfA, a transferase attaching 4-epi-L-vancosamine to a benzylic position, only utilizes donors that are closely related to its natural TDP sugar substrate. Our data also show that the spectrum of donors utilized by a given enzyme can depend on whether the natural acceptor or an analogue is used, and that GtfD is the most versatile enzyme for the synthesis of vancomycin analogues. 相似文献