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Simulating biochemical physics with ...

University of Minnesota., Chemical Physics.

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Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations./
Author:	Wong, Kin-Yiu.
Description:	342 p.
Notes:	Adviser: Jiali Gao.
Contained By:	Dissertation Abstracts International69-08B.
Subject:	Chemistry, Biochemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3323547
ISBN:	9780549751588

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations.
Wong, Kin-Yiu.

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations. - 342 p.

Adviser: Jiali Gao.

Thesis (Ph.D.)--University of Minnesota, 2008.

We have simulated two enzymatic reactions with molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) techniques. One reaction is the hydrolysis of the insecticide paraoxon catalyzed by phosphotriesterase (PTE). PTE is a bioremediation candidate for environments contaminated by toxic nerve gases (e.g., sarin) or pesticides. Based on the potential of mean force (PMF) and the structural changes of the active site during the catalysis, we propose a revised reaction mechanism for PTE. Another reaction is the hydrolysis of the second-messenger cyclic adenosine 3'-5'-monophosphate (cAMP) catalyzed by phosphodiesterase (PDE). Cyclicnucleotide PDE is a vital protein in signal-transduction pathways and thus a popular target for inhibition by drugs (e.g., ViagraRTM). A two-dimensional (2-D) free-energy profile has been generated showing that the catalysis by PDE proceeds in a two-step SN2-type mechanism.

ISBN: 9780549751588Subjects--Topical Terms:

1017722
Chemistry, Biochemistry.

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations.
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020 $a 9780549751588
035 $a (UMI)AAI3323547
035 $a AAI3323547
040 $a UMI $c UMI
100 1 $a Wong, Kin-Yiu. $3 1030705
245 1 0 $a Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations.
300 $a 342 p.
500 $a Adviser: Jiali Gao.
500 $a Includes supplementary digital materials.
500 $a Source: Dissertation Abstracts International, Volume: 69-08, Section: B, page: 4777.
502 $a Thesis (Ph.D.)--University of Minnesota, 2008.
520 $a We have simulated two enzymatic reactions with molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) techniques. One reaction is the hydrolysis of the insecticide paraoxon catalyzed by phosphotriesterase (PTE). PTE is a bioremediation candidate for environments contaminated by toxic nerve gases (e.g., sarin) or pesticides. Based on the potential of mean force (PMF) and the structural changes of the active site during the catalysis, we propose a revised reaction mechanism for PTE. Another reaction is the hydrolysis of the second-messenger cyclic adenosine 3'-5'-monophosphate (cAMP) catalyzed by phosphodiesterase (PDE). Cyclicnucleotide PDE is a vital protein in signal-transduction pathways and thus a popular target for inhibition by drugs (e.g., ViagraRTM). A two-dimensional (2-D) free-energy profile has been generated showing that the catalysis by PDE proceeds in a two-step SN2-type mechanism.
520 $a Furthermore, to characterize a chemical reaction mechanism in experiment, a direct probe is measuring kinetic isotope effects (KIEs). KIEs primarily arise from internuclear quantum-statistical effects, e.g., quantum tunneling and quantization of vibration. To systematically incorporate the quantum-statistical effects during MD simulations, we have developed an automated integration-free path-integral (AIF-PI) method based on Kleinert's variational perturbation theory for the centroid density of Feynman's path integral. Using this analytic method, we have performed ab initio pathintegral calculations to study the origin of KIEs on several series of proton-transfer reactions from carboxylic acids to aryl substituted alpha-methoxystyrenes in water. In addition, we also demonstrate that the AIF-PI method can be used to systematically compute the exact value of zero-point energy (beyond the harmonic approximation) by simply minimizing the centroid effective potential.
590 $a School code: 0130.
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Chemistry, Physical. $3 560527
650 4 $a Physics, Molecular. $3 1018648
690 $a 0487
690 $a 0494
690 $a 0609
710 2 $a University of Minnesota. $b Chemical Physics. $3 1030704
773 0 $t Dissertation Abstracts International $g 69-08B.
790 $a 0130
790 1 0 $a Cramer, Christopher J. $e committee member
790 1 0 $a Gao, Jiali, $e advisor
790 1 0 $a Truhlar, Donald G. $e committee member
790 1 0 $a York, Darrin M. $e committee member
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3323547