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Computational Chemistry and Enzymology
362. H.-Y. Mei; T. W. Karet and T. C. Bruice. A computational approach
to the mechanism of self-cleavage of hammerhead RNA. Proc. Natl.
Acad. Sci (USA) 1989, 86, 9727.
401. O. Almarsson and T. C. Bruice. Evaluation of the factors influencing
reactivity and steeospecificity in NAD(P)H dependent dehydrogenase
enzymes. J. Am. Chem. Soc. 1993, 115, 2125.
406. O. Almarsson; A. Sinha; E. Gopinath and T. C. Bruice. The Mechanism
of One-electron oxidationof NAD(P)H and the function of NADH Bound
to Catalase. J. Am. Chem. Soc. 1993, 115, 7093.
433. L. P. Olson and T. C. Bruice. Electron tunneling and ab initio
calculations related to the one-electron oxidation of NAD(P)H bound
to catalase. Biochemistry 1995, 34, 7335-7347.
438. F. C. Lightstone and T. C. Bruice. Ground state conformations
and entropic and enthalpic factors in the efficiency of intramolecular
and enzyme reactions. 1. Cyclic anhydride formation by substituted
glutarates, succinate and 3.6-endoxo-?4-tetrahydrophthalate monophenyl
esters. J. Am. Chem. Soc. 1996, 118, 2595-2605.
443. R. A. Torres; O. Almaesson and T. C. Bruice. Molecular mechanics
calculations of the riboacetal internucleotide linkage in double
and triple helices. Proc. Natl. Acad. Sci (USA) 1996, 93, 6875-6880.
444. L. P. Olson; J. Luo; O. Almarsson; and T. C. Bruice. Mechanism
of aldehyde oxidation catalyzed by horse liver alcohol dehydrogenase.
Biochemistry 1996, 35, 9782-9791.
445. H. Adelsteinsson; A. H. Maulitz and T. C. Bruice. Calculation
of the potential energy surface for the intermolecular amide hydrogen
bonds using semiempirical and ab initio methods. J. Am. Chem. Soc.
1996, 118, 7689-7693.
450. Y-J. Zheng & T. C. Bruice. On the Dehalogenation Mechnism
of 4-Chlorobenzoate by 4-Chlorobenzoyl CoA Dehydrogenase: Insights
from Study Based on Active Site Model. J. Am. Chem. Soc. 1997, 17,
3868-3877.
451. Y-Y. Zheng & T. C. Bruice. Is Strong Hydrogen Bonding in
the Transition State Enough To Account for the Observed Rate Acceleration
in a Mutant of Papain? Proc. Natl. Acad. Sci. 1997, 94, 4285.
453. A. H. Maulitz; F. C. Lightstone; Y-J. Zheng & T. C. Bruice.
Non- Enzymatic and Enzymatic Hydrolysis of Alkyl Halides. I. A Theoretical
Study of the SN2 Reactions of Acetate and Hydroxide Ions with Alkyl
Chlorides. Proc. Natl. Acad. Sci (USA). 1997, 94, 6591.
454. F. C. Lightstone; Y-J. Zheng; A. H. Maulitz & T. C. Bruice.
Non-enzymatic and Enzymatic Hydrolysis of Alkyl Halides. A Haloalkane
Dehalogenation Enzyme Evolved to Stabilized the Gas Phase Transition
State of an SN2 Displacement Reaction. Proc. Natl. Acad. Sci. (USA)
1997, 94, 8417.
455. J. Luo & T. C. Bruice. Nanosecond Molecular Dynamics Study
of a Polycation Ribonucleic Guanidine (RNG) Duples with a Complimentary
DNA Oligomer Strand. J. Am. Chem. Soc. 1997, 119, 6693.
457. Y-J. Zheng & T. C. Bruice. A Theoretical Examination of
the Factors Controlling the Catalytic Efficiency of a Transmethylation
Enzyme: Catechol O-Methyltransferase. J. Am. Chem. Soc. 1997, 119,
8137.
458. F. C. Lightstone & T. C. Bruice. Separation of Ground State
and Transition State Effects in Intramolecular and Enzymatic Reactions.
II. A Theoretical Study of the Formation of Transition States in
Cyclic Anhydride Formation. J. Am. Chem. Soc. 1997, 119, 9103.
459. Y-J. Zheng & T. C. Bruice. Conformation of coenzyme Pyrroloquinolinequinone
(PQQ) and the Role of Ca2+ in the Catalytic Mechanism of Quinoprotein
Methanol Dehydrogenase. Proc. Natl. Acad. Sci. (USA) 1997, 94, 11881.
460. J. Luo & T. C. Bruice. Nanosecond Molecular Dynamics of
Hybrid Triplex and Duplex of Polycation Deoxyribonucleic Guanidine
(DNG) Strands with a Complimentary DNA Strand. J. Am. Chem. Soc.
1998, 120, 1115.
461. Y-J. Zheng & T. C. Bruice. Rapid Enzyme-catalyzed Heterolytic
C-H Bond Cleavage by A Base Strength Amplification Mechanism: A
Theoretical Examination of the Mechanism of Oxidation of Vitamin
K. J. Am. Chem. Soc. 1998, 120, 1623.
462. H. Adalsteinsson & T. C. Bruice. What is the Mechanism of
Catalysis of Ester Aminolysis by Weak Amine Bases? Comparison of
Experimental Studies and Theoretical Investigation of the Aminolysis
of Substituted Phenyl Esters of Qunoline-6- and -8-Carboxylic Acids.
J. Am. Chem. Soc. 1998, 120, 3440.
463. Y-J. Zheng & T. C. Bruice. Role of a Critical Water in Scytalone
Dehydratase Calalyzed Reaction. Proc. Natl. Acad. Sci. (USA) 1998,
95, 4158.
464. Y-J. Zheng & T. C. Bruice. Identifying the Intermediate
in the Dioxygen Transfer from 4a-Hydroperoxyflavin Anion to Phenolate
and Indole Anions. Bioorganic Chem. 1998, 25, 331.
467. F. C. Lightstone; Y-J. Zheng & T. C. Bruice. Molecular Dynamics
Simulations of Ground and Transition States for the SN2 Displacement
of Cl- from 1,2- Dichloroethane at the Active Site of Xanthobacter
Autotrophicus Haloalkane Dehalogenase. J. Am. Chem. Soc. 1998, 120,
5611.
469. B. Schiøtt; Y.-J. Zheng & T. C. Bruice. Theorectical
Investigation of the Hydride Transfer from Formate to NAD+ and the
Implications for the Catalytic Mechanism of Formate Dehydrogenase.
J. Am. Chem. Soc. 1998, 120, 7192.
474. B. Shiøtt; B. B. Iversen; G. K. H. Madsen, & T.C.
Bruice. On the Electronic Nature of Low-Barrier Hydrogen Bonds in
Enzymatic Reactions. Proc. Natl. Acad. Sci. (USA) 1998, 95, 12799.
472. F. C. Lightstone; Y-J. Zheng & T. C. Bruice. The Structure
of the ES Complex and Transition State Formed in the SN2 Displacement
of Cl- from 1,2-Dichloroethane at the Active Site of Xanthobacter
autothropicus Haloalkane Dehalogenase. Bioorganic Chem. 1998, 26,
169.
473. F. C. Lightstone & T. C. Bruice. Enthalpy and Entropy
in Ring Closure Reactions. Bioorganic Chem. 1998, 26, 193.
474. B. Shiøtt; B. B. Iversen; G. K. H. Madsen; & T.C.
Bruice. On the Electronic Nature of Low-Barrier Hydrogen Bonds in
Enzymatic Reactions. Proc. Natl. Acad. Sci. (USA) 1998, 95, 12799.
475. E. Y. Lau & T. C. Bruice. Importance of Correlated Motions
in Forming Highly Reactive Near Attack Conformations in Catechol
O Methyltransferase. J. Am. Chem. Soc. 1998, 120, 12387.
477. B. Shiøtt; B. B. Iversen; G. K. H. Madsen; & T.C.
Bruice. Characterization of the Short Strong Hydrogen Bond in Benzoylacetone
by Ab Initio Calculations and Accurate Diffraction Experimentts.
Implications for the Electronic Nature of Low-Barrier Hydrogen Bonds
in Enzyme Reactions. J. Am. Chem. Soc. 1998, 120, 12117.
478. T. C. Bruice & F. C. Lightstone. Ground State and Transition
State Contributions to Intramolecular and Enzymatic Reactions. Acc.
Chem Res. 1999, 32, 127. PDF
482. J. Luo; K. Kahn; & T. C. Bruice. The Linear Dependence of
log(kcat/Km) for Reduction of NAD+ by PhCH2OH on the Distance Between
Reactants when Catalyzed by Horse Liver Alcohol Dehydrogenase and
203 Single Point Mutants. Bioorg. Chem. 1999, 27, 289. PDF
483. E. Y. Lau & T. C. Bruice. Consequences of Breaking the Asp-His
Hydrogen Bond of the Catalytic Triad: Effects on the Structure and
Dynamics of the Serine Esterase Cutinase. J. Biophys. 1999, 77,
85.
484. R. Torres; B. Schiott; & T. C. Bruice. Molecular Dynamics
Simulations of Ground and Transition States for the Hydrid Transfer
from Formate to NAD+ in Formate Dehydrogenase. J. Am. Chem. Soc.
1999, 121, 8164.
485. E. Y. Lau & T. C. Bruice. Active Site Dynamics of the HhaI
Methyltransferase: Insights from Computer Simulation. J. Mol. Bio.
1999, 293, 9.
488. R. Torres & T. C. Bruice. Theoretical Investigation of the
(1,2)-Sigmatropic Hydrogen Migration in the Mechanism of Oxidation
of 2-Aminobenzoyl-CoA by 2- Aminobenzoyl-CoA Monooxygenase/Reductase.
Proc. Natl. Acad. Sci. (USA) 1999, 96, 14748.
490. Kahn, K.; Bruice, T. C.. Transition state and ground state structures
and their interaction with the active site residues in catechol
O–methyltransferase. J. Am. Chem. Soc. 2000, 122, 46–51.
492. Adalsteinsson, H.; Bruice, T. C.. Generation of putative neuroregenerative
drugs. 1. Virtual point mutations to the polyketide rapamycin. Bioorg.
Med. Chem. 2000, 8, 617–624. PDF
493. Adalsteinsson, H.; Bruice, T. C.. Generation of putative neuroregenerative
drugs. 2. Screening virtual libraries of novel polyketides which
possess the binding domain of rapamycin. Bioorg. Med. Chem. 2000,
8, 625–635. PDF
494. Luo, J.; Bruice, T. C.. Structural properties of hybrid triplex
of polycation deoxyribonucleic S–methylthiourea (DNmt) strands
with a complementary DNA strand, probed by nanosecond molecular
dynamics. J. Biomol. Stru. Dyn. 2000, 17, 629–643.
495. Torres, R. A.; Bruice, T. C.. The mechanism of phosphodiester
hydrolysis: near in-line attack conformations in the hammerhead
ribozyme. J. Am. Chem. Soc. 2000, 122, 781–791.
497. Bruice, T. C.; Benkovic, S. J.. Chemical basis for enzyme catalysis.
Biochemistry 2000, 39, 6267–74. PDF
500. Kahn, K.; Bruice, T. C.. a-Ketoamides and a-ketocarbonyls: Conformational
analysis and development of all-atom OPLS force field. Bioorg. Med.
Chem. 2000, 8, 1881-1891. PDF
501. Lau, E.; Bruice, T. C.. Comparison of the dynamics for ground-state
and transition-state structures in the active site of catechol O-methyltransferase.
J. Am. Chem. Soc. 2000, 122, 7165-7171.
503. Lau, E. Y.; Kahn, K.; Bash, P. A.; Bruice, T. C.. The importance
of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular
mechanics study of a haloalkane dehalogenase. Proc. Natl. Acad.
Sci. (USA) 2000, 97, 9937-9942.
504. Bruice, T. C.; Kahn, K.. Computational enzymology. Curr. Opin.
Chem. Biol. 2000, 4, 540-544.
505. Zheng, Y.-J.; Xia, Z.-X.; Chen, Z.-W.; Mathews, F. S.; Bruice,
T. C.. Catalytic mechanism of quinoprotein methanol dehydrogenase:
a theoretical and x-ray crystallographic investigation. Proc. Natl.
Acad. Sci. (USA) 2001, 98, 432-434.
506. Lau, E. Y.; Newby, Z. E.; Bruice, T. C.. A theoretical examination
of the acid-catalyzed and noncatalyzed ring-opening reaction of
an oxirane by nucleophilic addition of acetate. Implications to
epoxide hydrolases. J. Am. Chem. Soc. 2001, 123, 3350-3357.
510. Lau, E. Y.; Bruice, T. C.. The active site dynamics of 4-chlorobenzoyl-CoA
dehalogenase. Proc. Natl. Acad. Sci. (USA) 2001, 98, 9527-32.
513. Luo, J.; Bruice, T. C.. Dynamic structures of horse liver alcohol
dehydrogenase (HLADH): Results of molecular dynamics simulations
of HLADH-NAD+-PhCH2OH, HLADH-NAD+-PhCH2O-, and HLADH-NADH-PhCHO.
J. Am. Chem. Soc. 2001, 123, 11952-59. PDF
514. Kahn, K.; Bruice, T. C.. Diphtheria toxin catalyzed hydrolysis
of NAD+: Molecular dynamics study of enzyme-bound substrate, transition
state, and inhibitor. J. Am. Chem. Soc. 2001, 123, 11960-69.
519. Hur, S.; Bruice, T, C.. The mechanism of catalysis of the chorismate
to prephenate reaction by the Escherichia coli mutase enzyme. Proc.
Natl. Acad. Sci. (USA) 2002, 99, 1176-1181. PDF
520. Bruice, T. C.. A view at the millennium: the efficiency of enzymatic
catalysis. Acc. Chem. Res. 2002, 35, 139-146. PDF
521. Newby, Z. E. R.; Lau, E.; Bruice, T. C.. A theoretical examination
of factors controlling the catalytic efficiency of the DNA-(adenine-N6)-methyltransferase
from Thermus aquaticus. Proc. Natl. Acad. Sci. (USA) 2002, 7922-7927.
522. Kahn, K.; Bruice, T. C.. Parameterization of OPLS–AA force
field for the conformational analysis of macrocyclic polyketides.
J. Comput. Chem. 2002, 23, 977-996. PDF
523. Hur, S.; Bruice, T. C.. The mechanism of cis-trans isomerization
of prolyl peptides by cyclophilin. J. Am. Chem. Soc. 2002, 124,
7303-7313. PDF
524. Mazumder, D.; Kahn, K.; Bruice, T. C., Computer Simulations
of trypanosomal nucleoside hydrolase: Determination of the protonation
state of the bound transition state analog. J. Am. Chem. Soc. 2002,
124, In press. PDF
525. Hur, S.; Bruice, T. C.. Molecular dynamics study of orotidine
5’-monophosphate decarboxylase in ground state and in intermediate
state: A role of the 203-218 loop dynamics. Proc. Natl. Acad. Sci.
(USA) 2002, 15, 9668-9673.
526. Reddy, S.Y.; Kahn, K.; Zheng; Y. J.; Bruice, T. C.. Protein
engineering of nitrile hydratase activity of papain: Molecular dynamics
study of a mutant and wild-type enzyme. J.Am. Chem. Soc. 2002, 124,
12979-90. PDF
and Supporting
Info
527. Schiøtt, B. & Bruice, T. C.. The reaction mechanism
of soluble epoxide hydrolase: Insights from molecular dynamics simulations.
J. Am. Chem. Soc. 2002, 124, 14558-14570.
528. Mazumder, D. & Bruice, T. C., Exploring nucleoside hydrolase
catalysis in silico: Molecular dynamic study of enzyme-bound substrate
and transition state. J. Am. Chem. Soc. 2002, 124, 14591-14600.
PDF
529. Luo, J. & Bruice, T. C.. Ten nanosecond molecular dynamics
simulation of the motions of the horse liver alcohol dehydrogenase•PhCH2O-
complex. Proc. Natl. Acad. Sci (USA), 2002, 99, 16597-16600.
530. Hur, S. & Bruice, T. C.. Comparison of formation of reactive
conformers for the SN2 displacements by CH3CO2- in water and by
Asp124- CO- in a haloalkane dehalogenase. Proc. Natl. Acad. Sci.
2003, 100, 2215-2219. PDF
531. Hur, S. & Bruice, T. C.. Enzymes Do What is Expected (Chalcone
isomerase vs. Chorismate mutase). J. Am. Chem. Soc. 2002, 125, 1472-1473.
Editors Choice: Highlights of recent literature, Laussez-faire Versus
Keynesian, Science, February 2003, 299, issue 7 PDF
533. Hur, S. & Bruice, T. C.. Comparison of formation of reactive
conformers (NACs) for the Claisen rearrangement of chorismate to
prephenate in water and in E. coli Mutase: The Efficiency of the
Enzyme Catalysis. J. Am. Chem. Soc. 2003, 125, 5964-5972. PDF
534. Reddy, S. Y., Mathews, F. S., Zheng, Y-J. and Bruice, T. C..
Quinoprotein methanol dehydrogenase: A molecular dynamic study and
comparison with crystal structure. J. Mol. Struct. 2003, 655 (2),
269-277. PDF
535. Mazumder, D., Kahn, K. & Bruice, T. C.. Computational
study of ketosteroid isomerase: Insights from molecular dynamic
simulation of enzyme bound substrate and intermediate. J. Am. Chem.
Soc., 2003, 125, 7553-7561.
537. Kahn, K. and Bruice, T. C.. Comparison of reaction energetics
and leaving group interactions during the enzyme-catlyzed and uncatalyzed
displacement of chloride from haloalkanes, J. Pys. Chem. B, 2003,
107, 6876-6885.
538. Reddy, S. Y. and Bruice, T. C.. In silico studies of the mechanism
of methanol oxidation by quinoprotein methanol dehydrogenase. J.
Am. Chem. Soc. 2003, 125, 8141-8150. PDF
and Supporting
Info
539. Torres, R. A.; Himo, F; Bruice, T. C.; Noodleman, L. &
Lovell, T.. Theoretical examination of Mg2+ mediated hydrolysis
in the Hammerhead ribozyme. J. Am. Chem. Soc. 2003, 125, 9861-9867.
540. Obika, S., Reddy, S. Y., Bruice, T. C.. Sequence specific
DNA binding of Ets-1 Transcription Factor: Molecular dynamics study
on the ETS domain-DNA complexes, J. Mol. Biol. 2003, 331, 345-369.
PDF,
Supporting
Figure and Supporting
Table
541. Hur, S. & Bruice, T. C.. Just a Near Attack Conformer
for Catalysis (Chorismate to Prephenate Rearrangements in Water,
Antibody, Enzymes, and Their Mutants). J. Am. Chem. Soc. 2003, 125,
10540-10542.
542. Hur, S. & Bruice, T. C.. The NAC approach to the study
of the chorismate to prephenate reaction. Proc. Natl. Acad. Sci.
2003, 100, 12015-12020.
543. Reddy, S. Y., Obika, S., Bruice, T. C.. Conformational and
dynamics of Ets-1 ETS domain-DNA complexes. Proc. Natl. Acad. Sci.
2003, 100, 15475-15480. PDF,
Supporting
Figure, Supporting
Table, Supporting
Method
545. Hur, S. & Bruice, T. C., Transition state stabilization
by general acid catalysis, water expulsion and enzyme reorganization
in Medieago sativa Chalcone isomerase. Proc. Natl. Acad. Sci., 2004,
101, 2730-2735.
546. Kahn, K. and Bruice, T. C.. Systematic convergence of energies
to basis set and treatment of electron correlation: focal point
conformational analysis of methanol. Theor. Chem. Acc. 2004, 111,
18-24.
547. Reddy, S. Y. & Bruice, T. C., Mechanism of glucose oxidation
by quinoprotein soluble glucose dehydrogenase: Insights from molecular
dynamics studies. J. Am. Chem. Soc., 2004, 126, 2431-2438. PDF,
Supporting
Information
549. Mazumder, D., Kahn, K. &
Bruice, T. C., Structural alterations of the thermophilic indole
glycerol phosphate synthase with temperature. J. Am. Chem. Soc.,
2004, 126, 5936-5937.
552. Moebitz, H. & Bruice, T.C.,
Multiple substrate binding states and chiral recognition in cofactor-independent
Glutamate racemase: A molecular dynamic study. Biochemistry, 2004,
43, 9685-9694.
553. Reddy, S.Y. & Bruice, T.C.,
Review: Determination of enzyme mechanisms by molecular dynamic
studies on quinoproteins, methanol dehydrogenase and soluble glucose
dehydrogenase, Protein Science, 2004, 13, 1965-1978. PDF
554. Reddy, S.Y. & Bruice, T.C.,
Mechanisms of ammonia activation and ammonium ion inhibition of
quinoprotein methanol dehydrogenase: A computational approach. Proc.
Natl. Acad. Sci. (USA), 2004, 101(45), 15887-15892. PDF
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