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2000-Present
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.
491. Kojima, N.; Bruice, T. C.. Replacement of the phosphorodiester
linkages of RNA with guanidinium linkages: The solid-phase synthesis
of ribonucleic guanidine. Org. Lett. 2000, 2, 81–84.
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. 496. Arya, D. P.; Bruice, T. C.. Solid-phase synthesis of oligomeric
deoxynucleic-thiourea (DNT) and deoxynucleic S–methylthiourea
(DNmt): a neutral/polycationic analogue of DNA. Bioorg. Med. Chem.
Lett. 2000, 10, 691-693. 497. Bruice, T. C.; Benkovic, S. J.. Chemical basis for enzyme catalysis.
Biochemistry 2000, 39, 6267–74. PDF
498. Linkletter, B. A.; Bruice, T. C.. Solid-phase synthesis of positively
charged deoxynucleic guanidine (DNG) modified oligonucleotides containing
neutral urea linkages: effect of charge deletions on binding and
fidelity. Bioorg. Med. Chem. 2000, 8, 1893-1901. 499. Barakar, D. A.; Kwok; Y.; Bruice, T. W. and Bruice, T. C.. Deoxynucleic
Guanidine/Peptide Nucleic Acid Chimeras: Synthesis, Binding and
Invasion Studies with DNA. J. Am. Chem Soc. 2000, 122, 5244. 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. 502. Satz, A. L. & Bruice, T. C.. Synthesis of Fluorescent Microgonotropens
(FMGTs) and Their Interactions with dsDNA. Bioorg. Med. Chem. 2000,
8, 1871-1880. PDF
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.
507. Satz, A.. L. & Bruice, T. C.. Recognition of nine base pairs
in the minor groove of dsDNA by a Tripyrrole Peptide-Hoechst Conjugate.
J. Am. Chem. Soc. 2001, 123, 2469-2477. PDF
508. Linkletter, B.; Szabo, I. E. and Bruice, T. C.. Solid phase
synthesis of oligopurine deoxynucleic guanidine (DNG) and analysis
of binding with DNA oligomers. Nucleic Acid Res. 2001, 29, 2370-2376.
509. Satz, L. S.; White, C. M.; Beerman, T. A. & Bruice, T. C..
Double -stranded DNA binding characteristics and subcellular distribution
of a minor groove binding diphenylether bisbenzimidazole. Biochemistry
2001, 40, 6465-6467. 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. 511. White, C. M.; Satz, A. L.; Bruice, T. C. & Beerman, T. A..
Inhibition of transcription factor-DNA complexes and gene expression
by a novel microgonotropen. Proc. Natl. Acad. (USA) 2001, 98, 10590-10595.
512. Challa, H. & Bruice, T. C.. Incorporation of positively
charged deoxynucleic S-methylthiourea linkages into oligonucleotides:
Synthesis and characterization of DNmt/DNA chimera. Bioorg. Med.
Chem. Lett. 2001, 11, 2423-2427. PDF
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. 515. White, C. M.; Satz, A. L.; Gawron, L. S.; Bruice, T. C. &
Beerman, T. A.. Inhibiting transcription factor/DNA complexes using
fluorescent microgonotropens. Biochemica et Biophysica Acta gene
expression. 2001, 1574, 100-108. 516. Satz, L. S. & Bruice, T. C.. Recognition of nine base pair
sequence in the minor groove of DNA at subpicomolar concemntrations
by a novel microgonotropen. Bioorg. & Med. Chem. 2002, 10, 241-262.
517. Kojima, N.; Szabo, I. E. & Bruice, T. C.. Synthesis of ribonucleic
guanidine: Replacement of the negative phosphodiester linkages of
RNA with positive guanidinium linkages. Tetrahedron 2002, 58, 867-879.
PDF
518. Satz, L. S. & Bruice, T. C.. Recognition in the Minor Groove
of double-stranded DNA by microgonotropens. Acc. Chem. Res. 2002,
35, 86-95. PDF
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, 8825-8833. 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
532. Reddy, P. M. & Bruice, T. C.. Solid phase synthesis of
positively charged deoxynucleic guanidine (DNG) oligonucleotide
mixed sequences. Bioorg. & Med. Chem. Lett. 2003, 1281-1285.
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.
536. Reddy, P. M., Jindra, P., Satz, L. S. & Bruice, T. C..
Sequence selective recognition in the minor groove of dsDNA by pyrrole,
imidazole-Hochst conjugates. J. Am. Chem. Soc., 2003, 125, 7843-7848.
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, 2004,
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
544. Challa, H. & Bruice, T. C., Deoxynucleic Guanidine: Synthesis
and incorporation of purine nucleosides into positively charged
DNG oligonucleotides. Bioorganic & Med. Chem. Lett., 2004, 12,
1475-1481.
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
548. Reddy, P.M. and Bruice, T.C., Solid-Phase Synthesis of Positively
Charged Deoxynucleic Guanidine (DNG) Tethering a Hoechst 33258 Analogue:
Triplex and Duplex Stabilization by Simultaneous Minor Groove Binding.
J. Am. Chem. Soc. 2004, 126, 3736-3747. 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.
550. Szabo, I. & Bruice, T. C.,
DNG Cytidine: Synthesis and binding properties of octomeric guanidinium-linked
deoxycytidine oligomer. Bioorganic & Med. Chem., 2004, 12, 4233-4244.
551. Reddy, M. P., Dexter, R. &
Bruice, T.C., DNA sequence recognition in the minor groove by hairpin
pyrrole polyamide-Hochst 33258 analog conjugate. Bioorganic &
Med. Chem. Lett., 2004, 14, 3803-3807.
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
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