490. Kahn, K.; Bruice, T. C Transition State and Ground State Structures and Their Interaction

6

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.

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.

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.

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.

500. Kahn, K.; Bruice, T. C.. α-Ketoamides and α-ketocarbonyls: Conformational analysis and development of all-atom OPLS force field. Bioorg. Med. Chem. 2000, 8, 1881-1891.

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.

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.

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.

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.

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.

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.

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.

520. Bruice, T. C.. A view at the millennium: the efficiency of enzymatic catalysis. Acc. Chem. Res. 2002, 35, 139-146.

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.

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.

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.

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.

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.

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.

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

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.

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.

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, 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.

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.

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. COMMENTARY. R. L. Schowen, How an enzyme surmounts the activation barrier, Proc. Natl. Acad. Sci., 2003, 100, 15475-15480.

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.

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.

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.

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.

554. Luo, J. & Bruice, T.C., Anti-correlated motions as a driving force in enzyme catalysis. The dehydrogenase reaction. Proc. Natl. Acad. Sci, 2004, In Press.

555. Mazumder, D. & Bruice, T.C., Molecular dynamics studies of ground state and intermediate of the hyperthermophilic indole-3-glycerol phosphate synthase, Proc. Natl. Acad. Sci, 2004, Submitted.

556. Valina, A.L.B., Mazumder, D. & Bruice, T.C., Probing the Ser-Ser-Lys catalytic triad mechanism of peptide amidase. Computational studies of the ground state, transition state, and intermediate, Biochemistry, 2004, Submitted.

557. Estabrook, R., Luo, J., Matthew, P., Vyas, S., Rannganarhan, R., Bruice, T.C. & Reich, N.O., Identification of dynamically and energetically coupled residues involved in enzyme catalysis, Science, 2004, Submitted.