Stephen J. Benkovic - Publications

Affiliations: 
Pennsylvania State University, State College, PA, United States 
Area:
mechanistic enzymology
Website:
http://research.chem.psu.edu/sjbgroup/

232 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Perumal SK, Xu X, Yan C, Ivanov I, Benkovic SJ. Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps. Journal of Molecular Biology. PMID 31051173 DOI: 10.1016/j.jmb.2019.04.035  0.64
2019 Liu C, Knudsen GM, Pedley AM, He J, Johnson JL, Yaron TM, Cantley LC, Benkovic SJ. Mapping post-translational modifications of de novo purine biosynthetic enzymes: Implications for pathway regulation. Journal of Proteome Research. PMID 30964683 DOI: 10.1021/acs.jproteome.8b00969  0.36
2018 Chan CY, Pedley AM, Kim D, Xia C, Zhuang X, Benkovic SJ. Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria. Proceedings of the National Academy of Sciences of the United States of America. PMID 30509995 DOI: 10.1073/pnas.1814042115  0.36
2018 Pedley AM, Benkovic SJ. Detecting Purinosome Metabolon Formation with Fluorescence Microscopy. Methods in Molecular Biology (Clifton, N.J.). 1764: 279-289. PMID 29605921 DOI: 10.1007/978-1-4939-7759-8_17  0.36
2018 Pedley AM, Karras GI, Zhang X, Lindquist SL, Benkovic SJ. The Role of HSP90 in the Regulation of de novo Purine Biosynthesis. Biochemistry. PMID 29553718 DOI: 10.1021/acs.biochem.8b00140  0.36
2018 Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A. Substrate-driven chemotactic assembly in an enzyme cascade. Nature Chemistry. 10: 311-317. PMID 29461522 DOI: 10.1038/nchem.2905  0.72
2017 Benkovic SJ, Spiering MM. Understanding DNA replication by the bacteriophage T4 replisome. The Journal of Biological Chemistry. PMID 28972188 DOI: 10.1074/jbc.R117.811208  0.72
2017 Spiering MM, Hanoian P, Gannavaram S, Benkovic SJ. RNA primer-primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication. Proceedings of the National Academy of Sciences of the United States of America. PMID 28507156 DOI: 10.1073/pnas.1620459114  0.72
2016 Pedley AM, Benkovic SJ. A New View into the Regulation of Purine Metabolism: The Purinosome. Trends in Biochemical Sciences. PMID 28029518 DOI: 10.1016/j.tibs.2016.09.009  0.36
2016 French JB, Jones SA, Deng H, Pedley AM, Kim D, Chan CY, Hu H, Pugh RJ, Zhao H, Zhang Y, Huang TJ, Fang Y, Zhuang X, Benkovic SJ. Spatial colocalization and functional link of purinosomes with mitochondria. Science (New York, N.Y.). 351: 733-7. PMID 26912862 DOI: 10.1126/science.aac6054  0.44
2016 French JB, Jones SA, Deng H, Pedley AM, Kim D, Chan CY, Hu H, Pugh RJ, Zhao H, Zhang Y, Huang TJ, Fang Y, Zhuang X, Benkovic SJ. Spatial colocalization and functional link of purinosomes with mitochondria Science. 351: 733-737. DOI: 10.1126/science.aac6054  1
2015 Choi JS, Dasari A, Hu P, Benkovic SJ, Berdis AJ. The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta. Nucleic Acids Research. PMID 26717984 DOI: 10.1093/nar/gkv1509  0.52
2015 Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Mathilakathu Madathil M, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA-Protein Interaction. Biochemistry. PMID 26618501 DOI: 10.1021/acs.biochem.5b01085  1
2015 Moree B, Connell K, Mortensen RB, Liu CT, Benkovic SJ, Salafsky J. Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation. Biophysical Journal. 109: 806-15. PMID 26287632 DOI: 10.1016/j.bpj.2015.07.016  1
2015 Noble E, Spiering MM, Benkovic SJ. Coordinated DNA Replication by the Bacteriophage T4 Replisome. Viruses. 7: 3186-200. PMID 26102578 DOI: 10.3390/v7062766  1
2015 Hedglin M, Benkovic SJ. Regulation of Rad6/Rad18 Activity During DNA Damage Tolerance. Annual Review of Biophysics. 44: 207-28. PMID 26098514 DOI: 10.1146/annurev-biophys-060414-033841  1
2015 Chan CY, Zhao H, Pugh RJ, Pedley AM, French J, Jones SA, Zhuang X, Jinnah H, Huang TJ, Benkovic SJ. Purinosome formation as a function of the cell cycle. Proceedings of the National Academy of Sciences of the United States of America. 112: 1368-73. PMID 25605889 DOI: 10.1073/pnas.1423009112  1
2015 Zhao H, Chiaro CR, Zhang L, Smith PB, Chan CY, Pedley AM, Pugh RJ, French JB, Patterson AD, Benkovic SJ. Quantitative analysis of purine nucleotides indicates that purinosomes increase de novo purine biosynthesis. The Journal of Biological Chemistry. 290: 6705-13. PMID 25605736 DOI: 10.1074/jbc.M114.628701  1
2015 Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Accounts of Chemical Research. 48: 482-9. PMID 25565178 DOI: 10.1021/ar500390e  1
2015 Guo F, Li P, French JB, Mao Z, Zhao H, Li S, Nama N, Fick JR, Benkovic SJ, Huang TJ. Controlling cell-cell interactions using surface acoustic waves. Proceedings of the National Academy of Sciences of the United States of America. 112: 43-8. PMID 25535339 DOI: 10.1073/pnas.1422068112  1
2015 Tony Liu C, Tomsho JW, Benkovic SJ. Corrigendum to "The unique chemistry of benzoxaboroles: Current and emerging applications in biotechnology and therapeutic treatments" [Bioorg. Med. Chem. 22 (2014) 4462-4473] Bioorganic and Medicinal Chemistry. DOI: 10.1016/j.bmc.2015.04.043  1
2014 Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ. Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proceedings of the National Academy of Sciences of the United States of America. 111: 18231-6. PMID 25453098 DOI: 10.1073/pnas.1415940111  1
2014 Ahmed D, Muddana HS, Lu M, French JB, Ozcelik A, Fang Y, Butler PJ, Benkovic SJ, Manz A, Huang TJ. Acoustofluidic chemical waveform generator and switch. Analytical Chemistry. 86: 11803-10. PMID 25405550 DOI: 10.1021/ac5033676  0.44
2014 Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM. Tryptophan-based fluorophores for studying protein conformational changes. Bioorganic & Medicinal Chemistry. 22: 5924-34. PMID 25284250 DOI: 10.1016/j.bmc.2014.09.015  1
2014 Liu CT, Layfield JP, Stewart RJ, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. Journal of the American Chemical Society. 136: 10349-60. PMID 24977791 DOI: 10.1021/ja5038947  1
2014 Liu CT, Tomsho JW, Benkovic SJ. The unique chemistry of benzoxaboroles: current and emerging applications in biotechnology and therapeutic treatments. Bioorganic & Medicinal Chemistry. 22: 4462-73. PMID 24864040 DOI: 10.1016/j.bmc.2014.04.065  1
2014 Zhao Y, Chen D, Yue H, Spiering MM, Zhao C, Benkovic SJ, Huang TJ. Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions. Nano Letters. 14: 1952-60. PMID 24628474 DOI: 10.1021/nl404802f  1
2014 Sengupta S, Spiering MM, Dey KK, Duan W, Patra D, Butler PJ, Astumian RD, Benkovic SJ, Sen A. DNA polymerase as a molecular motor and pump. Acs Nano. 8: 2410-8. PMID 24601532 DOI: 10.1021/nn405963x  1
2014 Zhao Y, Chen D, Benkovic SJ, Huang TJ. High-throughput single molecule detection using nanophotonic/microfluidic hybrid chip 18th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2014. 1811-1813.  1
2013 Fang Y, French J, Zhao H, Benkovic S. G-protein-coupled receptor regulation of de novo purine biosynthesis: a novel druggable mechanism. Biotechnology & Genetic Engineering Reviews. 29: 31-48. PMID 24568251 DOI: 10.1080/02648725.2013.801237  1
2013 van Dongen SF, Clerx J, Nørgaard K, Bloemberg TG, Cornelissen JJ, Trakselis MA, Nelson SW, Benkovic SJ, Rowan AE, Nolte RJ. A clamp-like biohybrid catalyst for DNA oxidation. Nature Chemistry. 5: 945-51. PMID 24153373 DOI: 10.1038/nchem.1752  0.96
2013 Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM. Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification. Biochemistry. 52: 8580-9. PMID 24152169 DOI: 10.1021/bi401275v  1
2013 Liu CT, Benkovic SJ. Capturing a sulfenic acid with arylboronic acids and benzoxaborole. Journal of the American Chemical Society. 135: 14544-7. PMID 24050501 DOI: 10.1021/ja407628a  1
2013 Manosas M, Perumal SK, Bianco PR, Bianco P, Ritort F, Benkovic SJ, Croquette V. RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue. Nature Communications. 4: 2368. PMID 24013402 DOI: 10.1038/ncomms3368  1
2013 Chen S, Fahmi NE, Wang L, Bhattacharya C, Benkovic SJ, Hecht SM. Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. Journal of the American Chemical Society. 135: 12924-7. PMID 23941571 DOI: 10.1021/ja403007r  1
2013 Liu CT, Wang L, Goodey NM, Hanoian P, Benkovic SJ. Temporally overlapped but uncoupled motions in dihydrofolate reductase catalysis. Biochemistry. 52: 5332-4. PMID 23883151 DOI: 10.1021/bi400858m  1
2013 Guo F, French JB, Li P, Zhao H, Chan CY, Fick JR, Benkovic SJ, Huang TJ. Probing cell-cell communication with microfluidic devices. Lab On a Chip. 13: 3152-62. PMID 23843092 DOI: 10.1039/c3lc90067c  1
2013 Wang L, Xu X, Kumar R, Maiti B, Liu CT, Ivanov I, Lee TH, Benkovic SJ. Probing DNA clamps with single-molecule force spectroscopy. Nucleic Acids Research. 41: 7804-14. PMID 23783571 DOI: 10.1093/nar/gkt487  1
2013 Boehr DD, Schnell JR, McElheny D, Bae SH, Duggan BM, Benkovic SJ, Dyson HJ, Wright PE. A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase. Biochemistry. 52: 4605-19. PMID 23758161 DOI: 10.1021/bi400563c  1
2013 Liu CT, Hanoian P, French JB, Pringle TH, Hammes-Schiffer S, Benkovic SJ. Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proceedings of the National Academy of Sciences of the United States of America. 110: 10159-64. PMID 23733948 DOI: 10.1073/pnas.1307130110  1
2013 Perumal SK, Nelson SW, Benkovic SJ. Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail. Journal of Molecular Biology. 425: 2823-39. PMID 23732982 DOI: 10.1016/j.jmb.2013.05.012  1
2013 Chen D, Yue H, Spiering MM, Benkovic SJ. Insights into Okazaki fragment synthesis by the T4 replisome: the fate of lagging-strand holoenzyme components and their influence on Okazaki fragment size. The Journal of Biological Chemistry. 288: 20807-16. PMID 23729670 DOI: 10.1074/jbc.M113.485961  1
2013 Zhao Y, Chen D, Yue H, French JB, Rufo J, Benkovic SJ, Huang TJ. Lab-on-a-chip technologies for single-molecule studies. Lab On a Chip. 13: 2183-98. PMID 23670195 DOI: 10.1039/c3lc90042h  1
2013 Hedglin M, Perumal SK, Hu Z, Benkovic S. Stepwise assembly of the human replicative polymerase holoenzyme. Elife. 2: e00278. PMID 23577232 DOI: 10.7554/eLife.00278  1
2013 Zhao H, French JB, Fang Y, Benkovic SJ. The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans. Chemical Communications (Cambridge, England). 49: 4444-52. PMID 23575936 DOI: 10.1039/c3cc41437j  1
2013 Hedglin M, Kumar R, Benkovic SJ. Replication clamps and clamp loaders. Cold Spring Harbor Perspectives in Biology. 5: a010165. PMID 23545418 DOI: 10.1101/cshperspect.a010165  1
2013 Benkovic SJ, Theriot J, Ringe D. Open questions - in brief: beyond -omics, missing motor proteins, and getting from molecules to organisms. Bmc Biology. 11: 8. PMID 23369202 DOI: 10.1186/1741-7007-11-8  1
2013 French JB, Zhao H, An S, Niessen S, Deng Y, Cravatt BF, Benkovic SJ. Hsp70/Hsp90 chaperone machinery is involved in the assembly of the purinosome. Proceedings of the National Academy of Sciences of the United States of America. 110: 2528-33. PMID 23359685 DOI: 10.1073/pnas.1300173110  1
2013 Ahmed D, Chan CY, Lin SC, Muddana HS, Nama N, Benkovic SJ, Huang TJ. Tunable, pulsatile chemical gradient generation via acoustically driven oscillating bubbles. Lab On a Chip. 13: 328-31. PMID 23254861 DOI: 10.1039/c2lc40923b  1
2013 Perumal SK, Ren W, Lee TH, Benkovic SJ. How a holoenzyme for DNA replication is formed. Proceedings of the National Academy of Sciences of the United States of America. 110: 99-104. PMID 23248268 DOI: 10.1073/pnas.1212748110  1
2013 Liu CT, Stewart RJ, Benkovic SJ. Too fast for catalysis Biocatalysis and Biotransformation. 31: 269-271. DOI: 10.3109/10242422.2013.836809  1
2012 Tomsho JW, Pal A, Hall DG, Benkovic SJ. Ring Structure and Aromatic Substituent Effects on the pK a of the Benzoxaborole Pharmacophore. Acs Medicinal Chemistry Letters. 3: 48-52. PMID 24900370 DOI: 10.1021/ml200215j  1
2012 Manosas M, Perumal SK, Croquette V, Benkovic SJ. Direct observation of stalled fork restart via fork regression in the T4 replication system. Science (New York, N.Y.). 338: 1217-20. PMID 23197534 DOI: 10.1126/science.1225437  1
2012 Tomsho JW, Benkovic SJ. Examination of the reactivity of benzoxaboroles and related compounds with a cis-diol. The Journal of Organic Chemistry. 77: 11200-9. PMID 23116424 DOI: 10.1021/jo302264g  1
2012 Chen S, Wang L, Fahmi NE, Benkovic SJ, Hecht SM. Two pyrenylalanines in dihydrofolate reductase form an excimer enabling the study of protein dynamics. Journal of the American Chemical Society. 134: 18883-5. PMID 23116258 DOI: 10.1021/ja307179q  1
2012 Deng Y, Gam J, French JB, Zhao H, An S, Benkovic SJ. Mapping protein-protein proximity in the purinosome. The Journal of Biological Chemistry. 287: 36201-7. PMID 22955281 DOI: 10.1074/jbc.M112.407056  1
2012 Hu Z, Perumal SK, Yue H, Benkovic SJ. The human lagging strand DNA polymerase δ holoenzyme is distributive. The Journal of Biological Chemistry. 287: 38442-8. PMID 22942285 DOI: 10.1074/jbc.M112.404319  1
2012 Spurr IB, Birts CN, Cuda F, Benkovic SJ, Blaydes JP, Tavassoli A. Targeting tumour proliferation with a small-molecule inhibitor of AICAR transformylase homodimerization. Chembiochem : a European Journal of Chemical Biology. 13: 1628-34. PMID 22764122 DOI: 10.1002/cbic.201200279  1
2012 Ding X, Lin SC, Kiraly B, Yue H, Li S, Chiang IK, Shi J, Benkovic SJ, Huang TJ. On-chip manipulation of single microparticles, cells, and organisms using surface acoustic waves. Proceedings of the National Academy of Sciences of the United States of America. 109: 11105-9. PMID 22733731 DOI: 10.1073/pnas.1209288109  1
2012 Manosas M, Spiering MM, Ding F, Bensimon D, Allemand JF, Benkovic SJ, Croquette V. Mechanism of strand displacement synthesis by DNA replicative polymerases. Nucleic Acids Research. 40: 6174-86. PMID 22434889 DOI: 10.1093/nar/gks253  1
2012 Manosas M, Spiering MM, Ding F, Croquette V, Benkovic SJ. Collaborative coupling between polymerase and helicase for leading-strand synthesis. Nucleic Acids Research. 40: 6187-98. PMID 22434886 DOI: 10.1093/nar/gks254  1
2012 Ding F, Manosas M, Spiering MM, Benkovic SJ, Bensimon D, Allemand JF, Croquette V. Single-molecule mechanical identification and sequencing. Nature Methods. 9: 367-72. PMID 22406857 DOI: 10.1038/nmeth.1925  1
2012 Tomsho JW, Benkovic SJ. Elucidation of the mechanism of the reaction between phenylboronic acid and a model diol, Alizarin Red S. The Journal of Organic Chemistry. 77: 2098-106. PMID 22283713 DOI: 10.1021/jo202250d  1
2012 Stojkovi? V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A. Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. Journal of the American Chemical Society. 134: 1738-45. PMID 22171795 DOI: 10.1021/ja209425w  1
2011 Hammes GG, Benkovic SJ, Hammes-Schiffer S. Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry. 50: 10422-30. PMID 22029278 DOI: 10.1021/bi201486f  1
2011 Verrier F, An S, Ferrie AM, Sun H, Kyoung M, Deng H, Fang Y, Benkovic SJ. GPCRs regulate the assembly of a multienzyme complex for purine biosynthesis. Nature Chemical Biology. 7: 909-15. PMID 22020552 DOI: 10.1038/nchembio.690  1
2011 Benkovic SJ, Raney KD. Mechanisms: molecular machines. Current Opinion in Chemical Biology. 15: 577-9. PMID 21920800 DOI: 10.1016/j.cbpa.2011.08.013  1
2011 Young TS, Young DD, Ahmad I, Louis JM, Benkovic SJ, Schultz PG. Evolution of cyclic peptide protease inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 108: 11052-6. PMID 21690365 DOI: 10.1073/pnas.1108045108  1
2011 Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science (New York, N.Y.). 332: 234-8. PMID 21474759 DOI: 10.1126/science.1198542  1
2011 Baker SJ, Tomsho JW, Benkovic SJ. Boron-containing inhibitors of synthetases. Chemical Society Reviews. 40: 4279-85. PMID 21298158 DOI: 10.1039/c0cs00131g  1
2011 Herdendorf TJ, Albrecht DW, Benkovic SJ, Nelson SW. Biochemical characterization of bacteriophage T4 Mre11-Rad50 complex. The Journal of Biological Chemistry. 286: 2382-92. PMID 21081488 DOI: 10.1074/jbc.M110.178871  1
2010 Krauss U, Lee J, Benkovic SJ, Jaeger KE. LOVely enzymes - towards engineering light-controllable biocatalysts. Microbial Biotechnology. 3: 15-23. PMID 21255302 DOI: 10.1111/j.1751-7915.2009.00140.x  1
2010 Kumar R, Nashine VC, Mishra PP, Benkovic SJ, Lee TH. Stepwise loading of yeast clamp revealed by ensemble and single-molecule studies. Proceedings of the National Academy of Sciences of the United States of America. 107: 19736-41. PMID 21041673 DOI: 10.1073/pnas.1014139107  1
2010 Stojkovi? V, Perissinotti LL, Lee J, Benkovic SJ, Kohen A. The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer. Chemical Communications (Cambridge, England). 46: 8974-6. PMID 20972508 DOI: 10.1039/c0cc02988b  1
2010 Schaerli Y, Stein V, Spiering MM, Benkovic SJ, Abell C, Hollfelder F. Isothermal DNA amplification using the T4 replisome: circular nicking endonuclease-dependent amplification and primase-based whole-genome amplification. Nucleic Acids Research. 38: e201. PMID 20921065 DOI: 10.1093/nar/gkq795  1
2010 Nashine VC, Hammes-Schiffer S, Benkovic SJ. Coupled motions in enzyme catalysis. Current Opinion in Chemical Biology. 14: 644-51. PMID 20729130 DOI: 10.1016/j.cbpa.2010.07.020  1
2010 Manosas M, Meglio A, Spiering MM, Ding F, Benkovic SJ, Barre FX, Saleh OA, Allemand JF, Bensimon D, Croquette V. Magnetic tweezers for the study of DNA tracking motors. Methods in Enzymology. 475: 297-320. PMID 20627163 DOI: 10.1016/S0076-6879(10)75013-8  1
2010 An S, Deng Y, Tomsho JW, Kyoung M, Benkovic SJ. Microtubule-assisted mechanism for functional metabolic macromolecular complex formation. Proceedings of the National Academy of Sciences of the United States of America. 107: 12872-6. PMID 20615962 DOI: 10.1073/pnas.1008451107  1
2010 Nelson SW, Benkovic SJ. Response of the bacteriophage T4 replisome to noncoding lesions and regression of a stalled replication fork. Journal of Molecular Biology. 401: 743-56. PMID 20600127 DOI: 10.1016/j.jmb.2010.06.027  1
2010 Perumal SK, Raney KD, Benkovic SJ. Analysis of the DNA translocation and unwinding activities of T4 phage helicases. Methods (San Diego, Calif.). 51: 277-88. PMID 20170733 DOI: 10.1016/j.ymeth.2010.02.011  1
2010 An S, Kyoung M, Allen JJ, Shokat KM, Benkovic SJ. Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2. The Journal of Biological Chemistry. 285: 11093-9. PMID 20157113 DOI: 10.1074/jbc.M110.101139  0.4
2010 Lee J, Yennawar NH, Gam J, Benkovic SJ. Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae. Biochemistry. 49: 195-206. PMID 19950924 DOI: 10.1021/bi901614m  1
2010 Perumal SK, Yue H, Hu Z, Spiering MM, Benkovic SJ. Single-molecule studies of DNA replisome function. Biochimica Et Biophysica Acta. 1804: 1094-112. PMID 19665592 DOI: 10.1016/j.bbapap.2009.07.022  1
2009 Manosas M, Spiering MM, Zhuang Z, Benkovic SJ, Croquette V. Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome. Nature Chemical Biology. 5: 904-12. PMID 19838204 DOI: 10.1038/nchembio.236  1
2009 Arumugam SR, Lee TH, Benkovic SJ. Investigation of stoichiometry of T4 bacteriophage helicase loader protein (gp59). The Journal of Biological Chemistry. 284: 29283-9. PMID 19700405 DOI: 10.1074/jbc.M109.029926  1
2009 Li H, Fast W, Benkovic SJ. Structural and functional modularity of proteins in the de novo purine biosynthetic pathway. Protein Science : a Publication of the Protein Society. 18: 881-92. PMID 19384989 DOI: 10.1002/pro.95  1
2009 Nelson SW, Perumal SK, Benkovic SJ. Processive and unidirectional translocation of monomeric UvsW helicase on single-stranded DNA. Biochemistry. 48: 1036-46. PMID 19154117 DOI: 10.1021/bi801792q  1
2009 Nelson SW, Zhuang Z, Spiering MM, Benkovic SJ. T4 phage replisome Viral Genome Replication. 337-364. DOI: 10.1007/b135974_16  1
2008 Tavassoli A, Lu Q, Gam J, Pan H, Benkovic SJ, Cohen SN. Inhibition of HIV budding by a genetically selected cyclic peptide targeting the Gag-TSG101 interaction. Acs Chemical Biology. 3: 757-64. PMID 19053244 DOI: 10.1021/cb800193n  1
2008 Spiering MM, Nelson SW, Benkovic SJ. Repetitive lagging strand DNA synthesis by the bacteriophage T4 replisome. Molecular Biosystems. 4: 1070-4. PMID 18931782 DOI: 10.1039/b812163j  1
2008 Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R. Surface sites for engineering allosteric control in proteins. Science (New York, N.Y.). 322: 438-42. PMID 18927392 DOI: 10.1126/science.1159052  1
2008 Goodey NM, Benkovic SJ. Allosteric regulation and catalysis emerge via a common route. Nature Chemical Biology. 4: 474-82. PMID 18641628 DOI: 10.1038/nchembio.98  1
2008 Nelson SW, Kumar R, Benkovic SJ. RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins. The Journal of Biological Chemistry. 283: 22838-46. PMID 18511422 DOI: 10.1074/jbc.M802762200  1
2008 An S, Kumar R, Sheets ED, Benkovic SJ. Reversible compartmentalization of de novo purine biosynthetic complexes in living cells. Science (New York, N.Y.). 320: 103-6. PMID 18388293 DOI: 10.1126/science.1152241  1
2008 Zhuang Z, Johnson RE, Haracska L, Prakash L, Prakash S, Benkovic SJ. Regulation of polymerase exchange between Poleta and Poldelta by monoubiquitination of PCNA and the movement of DNA polymerase holoenzyme. Proceedings of the National Academy of Sciences of the United States of America. 105: 5361-6. PMID 18385374 DOI: 10.1073/pnas.0801310105  1
2008 Benkovic SJ, Hammes GG, Hammes-Schiffer S. Free-energy landscape of enzyme catalysis. Biochemistry. 47: 3317-21. PMID 18298083 DOI: 10.1021/bi800049z  1
2008 Tomsho JW, Benkovic SJ. Unnatural translation initiation. Acs Chemical Biology. 3: 87-8. PMID 18278847 DOI: 10.1021/cb8000233  1
2008 Naumann TA, Tavassoli A, Benkovic SJ. Genetic selection of cyclic peptide Dam methyltransferase inhibitors. Chembiochem : a European Journal of Chemical Biology. 9: 194-7. PMID 18085543 DOI: 10.1002/cbic.200700561  1
2007 Lionnet T, Spiering MM, Benkovic SJ, Bensimon D, Croquette V. Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 104: 19790-5. PMID 18077411 DOI: 10.1073/pnas.0709793104  1
2007 Cheng L, Naumann TA, Horswill AR, Hong SJ, Venters BJ, Tomsho JW, Benkovic SJ, Keiler KC. Discovery of antibacterial cyclic peptides that inhibit the ClpXP protease. Protein Science : a Publication of the Protein Society. 16: 1535-42. PMID 17600141 DOI: 10.1110/ps.072933007  1
2007 Rock FL, Mao W, Yaremchuk A, Tukalo M, Crépin T, Zhou H, Zhang YK, Hernandez V, Akama T, Baker SJ, Plattner JJ, Shapiro L, Martinis SA, Benkovic SJ, Cusack S, et al. An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science (New York, N.Y.). 316: 1759-61. PMID 17588934 DOI: 10.1126/science.1142189  1
2007 Tavassoli A, Benkovic SJ. Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli. Nature Protocols. 2: 1126-33. PMID 17546003 DOI: 10.1038/nprot.2007.152  1
2007 Nelson SW, Benkovic SJ. The T4 phage UvsW protein contains both DNA unwinding and strand annealing activities. The Journal of Biological Chemistry. 282: 407-16. PMID 17092935 DOI: 10.1074/jbc.M608153200  1
2007 Benkovic SJ, Hammes-Schiffer S. Dihydrofolate Reductase: Hydrogen Tunneling and Protein Motion Hydrogen-Transfer Reactions. 4: 1439-1454. DOI: 10.1002/9783527611546.ch46  1
2007 Smithrud DB, Benkovic SJ. Macrocycles and Antibodies as Catalysts The Lock-and-Key Principle, the State of the Art--100 Years On. 1: 149-172. DOI: 10.1002/9780470511411.ch5  1
2006 Horswill AR, Benkovic SJ. Identifying small-molecule modulators of protein-protein interactions. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 19.15. PMID 18429304 DOI: 10.1002/0471140864.ps1915s46  1
2006 Wang L, Goodey NM, Benkovic SJ, Kohen A. Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proceedings of the National Academy of Sciences of the United States of America. 103: 15753-8. PMID 17032759 DOI: 10.1073/pnas.0606976103  1
2006 Baker SJ, Akama T, Zhang YK, Sauro V, Pandit C, Singh R, Kully M, Khan J, Plattner JJ, Benkovic SJ, Lee V, Maples KR. Identification of a novel boron-containing antibacterial agent (AN0128) with anti-inflammatory activity, for the potential treatment of cutaneous diseases. Bioorganic & Medicinal Chemistry Letters. 16: 5963-7. PMID 16997550 DOI: 10.1016/j.bmcl.2006.08.130  1
2006 Wang L, Goodey NM, Benkovic SJ, Kohen A. The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1307-15. PMID 16873118 DOI: 10.1098/rstb.2006.1871  1
2006 Smiley RD, Zhuang Z, Benkovic SJ, Hammes GG. Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation. Biochemistry. 45: 7990-7. PMID 16800624 DOI: 10.1021/bi0603322  1
2006 Zhuang Z, Berdis AJ, Benkovic SJ. An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex. Biochemistry. 45: 7976-89. PMID 16800623 DOI: 10.1021/bi0601205  1
2006 Hammes-Schiffer S, Benkovic SJ. Relating protein motion to catalysis. Annual Review of Biochemistry. 75: 519-41. PMID 16756501 DOI: 10.1146/annurev.biochem.75.103004.142800  1
2006 Benkovic SJ, Hammes-Schiffer S. Biochemistry. Enzyme motions inside and out. Science (New York, N.Y.). 312: 208-9. PMID 16614206 DOI: 10.1126/science.1127654  1
2006 Saraf MC, Moore GL, Goodey NM, Cao VY, Benkovic SJ, Maranas CD. IPRO: an iterative computational protein library redesign and optimization procedure. Biophysical Journal. 90: 4167-80. PMID 16513775 DOI: 10.1529/biophysj.105.079277  1
2006 Zhuang Z, Yoder BL, Burgers PM, Benkovic SJ. The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. Proceedings of the National Academy of Sciences of the United States of America. 103: 2546-51. PMID 16476998 DOI: 10.1073/pnas.0511263103  1
2006 Wang L, Tharp S, Selzer T, Benkovic SJ, Kohen A. Effects of a distal mutation on active site chemistry. Biochemistry. 45: 1383-92. PMID 16445280 DOI: 10.1021/bi0518242  1
2006 Park HS, Nam SH, Lee JK, Yoon CN, Mannervik B, Benkovic SJ, Kim HS. Design and evolution of new catalytic activity with an existing protein scaffold. Science (New York, N.Y.). 311: 535-8. PMID 16439663 DOI: 10.1126/science.1118953  1
2006 Yang J, Nelson SW, Benkovic SJ. The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication. Molecular Cell. 21: 153-64. PMID 16427006 DOI: 10.1016/j.molcel.2005.11.029  1
2006 Nelson SW, Yang J, Benkovic SJ. Site-directed mutations of T4 helicase loading protein (gp59) reveal multiple modes of DNA polymerase inhibition and the mechanism of unlocking by gp41 helicase. The Journal of Biological Chemistry. 281: 8697-706. PMID 16407253 DOI: 10.1074/jbc.M512185200  1
2005 Antikainen NM, Smiley RD, Benkovic SJ, Hammes GG. Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry. 44: 16835-43. PMID 16363797 DOI: 10.1021/bi051378i  1
2005 Benkovic SJ, Baker SJ, Alley MR, Woo YH, Zhang YK, Akama T, Mao W, Baboval J, Rajagopalan PT, Wall M, Kahng LS, Tavassoli A, Shapiro L. Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH. Journal of Medicinal Chemistry. 48: 7468-76. PMID 16279806 DOI: 10.1021/jm050676a  1
2005 Naumann TA, Savinov SN, Benkovic SJ. Engineering an affinity tag for genetically encoded cyclic peptides. Biotechnology and Bioengineering. 92: 820-30. PMID 16155946 DOI: 10.1002/bit.20644  1
2005 Griswold KE, Kawarasaki Y, Ghoneim N, Benkovic SJ, Iverson BL, Georgiou G. Evolution of highly active enzymes by homology-independent recombination. Proceedings of the National Academy of Sciences of the United States of America. 102: 10082-7. PMID 16009931 DOI: 10.1073/pnas.0504556102  1
2005 Xi J, Zhang Z, Zhuang Z, Yang J, Spiering MM, Hammes GG, Benkovic SJ. Interaction between the T4 helicase loading protein (gp59) and the DNA polymerase (gp43): unlocking of the gp59-gp43-DNA complex to initiate assembly of a fully functional replisome. Biochemistry. 44: 7747-56. PMID 15909989 DOI: 10.1021/bi047296w  1
2005 Yang J, Xi J, Zhuang Z, Benkovic SJ. The oligomeric T4 primase is the functional form during replication. The Journal of Biological Chemistry. 280: 25416-23. PMID 15897200 DOI: 10.1074/jbc.M501847200  1
2005 Horswill AR, Benkovic SJ. Cyclic peptides, a chemical genetics tool for biologists. Cell Cycle (Georgetown, Tex.). 4: 552-5. PMID 15876867  1
2005 Cheng H, Hwang I, Chong Y, Tavassoli A, Webb ME, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Synthesis and biological evaluation of N-[4-[5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoroacetyl)pentyl]benzoyl]-L-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine biosynthetic pathway. Bioorganic & Medicinal Chemistry. 13: 3593-9. PMID 15848772 DOI: 10.1016/j.bmc.2004.11.049  1
2005 Chong Y, Hwang I, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Synthesis and biological evaluation of alpha- and gamma-carboxamide derivatives of 10-CF3CO-DDACTHF. Bioorganic & Medicinal Chemistry. 13: 3587-92. PMID 15848771 DOI: 10.1016/j.bmc.2004.11.050  1
2005 Cheng H, Chong Y, Hwang I, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Design, synthesis, and biological evaluation of 10-methanesulfonyl-DDACTHF, 10-methanesulfonyl-5-DACTHF, and 10-methylthio-DDACTHF as potent inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorganic & Medicinal Chemistry. 13: 3577-85. PMID 15848770 DOI: 10.1016/j.bmc.2004.12.004  1
2005 Woo YH, Rajagopalan PT, Benkovic SJ. A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening. Analytical Biochemistry. 340: 336-40. PMID 15840507 DOI: 10.1016/j.ab.2005.01.059  1
2005 Tavassoli A, Benkovic SJ. Genetically selected cyclic-peptide inhibitors of AICAR transformylase homodimerization. Angewandte Chemie (International Ed. in English). 44: 2760-3. PMID 15830403 DOI: 10.1002/anie.200500417  1
2005 Wong KF, Selzer T, Benkovic SJ, Hammes-Schiffer S. Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proceedings of the National Academy of Sciences of the United States of America. 102: 6807-12. PMID 15811945 DOI: 10.1073/pnas.0408343102  1
2005 Norcum MT, Warrington JA, Spiering MM, Ishmael FT, Trakselis MA, Benkovic SJ. Architecture of the bacteriophage T4 primosome: electron microscopy studies of helicase (gp41) and primase (gp61). Proceedings of the National Academy of Sciences of the United States of America. 102: 3623-6. PMID 15738414 DOI: 10.1073/pnas.0500713102  1
2005 Zhang Z, Spiering MM, Trakselis MA, Ishmael FT, Xi J, Benkovic SJ, Hammes GG. Assembly of the bacteriophage T4 primosome: single-molecule and ensemble studies. Proceedings of the National Academy of Sciences of the United States of America. 102: 3254-9. PMID 15728347 DOI: 10.1073/pnas.0500327102  1
2005 Xi J, Zhuang Z, Zhang Z, Selzer T, Spiering MM, Hammes GG, Benkovic SJ. Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. Biochemistry. 44: 2305-18. PMID 15709743 DOI: 10.1021/bi0479508  1
2004 Venkitakrishnan RP, Zaborowski E, McElheny D, Benkovic SJ, Dyson HJ, Wright PE. Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry. 43: 16046-55. PMID 15609999 DOI: 10.1021/bi048119y  1
2004 Joyce CM, Benkovic SJ. DNA polymerase fidelity: Kinetics, structure, and checkpoints Biochemistry. 43: 14317-14324. PMID 15533035 DOI: 10.1021/bi048422z  1
2004 Horswill AR, Savinov SN, Benkovic SJ. A systematic method for identifying small-molecule modulators of protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 101: 15591-6. PMID 15498867 DOI: 10.1073/pnas.0406999101  1
2004 Millar D, Trakselis MA, Benkovic SJ. On the solution structure of the T4 sliding clamp (gp45). Biochemistry. 43: 12723-7. PMID 15461444 DOI: 10.1021/bi048349c  1
2004 Horswill AR, Naumann TA, Benkovic SJ. Using incremental truncation to create libraries of hybrid enzymes. Methods in Enzymology. 388: 50-60. PMID 15289061 DOI: 10.1016/S0076-6879(04)88006-6  1
2004 Zhuang Z, Spiering MM, Berdis AJ, Trakselis MA, Benkovic SJ. 'Screw-cap' clamp loader proteins that thread. Nature Structural & Molecular Biology. 11: 580-1. PMID 15221017 DOI: 10.1038/nsmb0704-580  1
2004 Yang J, Zhuang Z, Roccasecca RM, Trakselis MA, Benkovic SJ. The dynamic processivity of the T4 DNA polymerase during replication. Proceedings of the National Academy of Sciences of the United States of America. 101: 8289-94. PMID 15148377 DOI: 10.1073/pnas.0402625101  1
2004 Sikorski RS, Wang L, Markham KA, Rajagopalan PT, Benkovic SJ, Kohen A. Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis. Journal of the American Chemical Society. 126: 4778-9. PMID 15080672 DOI: 10.1021/ja031683w  1
2004 Saraf MC, Horswill AR, Benkovic SJ, Maranas CD. FamClash: a method for ranking the activity of engineered enzymes. Proceedings of the National Academy of Sciences of the United States of America. 101: 4142-7. PMID 14981242 DOI: 10.1073/pnas.0400065101  1
2004 Zhang Z, Rajagopalan PT, Selzer T, Benkovic SJ, Hammes GG. Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. Proceedings of the National Academy of Sciences of the United States of America. 101: 2764-9. PMID 14978269 DOI: 10.1073/pnas.0400091101  1
2003 Kawarasaki Y, Griswold KE, Stevenson JD, Selzer T, Benkovic SJ, Iverson BL, Georgiou G. Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers. Nucleic Acids Research. 31: e126. PMID 14576326  1
2003 Lee SG, Lutz S, Benkovic SJ. On the structural and functional modularity of glycinamide ribonucleotide formyltransferases. Protein Science : a Publication of the Protein Society. 12: 2206-14. PMID 14500878 DOI: 10.1110/ps.03139603  1
2003 Trakselis MA, Roccasecca RM, Yang J, Valentine AM, Benkovic SJ. Dissociative properties of the proteins within the bacteriophage T4 replisome. The Journal of Biological Chemistry. 278: 49839-49. PMID 14500719 DOI: 10.1074/jbc.M307405200  1
2003 Yang J, Trakselis MA, Roccasecca RM, Benkovic SJ. The application of a minicircle substrate in the study of the coordinated T4 DNA replication. The Journal of Biological Chemistry. 278: 49828-38. PMID 14500718 DOI: 10.1074/jbc.M307406200  1
2003 Desharnais J, Hwang I, Zhang Y, Tavassoli A, Baboval J, Benkovic SJ, Wilson IA, Boger DL. Design, synthesis and biological evaluation of 10-CF3CO-DDACTHF analogues and derivatives as inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorganic & Medicinal Chemistry. 11: 4511-21. PMID 13129587 DOI: 10.1016/S0968-0896(03)00458-9  1
2003 Marsilje TH, Hedrick MP, Desharnais J, Capps K, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. 10-(2-benzoxazolcarbonyl)-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid: a potential inhibitor of GAR transformylase and AICAR transformylase. Bioorganic & Medicinal Chemistry. 11: 4503-9. PMID 13129586 DOI: 10.1016/S0968-0896(03)00457-7  1
2003 Marsilje TH, Hedrick MP, Desharnais J, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Design, synthesis, and biological evaluation of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues as potential inhibitors of GAR transformylase and AICAR transformylase. Bioorganic & Medicinal Chemistry. 11: 4487-501. PMID 13129585 DOI: 10.1016/S0968-0896(03)00456-5  1
2003 Wolan DW, Greasley SE, Wall MJ, Benkovic SJ, Wilson IA. Structure of avian AICAR transformylase with a multisubstrate adduct inhibitor beta-DADF identifies the folate binding site. Biochemistry. 42: 10904-14. PMID 12974624 DOI: 10.1021/bi030106h  1
2003 Benkovic SJ, Hammes-Schiffer S. A perspective on enzyme catalysis. Science (New York, N.Y.). 301: 1196-202. PMID 12947189 DOI: 10.1126/science.1085515  1
2003 Pineda P, Kanter A, McIvor RS, Benkovic SJ, Rosowsky A, Wagner CR. Dihydrofolate reductase mutant with exceptional resistance to methotrexate but not to trimetrexate. Journal of Medicinal Chemistry. 46: 2816-8. PMID 12825924 DOI: 10.1021/jm034057i  1
2003 Huntley JJ, Fast W, Benkovic SJ, Wright PE, Dyson HJ. Role of a solvent-exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase. Protein Science : a Publication of the Protein Society. 12: 1368-75. PMID 12824483 DOI: 10.1110/ps.0305303  1
2003 Zhang Y, Desharnais J, Marsilje TH, Li C, Hedrick MP, Gooljarsingh LT, Tavassoli A, Benkovic SJ, Olson AJ, Boger DL, Wilson IA. Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid. Biochemistry. 42: 6043-56. PMID 12755606 DOI: 10.1021/bi034219c  1
2003 Savinov SN, Hirschmann R, Benkovic SJ, Smith AB. Investigation of an antibody-ligase. Evidence for strain-induced catalysis. Bioorganic & Medicinal Chemistry Letters. 13: 1321-4. PMID 12657273 DOI: 10.1016/S0960-894X(03)00123-9  1
2003 Trakselis MA, Berdis AJ, Benkovic SJ. Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. Journal of Molecular Biology. 326: 435-51. PMID 12559912 DOI: 10.1016/S0022-2836(02)01330-X  1
2003 Firestine SM, Salinas F, Benkovic SJ. Using transcriptional-based systems for in vivo enzyme screening. Methods in Molecular Biology (Clifton, N.J.). 205: 315-27. PMID 12491897  1
2003 Abel-Santos E, Scott CP, Benkovic SJ. Use of inteins for the in vivo production of stable cyclic peptide libraries in E. coli Methods in Molecular Biology (Clifton, N.J.). 205: 281-294. PMID 12491894  1
2003 Ishmael FT, Trakselis MA, Benkovic SJ. Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome. The Journal of Biological Chemistry. 278: 3145-52. PMID 12427736 DOI: 10.1074/jbc.M209858200  1
2002 Lutz S, Fast W, Benkovic SJ. A universal, vector-based system for nucleic acid reading-frame selection. Protein Engineering. 15: 1025-30. PMID 12601143  1
2002 Rajagopalan PT, Lutz S, Benkovic SJ. Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates. Biochemistry. 41: 12618-28. PMID 12379104 DOI: 10.1021/bi026369d  1
2002 Rajagopalan PT, Zhang Z, McCourt L, Dwyer M, Benkovic SJ, Hammes GG. Interaction of dihydrofolate reductase with methotrexate: ensemble and single-molecule kinetics. Proceedings of the National Academy of Sciences of the United States of America. 99: 13481-6. PMID 12359872 DOI: 10.1073/pnas.172501499  1
2002 Marsilje TH, Labroli MA, Hedrick MP, Jin Q, Desharnais J, Baker SJ, Gooljarsingh LT, Ramcharan J, Tavassoli A, Zhang Y, Wilson IA, Beardsley GP, Benkovic SJ, Boger DL. 10-Formyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid (10-formyl-DDACTHF): a potent cytotoxic agent acting by selective inhibition of human GAR Tfase and the de novo purine biosynthetic pathway. Bioorganic & Medicinal Chemistry. 10: 2739-49. PMID 12057663 DOI: 10.1016/S0968-0896(02)00102-5  1
2002 Thoden JB, Firestine SM, Benkovic SJ, Holden HM. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. The Journal of Biological Chemistry. 277: 23898-908. PMID 11953435 DOI: 10.1074/jbc.M202251200  1
2002 Rajagopalan PTR, Benkovic SJ. Preorganization and protein dynamics in enzyme catalysis Chemical Record. 2: 24-36. PMID 11933259 DOI: 10.1002/tcr.10009  1
2002 Ishmael FT, Alley SC, Benkovic SJ. Assembly of the bacteriophage T4 helicase: architecture and stoichiometry of the gp41-gp59 complex. The Journal of Biological Chemistry. 277: 20555-62. PMID 11927580 DOI: 10.1074/jbc.M111951200  1
2002 Agarwal PK, Billeter SR, Rajagopalan PT, Benkovic SJ, Hammes-Schiffer S. Network of coupled promoting motions in enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 2794-9. PMID 11867722 DOI: 10.1073/pnas.052005999  1
2002 Stevenson JD, Benkovic SJ. Combinatorial approaches to engineering hybrid enzymes Journal of the Chemical Society, Perkin Transactions 2. 1483-1493.  1
2002 Wall M, Benkovic SJ. Synthesis and biological evaluation of 9-thia-5,10-dideazafolic acid Journal of Heterocyclic Chemistry. 39: 1097-1099.  1
2001 Valentine AM, Ishmael FT, Shier VK, Benkovic SJ. A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase. Biochemistry. 40: 15074-85. PMID 11735390 DOI: 10.1021/bi0108554  1
2001 Trakselis MA, Benkovic SJ. Intricacies in ATP-dependent clamp loading: variations across replication systems. Structure (London, England : 1993). 9: 999-1004. PMID 11709164 DOI: 10.1016/S0969-2126(01)00676-1  1
2001 Greasley SE, Marsilje TH, Cai H, Baker S, Benkovic SJ, Boger DL, Wilson IA. Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase Biochemistry. 40: 13538-13547. PMID 11695901 DOI: 10.1021/bi011482+  1
2001 Lutz S, Ostermeier M, Moore GL, Maranas CD, Benkovic SJ. Creating multiple-crossover DNA libraries independent of sequence identity. Proceedings of the National Academy of Sciences of the United States of America. 98: 11248-53. PMID 11562494 DOI: 10.1073/pnas.201413698  1
2001 Trakselis MA, Mayer MU, Ishmael FT, Roccasecca RM, Benkovic SJ. Dynamic protein interactions in the bacteriophage T4 replisome. Trends in Biochemical Sciences. 26: 566-72. PMID 11551794 DOI: 10.1016/S0968-0004(01)01929-6  1
2001 Scott CP, Abel-Santos E, Jones AD, Benkovic SJ. Structural requirements for the biosynthesis of backbone cyclic peptide libraries Chemistry and Biology. 8: 801-815. PMID 11514229 DOI: 10.1016/S1074-5521(01)00052-7  1
2001 Alley SC, Trakselis MA, Mayer MU, Ishmael FT, Jones AD, Benkovic SJ. Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme. The Journal of Biological Chemistry. 276: 39340-9. PMID 11504721 DOI: 10.1074/jbc.M104956200  1
2001 Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE. Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry. 40: 9846-59. PMID 11502178 DOI: 10.1021/bi010621k  1
2001 Trakselis MA, Alley SC, Abel-Santos E, Benkovic SJ. Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proceedings of the National Academy of Sciences of the United States of America. 98: 8368-75. PMID 11459977 DOI: 10.1073/pnas.111006698  1
2001 Shim JH, Wall M, Benkovic SJ, Diaz N, Suárez D, Merz JM. Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations Journal of the American Chemical Society. 123: 4687-4696. PMID 11457277 DOI: 10.1021/ja010014k  1
2001 Wahnon DC, Shier VK, Benkovic SJ. Mechanism-based inhibition of an essential bacterial adenine DNA methyltransferase: rationally designed antibiotics. Journal of the American Chemical Society. 123: 976-7. PMID 11456633 DOI: 10.1021/ja003285o  1
2001 Benkovic SJ, Valentine AM, Salinas F. Replisome-mediated DNA replication. Annual Review of Biochemistry. 70: 181-208. PMID 11395406 DOI: 10.1146/annurev.biochem.70.1.181  1
2001 Stevenson JD, Lutz S, Benkovic SJ. Retracing Enzyme Evolution in the (betaalpha)(8)-Barrel Scaffold. Angewandte Chemie (International Ed. in English). 40: 1854-1856. PMID 11385654 DOI: 10.1002/1521-3773(20010518)40:10<1854::AID-ANIE1854>3.0.CO;2-F  1
2001 Gooljarsingh LT, Ramcharan J, Gilroy S, Benkovic SJ. Localization of GAR transformylase in Escherichia coli and mammalian cells. Proceedings of the National Academy of Sciences of the United States of America. 98: 6565-70. PMID 11381136 DOI: 10.1073/pnas.121182998  1
2001 Fast W, Wang Z, Benkovic SJ. Familial mutations and zinc stoichiometry determine the rate-limiting step of nitrocefin hydrolysis by metallo-β-lactamase from Bacteroides fragilis Biochemistry. 40: 1640-1650. PMID 11327823 DOI: 10.1021/bi001860v  1
2001 Greasley SE, Horton P, Ramcharan J, Beardsley GP, Benkovic SJ, Wilson IA. Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis. Nature Structural Biology. 8: 402-6. PMID 11323713 DOI: 10.1038/87555  1
2001 Ishmael FT, Alley SC, Benkovic SJ. Identification and mapping of protein-protein interactions between gp32 and gp59 by cross-linking. The Journal of Biological Chemistry. 276: 25236-42. PMID 11309384 DOI: 10.1074/jbc.M100783200  1
2001 Ishmael FT, Norcum MT, Benkovic SJ, Bond JS. Multimeric Structure of the Secreted Meprin A Metalloproteinase and Characterization of the Functional Protomer Journal of Biological Chemistry. 276: 23207-23211. PMID 11301339 DOI: 10.1074/jbc.M102654200  1
2001 Shier VK, Hancey CJ, Benkovic SJ. Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus. The Journal of Biological Chemistry. 276: 14744-51. PMID 11278726 DOI: 10.1074/jbc.M010688200  1
2001 Moore GL, Maranas CD, Lutz S, Benkovic SJ. Predicting crossover generation in DNA shuffling. Proceedings of the National Academy of Sciences of the United States of America. 98: 3226-31. PMID 11248060 DOI: 10.1073/pnas.051631498  1
2001 Miller GP, Wahnon DC, Benkovic SJ. Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase Biochemistry. 40: 867-875. PMID 11170407 DOI: 10.1021/bi001608n  1
2001 Lutz S, Ostermeier M, Benkovic SJ. Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides. Nucleic Acids Research. 29: E16. PMID 11160936  1
2001 Ostermeier M, Benkovic SJ. Construction of hybrid gene libraries involving the circular permutation of DNA Biotechnology Letters. 23: 303-310. DOI: 10.1023/A:1005642725295  1
2000 Benkovic SJ, Kenyon GL. Introduction. Bioorganic Chemistry. 28: 315. PMID 11352468 DOI: 10.1006/bioo.2001.1198  1
2000 Ostermeier M, Benkovic SJ. Evolution of protein function by domain swapping Advances in Protein Chemistry. 55: 29-78. PMID 11050932  1
2000 Wall M, Shim JH, Benkovic SJ. Human AICAR transformylase: Role of the 4-carboxamide of AICAR in binding and catalysis Biochemistry. 39: 11303-11311. PMID 10985775  1
2000 Lutz S, Benkovic SJ. Homology-independent protein engineering. Current Opinion in Biotechnology. 11: 319-24. PMID 10975450 DOI: 10.1016/S0958-1669(00)00106-3  1
2000 Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM. Molecular structure of Escherichia coli purT-encoded glycinamide ribonucleotide transformylase Biochemistry. 39: 8791-8802. PMID 10913290 DOI: 10.1021/bi000926j  1
2000 Boger DL, Marsilje TH, Castro RA, Hedrick MP, Jin Q, Baker SJ, Shim JH, Benkovic SJ. Design, synthesis, and biological evaluation of fluoronitrophenyl substituted folate analogues as potential inhibitors of GAR transformylase and AICAR transformylase Bioorganic and Medicinal Chemistry Letters. 10: 1471-1475. PMID 10888335 DOI: 10.1016/S0960-894X(00)00271-7  1
2000 Bruice TC, Benkovic SJ. Chemical basis for enzyme catalysis. Biochemistry. 39: 6267-74. PMID 10828939 DOI: 10.1021/bi0003689  1
2000 He L, Musick MD, Nicewarner SR, Salinas FG, Benkovic SJ, Natan MJ, Keating CD. Colloidal Au-enhanced surface plasmon resonance for ultrasensitive detection of DNA hybridization Journal of the American Chemical Society. 122: 9071-9077. DOI: 10.1021/ja001215b  1
2000 Alley SC, Ishmael FT, Jones AD, Benkovic SJ. Mapping protein - Protein interactions in the bacteriophage T4 DNA polymerase holoenzyme using a novel trifunctional photo-cross-linking and affinity reagent [11] Journal of the American Chemical Society. 122: 6126-6127. DOI: 10.1021/ja000591t  1
2000 Benkovic SJ, Perham R, Aebersold R. Protein technologies and commercial enzymes Current Opinion in Biotechnology. 11: 317-318. DOI: 10.1016/S0958-1669(00)00105-1  1
2000 Liu C, Shim JH, Benkovic SJ. The unexpected catalytic properties of a heterodimer of GAR transformylase Bioorganic Chemistry. 28: 316-323. DOI: 10.1006/bioo.2000.1186  1
2000 Baker SJ, Firestine SM, Smithrud D, Salinas F, Benkovic SJ. Synthesis of two bi-functional ligands for the QUEST three-hybrid system Tetrahedron Letters. 41: 7009-7012.  1
1999 Wang Z, Fast W, Valentine AM, Benkovic SJ. Metallo-beta-lactamase: structure and mechanism. Current Opinion in Chemical Biology. 3: 614-22. PMID 10508665 DOI: 10.1016/S1367-5931(99)00017-4  1
1999 Alley SC, Shier VK, Abel-Santos E, Sexton DJ, Soumillion P, Benkovic SJ. Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution. Biochemistry. 38: 7696-709. PMID 10387009 DOI: 10.1021/bi9827971  1
1998 Boger DL, Kochanny MJ, Cai H, Wyatt D, Kitos PA, Warren MS, Ramcharan J, Gooljarsingh LT, Benkovic SJ. Design, synthesis, and evaluation of potential GAR and AICAR transformylase inhibitors. Bioorganic & Medicinal Chemistry. 6: 643-59. PMID 9681131 DOI: 10.1016/S0968-0896(98)00040-6  0.32
1997 Boger DL, Haynes NE, Warren MS, Gooljarsingh LT, Ramcharan J, Kitos PA, Benkovic SJ. Functionalized analogues of 5,8,10-trideazafolate as potential inhibitors of GAR Tfase or AICAR Tfase. Bioorganic & Medicinal Chemistry. 5: 1831-8. PMID 9354238 DOI: 10.1016/S0968-0896(97)00121-1  1
1996 Crowder MW, Wang Z, Franklin SL, Zovinka EP, Benkovic SJ. Characterization of the metal-binding sites of the beta-lactamase from Bacteroides fragilis. Biochemistry. 35: 12126-32. PMID 8810919 DOI: 10.1021/bi960976h  1
1995 Carr RT, Balasubramanian S, Hawkins PC, Benkovic SJ. Mechanism of metal-independent hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase. Biochemistry. 34: 7525-32. PMID 7779797  0.48
1995 Wagner CR, Huang Z, Singleton SF, Benkovic SJ. Molecular basis for nonadditive mutational effects in Escherichia coli dihydrofolate reductase. Biochemistry. 34: 15671-80. PMID 7495797  1
1994 Balasubramanian S, Carr RT, Bender CJ, Peisach J, Benkovic SJ. Identification of metal ligands in Cu(II)-inhibited Chromobacterium violaceum phenylalanine hydroxylase by electron spin echo envelope modulation analysis of histidine to serine mutations. Biochemistry. 33: 8532-7. PMID 8031788  1
1994 Huang Z, Wagner CR, Benkovic SJ. Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase. Biochemistry. 33: 11576-85. PMID 7918371  1
1994 Peliska JA, Balasubramanian S, Giedroc DP, Benkovic SJ. Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity. Biochemistry. 33: 13817-23. PMID 7524664  0.48
1993 Balasubramanian S, Carr RT, Bender CJ, Peisach J, Benkovic SJ. Histidines 138 and 143 are copper binding ligands in Chromobacterium violaceum phenylalanine hydroxylase. Advances in Experimental Medicine and Biology. 338: 67-70. PMID 8304204  1
1992 Wagner CR, Thillet J, Benkovic SJ. Complementary perturbation of the kinetic mechanism and catalytic effectiveness of dihydrofolate reductase by side-chain interchange. Biochemistry. 31: 7834-40. PMID 1510969  1
1992 Wagner CR, Benkovic SJ. Probing the molecular basis of resistance to pyrimethamine by site-directed mutagenesis. Journal of Medicinal Chemistry. 35: 2912-5. PMID 1495020  1
1992 Gibbs RA, Taylor S, Benkovic SJ. Antibody-catalyzed rearrangement of the peptide bond. Science (New York, N.Y.). 258: 803-5. PMID 1439788  1
1991 Gibbs RA, Posner BA, Filpula DR, Dodd SW, Finkelman MA, Lee TK, Wroble M, Whitlow M, Benkovic SJ. Construction and characterization of a single-chain catalytic antibody. Proceedings of the National Academy of Sciences of the United States of America. 88: 4001-4. PMID 2023948  1
1991 Adams JA, Fierke CA, Benkovic SJ. The function of amino acid residues contacting the nicotinamide ring of NADPH in dihydrofolate reductase from Escherichia coli. Biochemistry. 30: 11046-54. PMID 1834173  1
1991 Onishi A, Liotta LJ, Benkovic SJ. Cloning and expression of Chromobacterium violaceum phenylalanine hydroxylase in Escherichia coli and comparison of amino acid sequence with mammalian aromatic amino acid hydroxylases. The Journal of Biological Chemistry. 266: 18454-9. PMID 1655752  1
1990 Wagner CR, Benkovic SJ. Site directed mutagenesis: a tool for enzyme mechanism dissection. Trends in Biotechnology. 8: 263-70. PMID 1366735 DOI: 10.1016/0167-7799(90)90189-5  1
1989 Andrews J, Fierke CA, Birdsall B, Ostler G, Feeney J, Roberts GC, Benkovic SJ. A kinetic study of wild-type and mutant dihydrofolate reductases from Lactobacillus casei. Biochemistry. 28: 5743-50. PMID 2505841  1
1989 Fierke CA, Benkovic SJ. Probing the functional role of threonine-113 of Escherichia coli dihydrofolate reductase for its effect on turnover efficiency, catalysis, and binding. Biochemistry. 28: 478-86. PMID 2496745  1
1988 Benkovic SJ, Fierke CA, Naylor AM. Insights into enzyme function from studies on mutants of dihydrofolate reductase. Science (New York, N.Y.). 239: 1105-10. PMID 3125607  1
1987 Fierke CA, Kuchta RD, Johnson KA, Benkovic SJ. Implications for enzymic catalysis from free-energy reaction coordinate profiles. Cold Spring Harbor Symposia On Quantitative Biology. 52: 631-8. PMID 3331348  1
1987 Fierke CA, Johnson KA, Benkovic SJ. Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry. 26: 4085-92. PMID 3307916  1
1986 Mayer RJ, Chen JT, Taira K, Fierke CA, Benkovic SJ. Importance of a hydrophobic residue in binding and catalysis by dihydrofolate reductase. Proceedings of the National Academy of Sciences of the United States of America. 83: 7718-20. PMID 3463995  1
1985 Chen JT, Mayer RJ, Fierke CA, Benkovic SJ. Site-specific mutagenesis of dihydrofolate reductase from Escherichia coli. Journal of Cellular Biochemistry. 29: 73-82. PMID 3905833 DOI: 10.1002/jcb.240290203  1
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