STEPHEN BENKOVIC

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2
    Songon An
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 285:11093-9. 2010
  2. pmc Probing DNA clamps with single-molecule force spectroscopy
    Lin Wang
    Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA and Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
    Nucleic Acids Res 41:7804-14. 2013
  3. pmc Collaborative coupling between polymerase and helicase for leading-strand synthesis
    Maria Manosas
    Departement de Physique, Laboratoire de Physique Statistique, Ecole Normale Superieure, Université Pierre et Marie Curie Université Paris 06, Universite Paris Diderot, Centre National de la Recherche Scientifique, Paris 75005, France
    Nucleic Acids Res 40:6187-98. 2012
  4. pmc Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome
    Maria Manosas
    Université Pierre et Marie Curie Paris, Universite Paris Diderot, Centre National de la Recherche Scientifique, France
    Nat Chem Biol 5:904-12. 2009
  5. pmc The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans
    Hong Zhao
    Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
    Chem Commun (Camb) 49:4444-52. 2013
  6. ncbi request reprint A perspective on enzyme catalysis
    Stephen J Benkovic
    Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Science 301:1196-202. 2003
  7. ncbi request reprint Biochemistry. Enzyme motions inside and out
    Stephen J Benkovic
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Science 312:208-9. 2006
  8. ncbi request reprint Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH
    Stephen J Benkovic
    Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, Pennsylvania 16802, USA
    J Med Chem 48:7468-76. 2005
  9. ncbi request reprint Replisome-mediated DNA replication
    S J Benkovic
    Pennsylvania State University, Department of Chemistry, 414 Wartik Laboratory, University Park, Pennsylvania 16802, USA
    Annu Rev Biochem 70:181-208. 2001
  10. ncbi request reprint Protein-protein and protein-DNA interactions at the bacteriophage T4 DNA replication fork. Characterization of a fluorescently labeled DNA polymerase sliding clamp
    D J Sexton
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 271:28045-51. 1996

Research Grants

  1. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2009
  2. THE TRANSFORMYLASE ENZYMES
    STEPHEN BENKOVIC; Fiscal Year: 1980
  3. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2009
  4. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2001
  5. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2001
  6. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2000
  7. TRANSFORMYLASE ENZYMES--DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2000
  8. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2000
  9. TRANSFORMYLASE ENZYMES--DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 1999
  10. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2002

Collaborators

Detail Information

Publications83

  1. pmc Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2
    Songon An
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 285:11093-9. 2010
    ..Collectively, we provide compelling cellular evidence that CK2-mediated pathways reversibly regulate purinosome assembly, and thus the purinosome may be one of the ultimate targets of kinase inhibitors...
  2. pmc Probing DNA clamps with single-molecule force spectroscopy
    Lin Wang
    Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA and Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
    Nucleic Acids Res 41:7804-14. 2013
    ..cerevisiae and E. coli clamps. These studies provide a vivid picture of the mechanics and energy landscape of clamp opening and reveal how the prokaryotic and eukaryotic clamps function through different mechanisms. ..
  3. pmc Collaborative coupling between polymerase and helicase for leading-strand synthesis
    Maria Manosas
    Departement de Physique, Laboratoire de Physique Statistique, Ecole Normale Superieure, Université Pierre et Marie Curie Université Paris 06, Universite Paris Diderot, Centre National de la Recherche Scientifique, Paris 75005, France
    Nucleic Acids Res 40:6187-98. 2012
    ..The model quantitatively reproduces homologous and heterologous coupling results under various experimental conditions...
  4. pmc Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome
    Maria Manosas
    Université Pierre et Marie Curie Paris, Universite Paris Diderot, Centre National de la Recherche Scientifique, France
    Nat Chem Biol 5:904-12. 2009
    ..Thus nature appears to use several strategies to couple the disparate helicase and primase activities within primosomes...
  5. pmc The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans
    Hong Zhao
    Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
    Chem Commun (Camb) 49:4444-52. 2013
    ..In particular we highlight advances made towards understanding the assembly, control and function of this protein complex and the attempts made to exploit this knowledge for drug discovery...
  6. ncbi request reprint A perspective on enzyme catalysis
    Stephen J Benkovic
    Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Science 301:1196-202. 2003
    ..Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering...
  7. ncbi request reprint Biochemistry. Enzyme motions inside and out
    Stephen J Benkovic
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Science 312:208-9. 2006
  8. ncbi request reprint Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH
    Stephen J Benkovic
    Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, Pennsylvania 16802, USA
    J Med Chem 48:7468-76. 2005
    ..Our data demonstrate the potential for further development of borinic esters as antibacterial agents as well as leads to explore more specific inhibitors against two essential bacterial enzymes...
  9. ncbi request reprint Replisome-mediated DNA replication
    S J Benkovic
    Pennsylvania State University, Department of Chemistry, 414 Wartik Laboratory, University Park, Pennsylvania 16802, USA
    Annu Rev Biochem 70:181-208. 2001
    ....
  10. ncbi request reprint Protein-protein and protein-DNA interactions at the bacteriophage T4 DNA replication fork. Characterization of a fluorescently labeled DNA polymerase sliding clamp
    D J Sexton
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 271:28045-51. 1996
    ..Upon ATP hydrolysis, the 44/62 complex triggers a conformational change in the 45 protein that may be attributed to the clamp loading onto DNA...
  11. pmc Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase
    Kim F Wong
    Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 102:6807-12. 2005
    ....
  12. ncbi request reprint Preorganization and protein dynamics in enzyme catalysis
    P T Ravi Rajagopalan
    Department of Chemistry, Pennsylvania State University, University Park, 16802, USA
    Chem Rec 2:24-36. 2002
    ..The general significance of protein dynamics in understanding other biological processes is briefly discussed...
  13. ncbi request reprint Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates
    P T Ravi Rajagopalan
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 41:12618-28. 2002
    ..Natl. Acad. Sci. U.S.A. 99, 2794-2799], the data suggest that a coupled dynamic motion of these distal residues enhances crossing of the chemical reaction barrier and imply an expanded nonstatic role for the protein fold in catalysis...
  14. pmc Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae
    Jeeyeon Lee
    Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 49:195-206. 2010
    ..Understanding the role of specific amino acids in the active site coupled with detailed structural analysis will inform us on how to better design inhibitors targeting drug-resistant pathogenic bacterial DHFRs...
  15. pmc Surface sites for engineering allosteric control in proteins
    Jeeyeon Lee
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Science 322:438-42. 2008
    ..PAS-DHFR serves as a proof of concept for engineering regulatory activities into proteins through interface design at conserved allosteric sites...
  16. pmc The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase
    Lin Wang
    Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
    Philos Trans R Soc Lond B Biol Sci 361:1307-15. 2006
    ..Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry...
  17. doi request reprint Free-energy landscape of enzyme catalysis
    Stephen J Benkovic
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 47:3317-21. 2008
    ..Experimental and theoretical evidence is presented to support this concept...
  18. ncbi request reprint Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase
    Nina M Antikainen
    Department of Chemistry, Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802, USA
    Biochemistry 44:16835-43. 2005
    ..These results are correlated with other measurements related to conformation coupled catalysis...
  19. doi request reprint Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
    Songon An
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Science 320:103-6. 2008
    ..Collectively, the data provide strong evidence for the formation of a multi-enzyme complex, the "purinosome," to carry out de novo purine biosynthesis in cells...
  20. ncbi request reprint Relating protein motion to catalysis
    Sharon Hammes-Schiffer
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Biochem 75:519-41. 2006
    ..This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction...
  21. pmc Effects of a distal mutation on active site chemistry
    Lin Wang
    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
    Biochemistry 45:1383-92. 2006
    ....
  22. pmc Microtubule-assisted mechanism for functional metabolic macromolecular complex formation
    Songon An
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 107:12872-6. 2010
    ..Collectively, we propose a microtubule-assisted mechanism for functional purinosome formation in HeLa cells...
  23. pmc Analysis of the DNA translocation and unwinding activities of T4 phage helicases
    Senthil K Perumal
    414 Wartik Laboratories, Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
    Methods 51:277-88. 2010
    ..These methods have been successfully employed to study the functions of helicases from large superfamilies...
  24. pmc Interaction of dihydrofolate reductase with methotrexate: ensemble and single-molecule kinetics
    P T Ravi Rajagopalan
    Department of Chemistry, Pennsylvania State University, 152 Davey Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:13481-6. 2002
    ..Thus the mechanism of methotrexate binding to DHFR involves multiple steps and protein conformational changes...
  25. pmc On the structural and functional modularity of glycinamide ribonucleotide formyltransferases
    Seung Goo Lee
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Protein Sci 12:2206-14. 2003
    ..The chimeras in general, however, are subject to temperature instability and misfolding; thus, they serve primarily as useful candidates for further rounds of optimization...
  26. ncbi request reprint 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
    Jun Xi
    Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, USA
    Biochemistry 44:7747-56. 2005
    ..We conclude that gp59 acts in a manner similar to the clamp loader to ensure proper assembly of the replisome and does not remain as a replisome component during active replication...
  27. ncbi request reprint An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex
    Zhihao Zhuang
    Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 45:7976-89. 2006
    ..The collective kinetic data allowed us to propose and evaluate a sequence of steps describing this alternative pathway for clamp loading and holoenzyme formation...
  28. ncbi request reprint Dissociative properties of the proteins within the bacteriophage T4 replisome
    Michael A Trakselis
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 278:49839-49. 2003
    ..The implications of these results for RNA priming and extension during the repetitive synthesis of Okazaki fragments are discussed...
  29. ncbi request reprint Synthesis and biological evaluation of alpha- and gamma-carboxamide derivatives of 10-CF3CO-DDACTHF
    Youhoon Chong
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 13:3587-92. 2005
    ..Like 1, 2 is transported into the cell by the reduced folate carrier. Unlike 1, the functional activity of 2 is not dependent upon FPGS polyglutamylation...
  30. ncbi request reprint 10-(2-benzoxazolcarbonyl)-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid: a potential inhibitor of GAR transformylase and AICAR transformylase
    Thomas H Marsilje
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 11:4503-9. 2003
    ..Ketone 1 and the corresponding alcohol 13 were evaluated for inhibition of GAR Tfase and AICAR Tfase and the former was found to be a potent inhibitor of recombinant human (rh) GAR Tfase (Ki=600 nM)...
  31. ncbi request reprint The application of a minicircle substrate in the study of the coordinated T4 DNA replication
    Jingsong Yang
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 278:49828-38. 2003
    ..This inhibition only becomes significant at later times of the reaction and may be associated with the accumulation of single-stranded DNA leading to the collapse of active replisomes...
  32. ncbi request reprint The T4 phage UvsW protein contains both DNA unwinding and strand annealing activities
    Scott W Nelson
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 282:407-16. 2007
    ..The dual activities of UvsW are well suited for the DNA repair pathways described for leading strand lesion bypass and synthesis-dependent strand annealing...
  33. pmc Network of coupled promoting motions in enzyme catalysis
    Pratul K Agarwal
    Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:2794-9. 2002
    ..This type of network has broad implications for an expanded role of the protein fold in catalysis as well as ancillaries such as the engineering of altered protein function and the action of drugs distal to the active site...
  34. pmc Structural and functional modularity of proteins in the de novo purine biosynthetic pathway
    Hui Li
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Protein Sci 18:881-92. 2009
    ..Implications for understanding the role of domain swapping in protein evolution are discussed...
  35. pmc FamClash: a method for ranking the activity of engineered enzymes
    Manish C Saraf
    Department of Chemistry, 414 Wartik Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 101:4142-7. 2004
    ..Comparisons of the predicted clash map as a function of crossover position revealed good agreement with activity data, reproducing the observed V shape and matching the location of a local peak in activity...
  36. ncbi request reprint Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis
    R Steven Sikorski
    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
    J Am Chem Soc 126:4778-9. 2004
    ..The data also suggested environmentally coupled tunneling and commitment to catalysis on pre-steady-state isotope effects...
  37. ncbi request reprint Investigation of an antibody-ligase. Evidence for strain-induced catalysis
    Sergey N Savinov
    Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA
    Bioorg Med Chem Lett 13:1321-4. 2003
    ..General mechanistic implications for de novo induced catalysis are presented...
  38. ncbi request reprint 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
    Heng Cheng
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 13:3593-9. 2005
    ..coli GAR Tfase as well as recombinant human AICAR Tfase. Compound 2 exhibited modest, purine-sensitive growth inhibitory activity against the CCRF-CEM cell line (IC50 = 6.0 microM)...
  39. pmc Stepwise loading of yeast clamp revealed by ensemble and single-molecule studies
    Ravindra Kumar
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 107:19736-41. 2010
    ..These findings redefine and deepen our understanding of the clamp-loading process and reveal that it is surprisingly one of trial and error to arrive at a heuristic solution...
  40. pmc Discovery of antibacterial cyclic peptides that inhibit the ClpXP protease
    Lin Cheng
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Protein Sci 16:1535-42. 2007
    ..The screen used here could be adapted to identify cyclic peptide inhibitors of any enzyme that can be expressed in E. coli in conjunction with a fluorescent reporter...
  41. ncbi request reprint Site-directed mutations of T4 helicase loading protein (gp59) reveal multiple modes of DNA polymerase inhibition and the mechanism of unlocking by gp41 helicase
    Scott W Nelson
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 281:8697-706. 2006
    ....
  42. ncbi request reprint Repetitive lagging strand DNA synthesis by the bacteriophage T4 replisome
    Michelle M Spiering
    Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Biosyst 4:1070-4. 2008
    ....
  43. ncbi request reprint The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication
    Jingsong Yang
    Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Mol Cell 21:153-64. 2006
    ..We formulate a signaling model capable of rationalizing the distribution of Okazaki fragments under various conditions for this and possibly other replisomes...
  44. pmc Processive and unidirectional translocation of monomeric UvsW helicase on single-stranded DNA
    Scott W Nelson
    Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 48:1036-46. 2009
    ..The ability of UvsW to unwind DNA duplexes is likely to be mechanistically linked to its ability to processively translocate on ssDNA in a 3' to 5' unidirectional fashion...
  45. pmc IPRO: an iterative computational protein library redesign and optimization procedure
    Manish C Saraf
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Biophys J 90:4167-80. 2006
    ..Computational results demonstrate that it is indeed feasible to improve the overall library quality as exemplified by binding energy scores through targeted mutations in the parental sequences...
  46. pmc Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase
    Lin Wang
    Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
    Proc Natl Acad Sci U S A 103:15753-8. 2006
    ..This observation is in accordance with the notion that these remote residues are part of a dynamic network that is coupled to the catalyzed chemistry...
  47. ncbi request reprint Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly
    Jun Xi
    Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, USA
    Biochemistry 44:2305-18. 2005
    ..Thus, continued assembly of the replisome through addition of the primosome components and elements of the lagging-strand holoenzyme can occur without leading-strand DNA replication...
  48. ncbi request reprint Design, synthesis and biological evaluation of 10-CF3CO-DDACTHF analogues and derivatives as inhibitors of GAR Tfase and the de novo purine biosynthetic pathway
    Joel Desharnais
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 11:4511-21. 2003
    ..120 microM) and very selective (> or =100-fold) for rh versus E. coli GAR Tfase. Additional key analogues of 1 were examined (7 and 8) and found to be much less active (1000-fold) highlighting the exceptional characteristics of 1...
  49. ncbi request reprint Genetically selected cyclic-peptide inhibitors of AICAR transformylase homodimerization
    Ali Tavassoli
    Department of Chemistry, Pennsylvania State University, University Park, 16802, USA
    Angew Chem Int Ed Engl 44:2760-3. 2005
  50. ncbi request reprint Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme
    Michael A Trakselis
    Department of Chemistry, 415 Wartik Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Biol 326:435-51. 2003
    ..Although this sequential assembly mechanism can be generally applied to most other replication systems studied to date, the specifics of ATP utilization seem to vary across replication systems...
  51. ncbi request reprint 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
    Heng Cheng
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 13:3577-85. 2005
    ..0 microM and 2, IC50 = 2.0 microM)...
  52. ncbi request reprint Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome
    Faoud T Ishmael
    Department of Biochemistry and Molecular Biology, Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania 17033, USA
    J Biol Chem 278:3145-52. 2003
    ..gp61.gp41 primosome complex. The resultant species is a complex of proteins that may allow coordinated leading and lagging strand synthesis, helicase DNA unwinding activity, and polymerase nucleotide incorporation...
  53. pmc Investigation of stoichiometry of T4 bacteriophage helicase loader protein (gp59)
    Sri Ranjini Arumugam
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 284:29283-9. 2009
    ..In addition, the presence of gp32 and gp41 proteins increases the stability of the gp59 complex, emphasizing their functional role in T4 DNA replication machinery...
  54. ncbi request reprint 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
    Thomas H Marsilje
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 10:2739-49. 2002
    ..coli enzyme (K(i) for 3, 14nM against rhGAR Tfase versus 6 microM against E. coli GAR Tfase) which also accounts for their exceptional cytotoxic potency...
  55. ncbi request reprint The oligomeric T4 primase is the functional form during replication
    Jingsong Yang
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 280:25416-23. 2005
    ..Collectively, these results provide strong evidence for the functional oligomerization of gp61. The potential roles of gp61 oligomerization during lagging strand synthesis are discussed...
  56. ncbi request reprint 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
    Thomas H Marsilje
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Bioorg Med Chem 11:4487-501. 2003
    ....
  57. pmc RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins
    Scott W Nelson
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 283:22838-46. 2008
    ..The interplay between gp32, primase, clamp, and clamp loader dictates the rate and efficiency of primer synthesis, polymerase recycling, and primer transfer to the polymerase...
  58. pmc Single-molecule studies of DNA replisome function
    Senthil K Perumal
    414 Wartik Laboratory, Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
    Biochim Biophys Acta 1804:1094-112. 2010
    ....
  59. ncbi request reprint Using incremental truncation to create libraries of hybrid enzymes
    Alexander R Horswill
    Department of Chemistry, Pennsylvania State University, University Park 16802, USA
    Methods Enzymol 388:50-60. 2004
  60. ncbi request reprint A universal, vector-based system for nucleic acid reading-frame selection
    Stefan Lutz
    Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
    Protein Eng 15:1025-30. 2002
    ....
  61. ncbi request reprint Assembly of the bacteriophage T4 helicase: architecture and stoichiometry of the gp41-gp59 complex
    Faoud T Ishmael
    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 277:20555-62. 2002
    ..As the helicase is loaded onto DNA, a conformational change in the gp41-gp59 complex occurs, which may serve to displace gp32 from the lagging strand and load the hexameric helicase in its place...
  62. pmc The dynamic processivity of the T4 DNA polymerase during replication
    Jingsong Yang
    Department of Chemistry, 414 Wartik Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 101:8289-94. 2004
    ....
  63. pmc The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer
    Zhihao Zhuang
    Department of Chemistry, 414 Wartik Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:2546-51. 2006
    ..The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm...
  64. ncbi request reprint A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening
    Youn Hi Woo
    414 Wartik Laboratory, Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Anal Biochem 340:336-40. 2005
    ..The methodology developed is suited to screen a large number of compounds for inhibitors of various methyltransferases...
  65. ncbi request reprint Structure of avian AICAR transformylase with a multisubstrate adduct inhibitor beta-DADF identifies the folate binding site
    Dennis W Wolan
    The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Biochemistry 42:10904-14. 2003
    ..Furthermore, the beta-DADF-bound structure provides a more optimal three-dimensional scaffold to improve the design of specific antineoplastic agents...
  66. ncbi request reprint Identification of a novel boron-containing antibacterial agent (AN0128) with anti-inflammatory activity, for the potential treatment of cutaneous diseases
    Stephen J Baker
    Anacor Pharmaceuticals, Inc, 1060 E Meadow Circle, Palo Alto, CA 94303, USA
    Bioorg Med Chem Lett 16:5963-7. 2006
    ..This compound is now in clinical development for dermatological conditions...
  67. ncbi request reprint Design and evolution of new catalytic activity with an existing protein scaffold
    Hee Sung Park
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373 1, Kusung dong, Yusung Gu, Daejon 305 701, Korea
    Science 311:535-8. 2006
    ..8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100...
  68. pmc Role of a solvent-exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase
    James J A Huntley
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Protein Sci 12:1368-75. 2003
    ..Rather, a more productive approach may be to design therapeutics directed towards this solvent-exposed tryptophan residue...
  69. ncbi request reprint 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
    Yan Zhang
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Biochemistry 42:6043-56. 2003
    ....
  70. pmc Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation
    R Derike Smiley
    Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, USA
    Biochemistry 45:7990-7. 2006
    ..In all cases, MgATP is required. The possible physiological significance of the various assembly pathways is discussed in the context of replication initiation and lagging strand synthesis during various stages of T4 phage replication...
  71. ncbi request reprint PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site
    James B Thoden
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Biol Chem 277:23898-908. 2002
    ..This sensitivity to nucleotide identity is in sharp contrast to that observed for the "P-loop"-containing enzymes, in which the conformation of the binding motif is virtually unchanged in the presence or absence of nucleotides...
  72. ncbi request reprint Dihydrofolate reductase mutant with exceptional resistance to methotrexate but not to trimetrexate
    Pamela Pineda
    Departments of Medicinal Chemistry and of Genetics and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Med Chem 46:2816-8. 2003
    ..5-fold higher for trimetrexate (TMTX). These findings suggest that F31A/F34A could be used for gene therapy to render normal cells resistant to MTX but sensitive to TMTX...
  73. ncbi request reprint 'Screw-cap' clamp loader proteins that thread
    Zhihao Zhuang
    Nat Struct Mol Biol 11:580-1. 2004
  74. ncbi request reprint Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle
    Rani P Venkitakrishnan
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Biochemistry 43:16046-55. 2004
    ..The G121V mutation, at a position distant from the active site, interferes with coupled loop movements and appears to impair catalysis by destabilizing the closed Michaelis complex and introducing an extra step into the kinetic pathway...
  75. ncbi request reprint DNA polymerase fidelity: kinetics, structure, and checkpoints
    Catherine M Joyce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Biochemistry 43:14317-24. 2004
    ....
  76. ncbi request reprint Using transcriptional-based systems for in vivo enzyme screening
    Steven M Firestine
    Department of Medicinal Chemistry, Mylan School of Pharmacy, Duquesne University, Pittsburgh, PA, USA
    Methods Mol Biol 205:315-27. 2003
  77. ncbi request reprint On the solution structure of the T4 sliding clamp (gp45)
    David Millar
    Department of Molecular Biology MB 19, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Biochemistry 43:12723-7. 2004
    ..The ramifications for replisome remodeling by this pathway are discussed...
  78. pmc Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers
    Yasuaki Kawarasaki
    Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
    Nucleic Acids Res 31:e126. 2003
    ..Expression and high-throughput flow cytometric screening of the chimeric GST library identified several chimeric progeny that retained rat-like parental substrate specificity...
  79. doi request reprint Allosteric regulation and catalysis emerge via a common route
    Nina M Goodey
    Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
    Nat Chem Biol 4:474-82. 2008
    ....
  80. ncbi request reprint Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli
    Ali Tavassoli
    School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
    Nat Protoc 2:1126-33. 2007
    ..This protocol is expected to take around 3-4 weeks to implement...
  81. pmc Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate
    Zhiquan Zhang
    Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 101:2764-9. 2004
    ..The results from stopped-flow and single-molecule methods are complementary and demonstrate that multiple conformations of both the enzyme and enzyme-substrate complexes exist...
  82. pmc Evolution of highly active enzymes by homology-independent recombination
    Karl E Griswold
    Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 102:10082-7. 2005
    ..These results highlight the power of combinatorial homology-independent and low-homology recombination methods for the generation of unique, highly active enzymes and also suggest a possible means of enzyme "humanization."..

Research Grants55

  1. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2009
    ..Individual enzymes within the pathway are biologically validated targets. Interference by small molecules with purinosome assembly provides a unique route to new pharmaceuticals. ..
  2. THE TRANSFORMYLASE ENZYMES
    STEPHEN BENKOVIC; Fiscal Year: 1980
    ....
  3. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2009
    ..In so far as these events are central to cell division in how helicases in particular function in normal and diseased states is of critical importance. ..
  4. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2001
    ..Computer models will be developed based on the determination of enzyme and metabolite levels in the cell to predict the flux of intermediates in the pathway. ..
  5. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2001
    ..These studies should greatly deepen our knowledge of how the T4 replicative system functions and serves as a paradigm for DNA replication in general. ..
  6. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2000
    ..These studies should greatly deepen our knowledge of how the T4 replicative system functions and serves as a paradigm for DNA replication in general. ..
  7. TRANSFORMYLASE ENZYMES--DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2000
    ..These folate requiring enzymes are important in one carbon unit transfer and have been the target of chemotherapy. Dihydrofolate reductase in particular serves as a paradigm for understanding the fundamentals of enzyme catalysis. ..
  8. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2000
    ..These studies should greatly deepen our knowledge of how the T4 replicative system functions and serves as a paradigm for DNA replication in general. ..
  9. TRANSFORMYLASE ENZYMES--DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 1999
    ..These folate requiring enzymes are important in one carbon unit transfer and have been the target of chemotherapy. Dihydrofolate reductase in particular serves as a paradigm for understanding the fundamentals of enzyme catalysis. ..
  10. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2002
    ..These studies should greatly deepen our knowledge of how the T4 replicative system functions and serves as a paradigm for DNA replication in general. ..
  11. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2002
    ..Computer models will be developed based on the determination of enzyme and metabolite levels in the cell to predict the flux of intermediates in the pathway. ..
  12. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    Stephen J Benkovic; Fiscal Year: 2010
    ..Individual enzymes within the pathway are biologically validated targets. Interference by small molecules with purinosome assembly provides a unique route to new pharmaceuticals. ..
  13. PHOSPHATE ACTIVATION MECHANISMS
    Stephen J Benkovic; Fiscal Year: 2010
    ....
  14. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2009
    ....
  15. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2007
    ....
  16. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2006
    ..abstract_text> ..
  17. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2004
    ..Computer models will be developed based on the determination of enzyme and metabolite levels in the cell to predict the flux of intermediates in the pathway. ..
  18. TRANSFORMYLASE ENZYMES DIHYDROFOLATE REDUCTASE
    STEPHEN BENKOVIC; Fiscal Year: 2003
    ..Computer models will be developed based on the determination of enzyme and metabolite levels in the cell to predict the flux of intermediates in the pathway. ..
  19. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 2003
    ..abstract_text> ..
  20. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1990
    ..The ultimate objective of this work is to elucidate the relationship between polymerase structure and function that results in the enzymes high catalytic efficiency and fidelity...
  21. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1999
    ..These studies should greatly deepen our knowledge of how the T4 replicative system functions and serves as a paradigm for DNA replication in general. ..
  22. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1991
    ..The ultimate objective of this work is to elucidate the relationship between polymerase structure and function that results in the enzymes high catalytic efficiency and fidelity...
  23. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1992
    ..The ultimate objective of this work is to elucidate the relationship between polymerase structure and function that results in the enzymes high catalytic efficiency and fidelity...
  24. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1980
    ..Petsko at M.I.T. to carry out X-ray crystallographic studies on FBPase; and 5) initiation of series of mechanistic studies on restriction endonucleases commencing with the chemical synthesis of small, potential substrate molecules. ..
  25. PHOSPHATE ACTIVATION MECHANISMS
    STEPHEN BENKOVIC; Fiscal Year: 1993
    ..The ultimate objective of this work is to elucidate the relationship between polymerase structure and function that results in the enzymes high catalytic efficiency and fidelity...