Stephen J. Benkovic

Stephen J. Benkovic

Main Content

  • Evan Pugh University Professor and Eberly Chair in Chemistry
Office:
414 Wartik Laboratory
University Park, PA 16802
Email:
(814) 865-2882

Education:

  1. B.S., Lehigh University; 1960
  2. Ph.D., Cornell University, 1963
  3. Postdoctoral Research Assoc., University of California at Santa Barbara, 1964-65

Honors and Awards:

  1. National Academy of Inventors (NAI) Fellow
  2. National Academy of Science Award in Chemical Sciences
  3. Ralph F. Hirschmann Award in Peptide Chemistry
  4. National Medal of Science
  5. Benjamin Franklin Medal in Life Science
  6. Royal Society Centenary Medal
  7. Nakanishi Prize (ACS)
  8. ASBMB-Merck Award
  9. American Philosophical Society
  10. Christian B. Anfinsen Award
  11. Chemical Pioneer, The American Institute of Chemists
  12. Honorary Doctorate of Science, Lehigh University
  13. Alfred Bader Award
  14. Institute of Medicine, National Academy of Sciences
  15. Bicentennial Scientific Achievement Award, City College of New York
  16. Repligen Award
  17. NIH Merit Award
  18. Arthur C. Cope Scholar Award
  19. The Eberly Chair in Chemistry
  20. Gowland Hopkins Award
  21. National Academy of Sciences
  22. American Academy of Arts and Sciences
  23. Pfizer Enzyme Award
  24. Guggenheim Fellowship
  25. NIH Career Development Award, The Pennsylvania State University
  26. Alfred P. Sloan Fellow, The Pennsylvania State University

Selected Publications:

  • Benkovic, S.J., Spiering, M.M. (2017) “Understanding DNA Replication by the Bacteriophage T4 Replisome”, JBC, doi 10.1074/jbc.R117.811208
  • Hedglin, M. and Benkovic, S.J. (2017) “Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours Around the Same Obstacle”; ACS Chem Review, 117, 7857-7877
  • Spiering, M.M., Hanoian, P., Gannavaram, S., and Benkovic, S.J. (2017) “RNA primer-primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication”; PNAS 114 (22):5635-5640
  • Hedglin, M., Perumal, S.K., Hu, Z., Benkovic, S.J., (2013) “Stepwise assembly of the human replicative polymerase holoenzyme”, eLife, 2013;2:e00278. DOI:  10.7554/eLife.00278Kumar, R., Nashine, V.C., Mishra, P,P., Benkovic, S.J. and Lee, T.H. (2010) Stepwise loading of yeast clamp revealed by ensemble and single-molecule studies,  PNAS USA 107 (46) 19736-19741
  • Huang, X., Liu, C.T., Benkovic, S.J. (2015) “Chapter 2:Protein Conformational Motions – Enzyme Catalysis:”, Understanding Enzymes: Function, Design, Engineering, and Analysis, PanStanford Publishing
  • Liu, C. T., Hanoian, P., French, J.B., Pringle, T. H., Hammes-Schiffer, S., Benkovic, S.J. (2013) “Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans”, PNAS, Vol. 110 (25), 10159-10164
  • Liu, C.T., Layfield, J.P., Stewart, III, R. J., French, J. B., Hanoian, P., Asbury, J.B., Hammes-Schiffer, S., Benkovic, S.J., (2014) “Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase”, JACS, 136 (29), 10349-10360
  • Liu, C.T.,Francis, K.,Layfield, J.,Huang,X.,Hammes-Schiffer, S.,Kohen,A.,Benkovic,S.J., (2014) “Eschericha coli Dihydrofolate Reductase Catalyzed Proton and Hydride Transfers: Temporal Order and the Roles of Asp27 and Tyr100”, PNAS, 111:51, 18231-18236; PMCID: 4280594
  • Boehr, D.D., Schnell, J.R., McElheny, D., Bae, S., Duggan, B.M., Benkovic, S.J., Dyson, H.J., and Wright, P.E., (2013) “A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase”, Biochemistry, 52 (27), 4605-4619
  • Pedley, A.M. and Benkovic, S.J. (2016) “A new view into the regulation of purine metabolism – the purinosome”, Trends Biochem Sci, 42(2):141-154
  • French, J. B., Jones, S.A., Deng, H., Hu, H., Pugh, R. J., Chan C. Y., Kim, D., Pedley, A. M., Zhao, H., Zhang, Y., Huang, T. J., Fang, Y., Zhuang, X., and Benkovic, S. J., (2016) “Spatial colocalization and functional link of purinosomes with mitochondria ”, Science, 351:6274, 733-736,
  • Zhao, H., Chiaro, C.R., Zhang, L., Smith, P.B., Chan, C.Y., Pedley, A.M., Pugh, R.J., French, J.B., Patterson, A.D., and Benkovic, S.J. (2015) “Quantitative Analysis of Purine Nucleotides Indicates Purinosomes Increase de novo Purine Biosynthesis”, JBC, doi 10.1074/ jbc.M114.628701
  • French,J. B., Zhao, H., An., S., Niessen, S., Deng, Y., Cravatt, B. J., and Benkovic, S. J. (2013) “The Hsp70/Hsp90 chaperone machinery is involved in the assembly of the purinosome”,  PNAS 110 (7) 2528-2533
  • An, S., Kumar, R., Sheets, E. D., and Benkovic, S. J. (2008) Reversible Compartmentalization of de Novo Purine Biosynthetic Complexes in Living Cells, Science 320, 103-106

Information:

Professor Benkovic has long been interested in various mechanisms used by enzymes that catalyze phosphoryl transfer reactions.  Historically their work began with bioorganic models of phosphoryl transfer reactions, e.g., the hydrolysis of phosphoenolpyruvate, progressed through a series of studies detailing the stereochemistry of the phosphoryl transfer, e.g., T4 DNA ligase, and the mechanism of action of fructose -1, 6- bisphosphatase.  Over the last three decades, the lab has focused on the mechanism of DNA replication using the eight protein T4 phage replisome as their model and in the last decade on translesion bypass by phage and human enzymes.  Their studies have made extensive use of a variety of kinetic techniques including single-turnover ensemble and single-molecule methods that feature magnetic tweezers (a long standing collaboration with the Croquette lab), and fluorescent FRET measurements.  The results have provided detailed insights into how holoenzymes involving polymerases/clamp proteins are assembled/disassembled and how they interact to coordinate leading/lagging strand synthesis despite the continuous replication of the leading strand and the stepwise, primed synthesis of the lagging strand.  The Benkovic lab is presently establishing the mechanistic basis for translesion bypass through in depth examination of the kinetics of human pol delta and pol eta.

A theme that underlies and connects all the research in Professor Benkovic’s laboratory is to discover and define the chemical principles that are responsible for enzymatic catalysis. With dihydrofolate reductase as a paradigm, they have examined the question of the importance of conformational changes and their contributions to catalysis.  A variety of collaborative approaches that include nuclear magnetic relaxation, pre-steady state kinetics, fluorescence resonance energy transfer, phylogentically coherent events, stark effects and molecular dynamic simulations have focused on the parent and mutant forms of the enzyme.  The collective findings support the presence of a network of residues within the protein fold that acts to generate a series of enzyme conformations along the reaction coordinate that optimize the reacting centers of the substrate and cofactor for the chemical transformation.  The optimization is manifest in favorable changes in the active site electrostatics for the series of complexes that comprise the reaction cycle and in an unexpected pH dependence of the chemical step.

Dr. Benkovic’s early research studies on the mechanism action of the tetrahydrofolate cofactors progressed from bioorganic model studies into examination of the folate requiring transformylase enzymes involved in de novo purine biosynthesis.   Their findings engendered inquiry into how these enzymes functioned within the context of the six enzymes that constitute the de novo purine biosynthetic pathway.  They were unable to demonstrate that such a reaction network functioned as a complex in vitro but were rewarded by the discovery that all participate in a cellular supra-molecular complex, the purinosome.  Their finding that the purinosome required an intracellular environment has encouraged the pursuit of such elusive metabolic complexes by others.  To date, plasmid constructs have been shared with more than a dozen laboratories.  The transient intracellular nature of the purinosome has challenged conventional in vitro purification and analysis techniques.  Consequently, experimental approaches have been inititated to identify its members-possibly not limited to enzymes in the de novo purine biosynthetic pathway-through the latest intracellular fluorescence, cross-linking, protein-protein reporter assays and confocal imaging techniques.  Similarly, these along with the identification and measurement of changes in metabolite levels as a function of purinosome status have demanded participation in collaborations that feature high resolution fluorescence based cellular imaging (STORM); high through put screens for finding clients of the Hsp90 chaperone complex; and  sensitive MALDI-MS/MS analysis of purinosome containing cells.  Another protocol, dynamic mass redistributoion (DMR) has been used to identify signaling molecules. The purinosomes present a different challenge than our studies on the T4 replisome where the protein-protein interactions are sufficiently strong in the absence of cellular factors that the replisome can be reconstituted in vitro.  The purinosome is among the first example of an intracellular, transient, supra-molecular complex and represents an emerging research area.

Research Interests:

Biological

Cellular metabolism and gene replication

Chemical Biology

Cellular metabolism and gene replication