|
|
|
2008
|
| 1. |
Nelson,
S. W., Kumar, R., and Benkovic, S. J. (2008) RNA Primer
Handoff in Bacteriophage T4 DNA Replication: The Role of
Single-stranded DNA-binding Protein and Polymerase Accessory
Proteins, J. Biol. Chem. 283 (33) 22838-22846.
|
| 2. |
Goodey,
N. M. and Benkovic, S. J. (2008) Allosteric Regulation and
Catalysis Emerge Via a Common Route, Nat. Chem. Biol. 4
(8) 474-482.
|
| 3. |
Zhuang,
Z., Johnson, R. E., Haracska, L., Prakash, L., Prakash, S.,
and Benkovic, S. J. (2008) Regulation of Polymerase Exchange
Between Polη and Polδ by Monoubiquitination of PCNA
and the Movement of DNA Polymerase Holoenzyme, Proc. Natl.
Acad. Sci. 105 (14) 5361-5366
|
| 4 |
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.
|
| 5. |
Benkovic, S.
J., Hammes, G. G., and Hammes-Schiffer, S. (2008) Free-Energy
Landscape of Enzyme Catalysis, Biochemistry 47 (11)
3317-3321.
|
| 6. |
Tomsho,
J. W. and Benkovic, S. J. (2008) Unnatural Translation
Initiation, ACS Chem. Biol. 3 (2) 87-88.
|
| 7. |
Naumann, T. A., Tavassoli, A., and Benkovic, S. J. (2008) Genetic Selection of Cyclic Peptide Dam Methyltransferase Inhibitors, Chembiochem 25 (9) 194-197.
|
| |
2007
|
| 1. |
Lionnet, T., Spiering, M. M., Benkovic, S. J., Bensimon, D., Croquette, V. (2007) Real-time Observation of Bacteriophage T4 gp41 Helicase Reveals an Unwinding Mechanism, Proc. Natl. Acad. Sci. USA 104 (50) 19790-19795.
|
| 2. |
Cheng, L., Naumann, T. A., Horswill, A. R., Hong, S.-J., Venters, B. J., Tomsho, J. W., Benkovic, S. J., Keiler, K. C. (2007) Discovery of Antibacterial Cyclic Peptides That Inhibit the ClpXP Protease, Protein Science 16, 1-8.
|
.
|
Rock,
F. L., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou,
Zhang, Y.-K., Hernandez, V., Akama, T., Baker, S. J., Plattner,
J. J., Shapiro, L., Martinis, S. A., Benkovic, S. J., Cusack,
S., Alley, M. R. K. (2007) An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by
Trapping tRNA in the Editing Site, Science 316 (5832) 1759-1761.
|
| 4. |
Tavassoli,
A. and Benkovic, S. J. (2007) Split-intein Mediated Circular Ligation Used in the Synthesis
of Cyclic Peptide Libraries in E. coli, Nature Protocols 2 (5)
1126-1133. |
| 5. |
Nelson,
S. W. and Benkovic, S. J. (2007) The T4 Phage UvsW Protein Contains Both DNA Unwinding and
Strand Annealing Activities, J. Biol. Chem. 282 (1) 407-416.
|
| 6. |
Benkovic,
S. J. and Hammes-Schiffer, S. (2007) Dihydrofolate Reductase: Hydrogen Tunneling and Protein Motion
in Hydrogen-Transfer Reactions, Vol. 4 (Schowen, R. L., Klinman,
J. P., Hynes, J. T., and Limbach, H. -H. (Eds), Wiley-VCH Verlag
GmbH & Co. Weinheim, pp. 1439-1454. |
| |
2006
|
| 1. |
Horswill,
A. R. and Benkovic, S. J. (2006)
Identifying Small-Molecule Modulators of Protein-Protein Interactions,
in Current Protocols in Protein Science, John Wiley & Sons,
Inc., pp. 19.15.1-19.15.19. |
| 2. |
Baker,
S. J., Akama, T., Zhang, Y.-K., Sauro, V., Pandit, C., Singh,
R., Kully, M., Khan, J., Plattner, J. J., Benkovic, S. J., Lee,
V., and Maples, K. R. (2006)
Identification of A Novel Boron-containing Antibacterial Agent
(AN0128) With Anti-inflammatory Activity, for the Potential
Treatment of Cutaneous Diseases, Bioorg. Med. Chem. Lett. 16,
5963-5967. |
| 3. |
Wang,
L., Goodey, N. M., Benkovic, S. J., and Kohen, A. (2006)
Coordinated Effects of Distal Mutations on Environmentally Coupled
Tunneling in Dihydrofolate Reductase, Proc. Natl. Acad. Sci.
USA 103 (43) 15753-15758. |
| 4. |
Saraf,
M. C., Moore, G. L., Goodey, N. M., Cao, V. Y., Benkovic,
S. J., and Maranas, C. D. (2006) IPRO:
An Iterative Computational Protein Library Redesign and Optimization
Procedure, Biophys. J. 90 (11) 4167-4180.
|
| 5. |
Wang,
L., Goodey, N. M., Benkovic, S. J., and Kohen, A. (2006)
The Role of Enzyme Dynamics and Tunneling in Catalysing Hydride
Transfer: Studies of Distal Mutants of Dihydrofolate Reductase,
Phil. Trans. R. Soc. B 361, 1307-1315. |
| 6. |
Hammes-Schiffer,
S. and Benkovic, S. J. (2006)
Relating Protein Motion to Catalysis, Annu. Rev. Biochem. 75,
519-541. |
| 7. |
Smiley,
R. D., Zhuang, Z., Benkovic, S. J., and Hammes, G. G. (2006)
Single-Molecule Investigation of the T4 Bacteriophage DNA Polymerase
Holoenzyme: Multiple Pathways of Holoenzyme Formation, Biochemistry
45, 7990-7997. |
| 8. |
Zhuang,
Berdis, A. J., and Benkovic, S. J. (2006)
An Alternative Clamp Loading Pathway via the T4 Clamp Loader,
Biochemistry 45, 7976-7989. |
| 9. |
Benkovic,
S. J. and Hammes-Schiffer, S. (2006)
Enzyme Motions Inside and Out, Science 312, 208-209. |
| 10. |
Nelson,
S. W., Yang, J., and Benkovic, S. J. (2006)
Site-directed Mutations of T4 Helicase Loading Protein (gp59)
Reveal Multiple Modes of DNA Polymerase Inhibition and the Mechanism
of Unlocking by gp41 Helicase, J. Biol. Chem. 281 (13) 8697-8706.
|
| 11. |
A.R.
Horswill and S.J. Benkovic
Cyclic Peptides, A Chemical Genetics Tool for Biologists,Cellcycle
4 (4) 552-555 (2006). |
| 12. |
Z.
Zhuang, B.L. Yoder, P.M.J. Burgers, and S.J. Benkovic
The Structure of a Ring-opened Proliferating Cell Nuclear Antigen-Replication
Factor C Complex Revealed by Fluorescence Energy Transfer, Proc.
Natl. Acad. Sci. U.S.A., 103 (8) 2546-2551 (2006). |
| 13. |
H-S.
Park, S-H. Nam, J.K. Lee, C.N. Yoon, B. Mannervik, S.J. Benkovic,
and H-S. Kim,
Design and Evolution of New Catalytic Activity with an Existing
Protein Scaffold," Science 311 (5760) 535-538 (2006).
|
| 14. |
L.
Wang, S. Tharp, T. Selzer, S.J. Benkovic, and A. Kohen
Effects of A distal Mutation on Active Site Chemistry. Biochemistry
45 (5) 1383-1392 (2006). |
| 15. |
J.
Yang, S.W. Nelson, and S.J. Benkovic
The Control Mechanism for Lagging Strand Polymerase Recycling
during Bacteriophage T4 DNA Replication, Mol. Cell 27, 153-164
(2006). |
| |
2005 |
| 1. |
Cheng,
H., Hwang, I., Chong, Y., Tavassoli, A., Webb, M. E., Zhang,
Y., Wilson, I. A., Benkovic, S. J., and Boger, D. L. (2005)
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, Bioorg. Med. Chem. 13 (10) 3593-3599. |
| 2. |
Tavassoli,
A., Naumann, T. A., and Benkovic, S. J. (2005)
Production of Cyclic Proteins and Peptides, in Nucleic Acids
and Molecular Biology, Vol. 16, Homing Endonucleases and Inteins
(Marlene Belfort et al. (Eds.), Springer-Verlag Berlin Heidelberg,
pp. 293-305. |
| 3. |
T.A.
Naumann, S.N. Savinov, and S.J. Benkovic
Engineering an Affinity Tag for Genetically Encoded Cyclic Peptides,
Biotechnol. Bioeng. 7, 820-830 (2005). |
| 4. |
N.M.
Antikainen, R.D. Smiley, S.J. Benkovic, and G.G. Hammes
Conformation Coupled Enzyme Catalysis: Single-Molecule and Transient
Kinetics Investigation of Dihydrofolate Reductase," Biochemistry
44, 16835-16843 (2005). |
| 5. |
S.J.
Benkovic, S.J. Baker, M.R.K. Alley, Y-H. Woo, Y-K. Zhang, T.
Akama, W. Mao, J. Baboval, P.T.R. Rajagopalan, M. Wall, L.S.
Kahng, A. Tavassoli, and L. Shapiro
Identification of Borinic Esters as Inhibitors of Bacterial
Cell Growth and Bacterial Methyltransferases, CcrM and MenH,"
J. Med. Chem. 48, 7468-7476, 2005. |
| 6. |
K.E.
Griswold, Y. Kawarasaki, N. Ghoneim, S.J. Benkovic, B.L. Iverson,
and G. Georgiou
Evolution of Highly Active Enzymes by Homology-Independent Recombination,
Proc. Natl. Acad. Sci. USA 102 (29) 10082-10087 (2005).
|
| 7. |
J.
Yang, J. Xi, Z. Zhuang, and S.J. Benkovic
The Oligomeric T4 Primase Is the Functional Form During Replication,J.
Biol. Chem. 280 (27) 25416-25423 (2005). |
| 8. |
J.
Xi, Z. Zhang, Z. Zhuang, J. Yang, M.M. Spiering, G.G. Hammes,
and S.J. Benkovic
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, 7747-7756 (2005). |
| 9. |
K.F.Wong,
T. Selzer, S.J. Benkovic, and S. Hammes-Schiffer
Impact of Distal Mutations on the Network of Coupled Motions
Correlated to Hydride Transfer in Dihydrofolate Reductase,"
Proc. Natl. Acad. Sci. USA 102 (19) 6807-6812 (2005). |
| 10. |
A.
Tavassoli and S.J. Benkovic
Genetically Selected Cyclic-Peptide Inhibitors of AICAR Transformylase
Homodimerization, Angew. Chem. 117, 2820-2823 (2005). |
| 11. |
Y.H. Woo,
P.T.R. Rajagopalan, S.J. Benkovic
A Nonradioactive DNA Methyltransferase Assay Adaptable to High-Throughput
Screening, Anal. Biochem. 304 (2) 336-340 (2005). |
| 12. |
M.T.
Norcum, J.A. Warrington, M.M. Spiering, F.T. Ishmael, M.A. Trakselis,
and S.J. Benkovic
Architecture of the Bacteriophage T4 Primosome: Electron Microscopy
Studies of Helicase (gp41) and Primase (gp61), Proc. Natl. Acad.
Sci. USA 102 (10) 3623-3626 (2005). |
| 13. |
Z.
Zhang, M.M. Spiering, M.A. Trakselis, F.T. Ishmael, J.Xi, S.J.
Benkovic, and G.G. Hammes
Assembly of the Bacteriophage T4 Primosome: Single-molecule
and Ensemble Studies, Proc. Natl. Acad. Sci. USA 102 (9) 3254-3259.
|
| 14. |
J.
Xi, Z. Zhuang, Z. Zhang, T. Selzer, M.M. Spiering, G.G. Hammes,
and S.J. Benkovic
Interaction Between the T4 Helicase-loading Protein (gp59) and
The DNA Polymerase (gp43): A Locking Mechanism To Delay Replication
During Replisome Assembly, Biochemistry 44 (7) 2305-2318 (2005).
|
| 15. |
Horswill
AR, Benkovic SJ.
Cyclic peptides, a chemical genetics tool for biologists.
Cell Cycle. 2005 Apr;4(4):552-5. Epub 2005 Apr 5. Review. |
| |
2004 |
| 1. |
R.P.
Venkitakrishnan, E. Zaborowski , D. McElheny, S.J. Benkovic,
H.J. Dyson, and P.E. Wright
“Conformational Changes in the Active Site Loops of Dihydrofolate
Reductase During the Catalytic Cycle,” Biochemistry 43,
16046-16055 (2004). |
| 2. |
C.M.
Joyce and S.J. Benkovic
"DNA Polymerase Fidelity: Kinetics, Structure, and Checkpoints,"
Biochemistry 43 (45) 2004. |
| 3. |
A.R.
Horswill, S.N. Savinov, and S.J. Benkovic
"A Systematic Method for Identifying Small-Molecule Modulators
of Protein-Protein Interactions," Proc. Natl. Acad. Sci.
USA 101 (44) 15591-15596 (2004). |
| 4. |
D.
Millar, M.A. Trakselis, and S.J. Benkovic
"On the Solution Structure of the T4 Sliding Clamp (gp45)",
Biochemistry 43, 12723-12727 (2004). |
| 5. |
A.R.
Horswill, T.A. Naumann, and S.J. Benkovic
"Using Incremental Truncation to Create Libraries of Hybrid
Enzymes," in Methods in Enzymology, Vol. 388, Protein Engineering,
Chapter 6 (D.E. Robertson, J.P. Noel, Eds) Elsevier Academic
Press, San Diego, CA pp. 50-60 (2004). |
| 6. |
Z.
Zhuang, M.M. Spiering, A.J. Berdis, M.A. Trakselis, and S.J.
Benkovic
"Screw-cap Clamp Loader Proteins That Thread", Nat.
Struct. Mol. Biol. 11 (7) 580-581 (2004). |
| 7. |
J.
Yang, Z. Zhuang, R. Roccasecca, M.A. Trakselis, and S.J. Benkovic
“The Dynamic Processivity of the T4 DNA Polymerase During
Replication,” Proc. Natl. Acad. Sci. USA 101 (22) 8289-8294
(2004). |
| 8. |
R.S.
Sikorski, L. Wang, K.A. Markham, P.T.R. Rajagopalan, S.J. Benkovic,
and A. Kohen
"Tunneling and Coupled Motion in the Escherichia coli Dihydrofolate
Reductase Catalysis," J. Am. Chem. Soc. 126, 4778-4779
(2004). |
| 9. |
M.C.
Saraf, A.R. Horswill, S.J. Benkovic, and C.D. Maranas
“FamClash: A Method for Ranking the Activity of Engineered
Enzymes,” Proc. Natl. Acad. Sci. USA 101 (12) 4142-4147
(2004). |
| 10. |
Z.
Zhang, P.T.R. Rajagoplan, T. Selzer, S.J. Benkovic, and G.G.
Hammes
"Single-Molecule and Transient Kinetics Investigation of
the Interaction of Dihydrofolate Reductase with NADPH and Dihydrofolate,"
Proc. Natl. Acad. Sci. USA 101 (9) 2764-2769 (2004). |
| |
2003 |
| 1. |
M.A.
Trakselis, R.M. Roccasecca, J. Yang, A.M. Valentine, and S.J.
Benkovic
"Dissociative Properties of the Proteins within the Bacteriophage
T4 Replisome," J. Biol. Chem. 278 (50) 49839-49849 (2003).
|
| 2. |
J.
Yang, M.A. Trakselis, R.M. Roccasecca, and S.J. Benkovic
"The Application of a Minicircle Substrate in the Study
of the Coordinated T4 DNA Replication," J. Biol. Chem.
278 (50) 49829-49838 (2003). |
| 3. |
Y.
Kawarasaki, Griswold, K.E., Stevenson, J.D., Selzer, T., Benkovic,
S.J., Iverson, B.L., and Georgiou, G.
“Enhanced Crossover SCRATCHY: Construction and High-throughput
Screening of a Combinatorial Library Containing Multiple Non-homologous
Crossovers,” Nucleic Acids Res. 31, 1-8 (2003). (Pubmed
Article) |
| 4. |
D.W.
Wolan, S.E. Greasley, M.J. Wall, S.J. Benkovic, and I.A. Wilson
"Structure of Avian AICAR Transformylase with a Multisubstrate
Adduct Inhibitor b-DADF Identifies the Folate Binding Site,"
Biochemistry 42, 10904-10914 (2003). |
| 5. |
S.G.
Lee, S. Lutz, and S.J. Benkovic
"On the Structural and Functional Modularity of Glycinamide
Ribonucleotide Formyltrasferases," Protein Science 12,
2206-2214 (2003). |
| 6. |
J.
Desharnais, I. Hwang, Y. Zhang, A. Tavassoli, J. Baboval, S.J.
Benkovic, I.A. Wilson, and D.L. Boger
“Design, Synthesis and Biological Evaluation of 10-CF3-CO-DDACTHF
Analogues and Derivatives as Inhibitors of GAR Tfase and the
De Novo Purine Biosynthetic Pathway,” Bioorg. Med. Chem.
11, 4511-4521 (2003). |
| 7. |
T.H.
Marsilje, M.P. Hedrick, J. Desharnais, K. Capps, A. Tavassoli,
Y. Zhang, I.A. Wilson, S.J. Benkovic, and D.L. Boger
“10-(2-Benzoxazolcarbonyl)-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic
Acid: A Potential Inhibitor of GAR Transformylase and AICAR
Transformylase,” Bioorg. Med. Chem. 11, 4503-4509 (2003).
|
| 8. |
T.H.
Marsilje, M.P. Hedrick, J. Desharnais, A. Tavassoli, Y. Zhang,
I.A. Wilson, S.J. Benkovic, and D.L. Boger
“Design, Synthesis, and Biological Evaluation of Simplified
a-Keto Heterocycle, Trifluoromethyl Ketone, and Formyl Substituted
Folate Analogues as Potential Inhibitors of GAR Transformylase
and AICAR Transformylase,” Bioorg. Med. Chem. 11, 4487-4501
(2003). |
| 9. |
S.J.
Benkovic and Sharon Hammes-Schiffer
"A Perspective on Enzyme Catalysis," Science 301 (5637)
1196-1202 (2003) |
| 10. |
J.J.A.
Huntley, W. Fast, S.J. Benkovic, P.E. Wright, and H. Jane Dyson
"Role of a Solvent-Exposed Tryptophan in the Recognition
and Binding of Antibiotic Substrates for a Metallo-b-Lactamase,"
Protein Science 12, 1368-1375 (2003). |
| 11. |
P.
Pineda, A. Kanter, R.S. McIvor, S.J. Benkovic, A. Rosowsky,
and C.R. Wagner
"Dihydrofolate Reductase Mutant with Exceptional Resistance
to Methotrexate but Not to Trimetrexate," J.Med. Chem.
46 (14) 2816-2818 (2003). |
| 12. |
Y.
Zhang, J. Desharnais, T.H. Marsilje, C. Li, M.P. Hedrick, L.T.
Gooljarsingh, A. Tavassoli, S.J. Benkovic, A.J. Olson, D.L.
Boger, and I.A. Wilson
"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 (20) 6043-6056 (2003). |
| 13. |
S.N.
Savinov, R. Hirschmann, S.J. Benkovic, and A.B. Smith, III
"Investigation of an Antibody-Ligase. Evidence for Strain-Induced
Catalysis," Bioorg. Med. Chem. Lett. 13, 1321-1324 (2003).
|
| 14. |
M.A.
Trakselis, A.J. Berdis, and S.J. Benkovic
"Examination of the Role of the Clamp-loader and ATP Hydrolysis
in the Formation of the Bacteriophage T4 Polymerase Holoenzyme,"
J. Mol. Biol. 326 (2), 435-451 (2003). |
| 15. |
F.T
Ishmael, M.A. Trakselis, and S.J. Benkovic
"Protein-Protein Interactions in the Bacteriophage T4 Replisome.
The Leading Strand Holoenzyme is Physically Linked to the Lagging
Strand Holoenzyme and the Primosome," J. Biol. Chem. 278
(5), 3145-3152 (2003). |
| |
2002 |
| 1. |
S.
Lutz, W. Fast, and S.J. Benkovic
"A University, Vector-Based System for Nucleic Acid Reading-Frame
Selection," Protein Eng. 15 (12) 1025-1030 (2002). |
| 2. |
M.
Wall and S.J. Benkovic
"Synthesis and Biological Evaluation of 9-Thia-5,10-dideazafolic
Acid," J. Heterocyclic Chem., 39, 1097-1099 (2002). |
| 3. |
S.M.
Firestine, F. Salinas, and S.J. Benkovic
"Using Transcriptional-Based Systems for In Vivo Enzyme
Screening," in Methods in Molecular Biology, Vol. 205,
E.coli Gene Expression Protocols, Chapter 22 (P.E. Vaillancourt,
Ed.) Humana Press Inc., Totowa, NJ pp. 315-327 (2002). |
| 4. |
E.
Abel-Santos, C.P. Scott, and S.J. Benkovic
"Use of Inteins for the In Vivo Production of Stable Cyclic
Peptide Libraries in E.coli," in Methods in Molecular Biology,
Vol. 205, E.coli Gene Expression Protocols, Chapter 19 (P.E.
Vaillancourt, Ed.) Humana Press Inc., Totowa, NJ pp. 281-294
(2002). |
| 5. |
P.T.R.
Rajagopalan, S. Lutz, and S.J. Benkovic
"Coupling Interactions of Distal Residues Enhance Dihydrofolate
Reductase Catalysis: Mutational Effects on Hydride Transfer
Rates," Biochemistry 41, 12618-12628 (2002). |
| 6. |
P.T.R.
Rajagopalan, Z. Zhang, L. McCourt, M. Dwyer, S.J. Benkovic,
and G.G. Hammes
"Interaction of Dihydrofolate Reductase With Methotrexate:
Ensemble and Single-molecule Kinetics," Proc. Natl. Acad.
Sci. USA 99 (21) 13481-13486 (2002). |
| 7.. |
J.D.
Stevenson and S.J. Benkovic
"Combinatorial Approaches to Engineering Hybrid Enzymes,"
J. Chem. Soc., Perkin Trans. 2 (9) 1483-1493 (2002). |
| 8. |
J.B.
Thoden, S.M. Firestine, S.J. Benkovic, and H.M. Holden
“PurT-encoded Glycinamide Ribonucleotide Transformylase.
Accommodation of Adenosine Nucleotide Analogs Within the Active
Site,” J. Biol. Chem. 277(26) 23898-23908 (2002). |
| 9. |
T.H.
Marsilje, M.A. Labroli, M.P. Hedrick, Q. Jin, J. Desharnais,
S.J. Baker, L.T. Gooljarsingh, J. Ramcharan, A. Tavassoli, Y.
Zhang, I.A. Wilson, G.P. Beardsley, S.J. Benkovic, and D.L.
Boger
"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," Bioorg. Med. Chem. 10, 2739-2749
(2002). |
| 10. |
F.T.
Ishmael, S.C. Alley, and S.J. Benkovic
"Assembly of the Bacteriophage T4 Helicase," J. Biol.
Chem. 277 (23) 20555-20562 (2002). |
| 11. |
S.
Lutz and S.J. Benkovic
"Engineering Protein Evolution" in Directed Molecular
Evolution of Proteins, Chapter 9 (S. Brakmann and K. Johnsson,
Eds.) Wiley-VCH Verlag GmbH, Germany pp. 177-214 (2002). |
| 12. |
P.K.
Agarwal, S.R. Billeter, P.T. Ravi Rajagopalan, S.J. Benkovic,
and S. Hammes-Schiffer
"Network of Coupled Promoting Motions in Enzyme Catalysis,"
Proc. Natl. Acad. USA 99 (5), 2794-2799 (2002). |
| 13. |
P.T.
Ravi Rajagopalan and S.J. Benkovic
"Preorganization and Protein Dynamics in Enzyme Catalysis,"
The Chemical Record 2, 24-36 (2002). |
| 14. |
M. Ostermeier,
S. Lutz, and S.J. Benkovic
"Generation of Protein Fragment Libraries by Incremental
Truncation," in Protein-Protein Interactions, Section 4,
Chapter 28 (E. Golemis, Ed.) Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, New York pp. 507-522 (2002). |
| 15. |
A.M. Valentine
and S.J. Benkovic
"Enzyme Mechanisms," in Encyclopedia of Physical Science
and Technology, Third Edition, Volume 5 (R.A. Meyers, Ed.) Academic
Press, San Diego pp. 627-639 (2002). |
| |
2001 |
| 1. |
S.J. Benkovic
in Perspectives in Catalysis--Future Directions of Catalysis
Science--Workshop, Catalysis Letters 76, 3-4 (2001). |
| 2. |
I. Lee and S.J.
Benkovic
"Catalytic Antibiotics," in Encyclopedia of Molecular
Medicine, Vol. 5 (T. Creighton, Ed.) John Wiley & Sons,
New York pp. 492-498 (2001). |
| 3. |
A.M.
Valentine, F.T. Ishmael, V.K. Shier, and S.J. Benkovic
"A Zinc Ribbon Protein in DNA Replication: Primer Synthesis
and Macromolecular Interactions by the Bacteriophage T4 Primase,"
Biochemistry 40 (50), 15074-15085 (2001). |
| 4. |
S.E.
Greasley, T.H. Marsilje, H. Cai, S. Baker, S.J. Benkovic, D.L.
Boger, and I.A. Wilson
"Unexpected Formation of an Epoxide-Derived Multisubstrate
Adduct Inhibitor on the Active Site of GAR Transformylase,"
Biochemistry 40, 13538-13547 (2001). |
| 5. |
Trakselis, M. A. and Benkovic, S. J.
"Intricacies in ATP-Dependent Clamp Loading: Variations
Across Replication Systems," Structure 9, 999-1004 (2001).
|
| 6. |
S.C.
Alley, M.A. Trakselis, M.U. Mayer, F.T. Ishmael, A.D. Jones,
and S.J. Benkovic
"Building a Replisome Solution Structure by Elucidation
of Protein-Protein Interactions in the Bacteriophage T4 DNA
Polymerase Holoenzyme," J. Biol. Chem. 276 (42) 39340-39349
(2001). |
| 7. |
S.
Lutz, M. Ostermeier, G.L. Moore, C.D. Maranas, and S.J. Benkovic
"Creating Multiple-Crossover DNA Libraries Independent
of Sequence Identity," Proc. Natl. Acad. Sci. USA 98 (20)
11248-11253 (2001). |
| 8. |
M.A.
Trakselis, M.U. Mayer, F.T. Ishmael, R.M. Roccasecca, and S.J.
Benkovic
"Dynamic Protein Interactions in the Bacteriophage T4 Replisome,"
TIBS, 26, 566-572 (2001). |
| 9. |
F.T.
Ishmael, S.C. Alley, and S.J. Benkovic
"Identification and Mapping of Protein-Protein Interactions
between gp32 and gp59 by Cross-linking," J. Biol. Chem.
276, 25236-25242 (2001). |
| 10. |
J.H.
Shim, M. Wall, S.J. Benkovic, N. Diaz, D. Suarez, and K.M. Merz.Jr.
"Evaluation of the Catalytic Mechanism of AICAR Transformylase
by pH-Dependent Kinetics, Mutagenesis, and Quantum Chemical
Calculations," J. Am. Chem. Soc. 123, 4687-4696 (2001).
|
| 11. |
M.J.
Osborne, J. Schnell, S.J. Benkovic, H.J. Dyson, and P.E. Wright
"Backbone Dynamics in Dihydrofolate Reductase Complexes:
Role of Loop Flexibility in the Catalytic Mechanism," Biochemistry
40, 9846-9859 (2001). |
| 12. |
C.P.
Scott, E. Abel-Santos, A.D. Jones, and S.J. Benkovic
"Structural Requirements for the Biosynthesis of Backbone
Cyclic Peptide Libraries," Chem. Biol. 8, 801-815 (2001).
|
| 13. |
F.T.
Ishmael, M.T. Norcum, S.J. Benkovic, and J.S. Bond
"Multimeric Structure of the Secreted Meprin A Metalloproteinase
and Characterization of the Functional Protomer," J. Biol.
Chem. 276 (25), 23207-23211 (2001). |
| 14. |
M.A.
Trakselis, S.C. Alley, E. Abel-Santos, and S.J. Benkovic
"Creating a Dynamic Picture of the Sliding Clamp During
T4 DNA Polymerase Holoenzyme Assembly by Using Fluorescence
Resonance Energy Transfer," Proc. Natl. Acad. Sci. USA
98 (15) 8368-8375 (2001). |
| 15. |
S.J.
Benkovic, A.M. Valentine, and F. Salinas
"Replisome-Mediated DNA Replication," Annu. Rev. Biochem.,
70, 181-208 (2001). |
| 16. |
J.D.
Stevenson, S. Lutz, and S.J. Benkovic
"Retracing Enzyme Evolution in the (Ba)8-Barrel Scaffold,"
Angew. Chem. Int. Ed. 40, 1854-1856 (2001). |
| 17. |
L.T.
Gooljarsingh, J. Ramcharan, S. Gilroy, and S.J. Benkovic
"Localization of GAR Transformylase in Escherichia coli
and Mammalian Cells," Proc. Natl. Acad. Sci. USA 98, 6565-6570
(2001). |
| 18. |
V.K.
Shier, C.J. Hancey, and S.J. Benkovic
"Identification of the Active Oligomeric State of an Essential
Adenine DNA Methyltransferase from Caulobacter crescentus,"
J. Mol. Biol. 276, 14744-14751 (2001). |
| 19. |
S.E.
Greasley, P. Horton, J. Ramcharan, G.P. Beardsley, S.J. Benkovic,
and I.A. Wilson
"Crystal Structure of a Bifunctional Transformylase and
Cyclohydrolase Enzyme in Purine Biosynthesis," Nature Struct.
Biol. 8, 402-406 (2001). |
| 20. |
G.L.
Moore, C.D. Maranas, S. Lutz, and S.J. Benkovic
"Predicting Crossover Generation in DNA Shuffling,"
Proc. Natl. Acad. Sci. USA 98, 3226-3231 (2001). |
| 21. |
M.
Ostermeier and S.J. Benkovic
"Construction of Hybrid Gene Libraries Involving the Circular
Permutation of DNA," Biotech. Lett. 23, 303-310 (2001).
|
| 22. |
W.
Fast, Z. Wang, S.J. Benkovic
"Familial Mutations and Zinc Stoichiometry Determine the
Rate-Limiting Step of Nitrocefin Hydrolysis by Metallo-b-lactamase
from Bacterioides fragilis," Biochemistry 40, 1640-1650
(2001). |
| 23. |
S.
Lutz, M. Ostermeier, and S.J. Benkovic
"Rapid Generation of Incremental Truncation Libraries for
Protein Engineering Using a-Phosphothioate," Nucleic Acids
Res. 29, 1-7 (2001). |
| 24. |
D.C.
Wahnon, V.K. Shier, and S.J. Benkovic
"Mechanism-Based Inhibition of an Essential Bacterial Adenine
DnA Methyltransferase: Rationally Designed Antibiotics,"
J. Am. Chem. Soc. 123, 976-977 (2001). |
| 25. |
G.P.
Miller, D.C. Wahnon, and S.J. Benkovic
"Interloop Contacts Modulate Ligand Cycling during Catalysis
by Escherichia coli Dihydrofolate Reductase," Biochemistry
40, 867-875 (2001). |
| |
2000 |
| 1. |
C.
Liu, J.H. Shim, and S.J. Benkovic
"The Unexpected Catalytic Properties of a Heterodimer of
GAR Transformylase," Bioorg. Chem. 28, 316-323 (2000).
|
| 2. |
M.
Ostermeier and S.J. Benkovic
"Evolution
of Protein Function by Domain Swapping' in Advances in Protein
Chemistry (Vol. 55) Evolutionary Protein Design (F.H. Arnold,
Ed.) Academic Press, San Diego pp. 29-77 (2000).
|
| 3. |
S.J.
Baker, S.M. Firestine, D. Smithrud, F. Salinas, and S.J. Benkovic
"Synthesis of Two Bi-functional Ligands for the QUEST Three-hybrid
System," Tetrahedron Lett. 41, 7009-7012 (2000). |
| 4. |
M.
Wall, J.-H. Shim, and S.J. Benkovic
"Role of the 4-Carboxamide of AICAR in Binding and Catalysis,"
Biochemistry 39, 11301-11311 (2000). |
| 5. |
S.C.
Alley, F.T. Ishmael, A.D. Jones, and S.J. Benkovic
"Mapping Protein-Protein Interactions in the Bacteriophage
T4 DNA Polymerase Holoenzyme Using a Novel Trifunctional Photo-cross-linking
and Affinity Reagent," J. Am. Chem. Soc. 122, 6126-6127
(2000). |
| 6. |
J.B.
Thoden, S. Firestine, A. Nixon, S.J. Benkovic, and H.M. Holden
"Molecular Structure of Escherichia coli PurT-Encoded Glycinamide
Ribonucleotide Transformylase," Biochemistry 39, 8791-8802
(2000). |
| 7. |
S.
Lutz and S.J. Benkovic
"Homology-Independent Protein Engineering," Curr.
Opin. Biotechnol. 11, 319-324 (2000). |
| 8. |
F.
Salinas and S.J. Benkovic
"Characterization of Bacteriophage T4-coordinated Leading-
and Lagging-strand Synthesis on a Minicircle Substrate,"
Proc. Natl. Acad. Sci. USA 97, 7196-7201 (2000). |
| 9. |
D.L.
Boger, T.H. Marsilje, R.A. Castro, M.P. Hedrick, Q. Jin, S.J.
Baker, J.H. Shim, and S.J. Benkovic
"Design, Synthesis, and Biological Evaluation of Fluoronitrophenyl
Substituted Folate Analogues as Potential Inhibitors of GAR
Transformylase and AICAR Transformylase," Bioorg. Med.
Chem. Lett. 10, 1471-1475 (2000). |
| 10. |
D.L.
Boger, M.A. Labroli, T.H. Marsilje, Q. Jin, M.P. Hedrick, S.J.
Baker, J.H. Shim, and S.J. Benkovic
"Conformationallly Restricted Analogues Designed for Selective
Inhibition of GAR Tfase Versus Thymidylate Synthase or Dihydrofolate
Reductase," Bioorg. Med. Chem. 8, 1075-1086 (2000). |
| 11. |
T.C.
Bruice and S.J. Benkovic
"Chemical Basis for Enzyme Catalysis," Biochemistry
39, 6267-6274 (2000). |
| 12. |
A.E.
Nixon and S.J. Benkovic
"Improvement in the Efficiency of Formyl Transfer of a
GAR Transformylase Hybrid Enzyme," Protein Engineering
13, 323-327 (2000). |
| 13. |
S.M.
Firestine, F. Salinas, A.E. Nixon, S.J. Baker, and S.J. Benkovic
"Using an AraC-based three-hybrid System to Detect Biocatalysts
in vivo," Nat. Biotechnol. 18, 544-547 (2000). |
| 14. |
D.B.
Smithrud, P.A. Benkovic, S.J. Benkovic, V. Roberts, J. Liu,
I. Neagu, S. Iwama, B.W. Phillips. A.B. Smith III, and R. Hirschmann
"Cyclic Peptide Formation Catalyzed by an Antibody Ligase,"
Proc. Natl. Acad. Sci., USA 97, 1953-1958 (2000). |
| 15. |
M.
Ostermeier and S.J. Benkovic
"A Two-phagemid System for the Creation of Non-phage Displayed
Antibody Libraries Approaching One Trillion Members," J.
of Immunological Methods 237, 175-186 (2000). |
| 16. |
S.C.
Alley, E. Abel-Santos, and S.J. Benkovic
"Tracking Sliding Clamp Opening and Closing during Bacteriophage
T4 DNA Polymerase Holoenzyme Assembly," Biochemistry 39,
3076-3090 (2000). |
| |
1999 |
| 1. |
S.E.Greasley,
M.M. Yamashita, H. Cai, S.J. Benkovic, D.L. Boger, and I.A.
Wilson
"New Insights into Inhibitor Design from the Crystal Structure
and NMR of Escherichia coli GAR Transformylase in Complex with
ß-GAR and 10-Formyl-5,8,10-trideazafolic Acid," Biochemistry
38, 16783-16793 (1999). |
| 2. |
M.
Ostermeier, J.-H. Shim, and S.J. Benkovic
"A Combinatorial Approach to Hybrid Enzymes Independent
of DNA Homology," Nat. Biotechnol. 17, 1205-1209
(1999). |
| 3. |
C.P.
Scott, E. Abel-Santos, M. Wall, D.C. Wahnon, and S.J. Benkovic
"Production of Cyclic Peptides and Proteins In vivo,"
Proc. Natl. Acad. Sci. USA 96, 13638-13643 (1999). |
| 4. |
S.D.B.
Scrofani, J. Chung, J.J.A. Huntley, S.J. Benkovic, P.E. Wright,
and H.J. Dyson
"NMR Characterization of the Metallo-B-lactamase from Bacterioides
fragilis and Its Interaction with a Tight-Binding Inhibitor:
Role of an Active-Stie Loop," Biochemistry 38, 14507-14514
(1999). |
| 5. |
I. Lee and S.J.
Benkovic
"Catalytic Antibodies," in Encyclopedia of Molecular
Biology (T.E. Creighton, Editor) John Wiley & Sons, Inc.,
New York pp. 353-354 (1999). |
| 6. |
M.
Ostermeier, A.E. Nixon, and S.J. Benkovic
"Incremental Truncation as a Strategy in the Engineering
of Novel Biocatalysts," Bioorg. Med. Chem. 7, 2139-2144
(1999). |
| 7. |
M.M.
Thayer, E.H. Olender, A.S. Arvai, C.K. Koike, I.L. Canestrelli,
J.D. Stewart, S.J. Benkovic, E.D. Getzoff, and V.A. Roberts
"Structural Basis for Amide Hydrolysis Catalyzed by the
43C9 Antibody," J. Mol. Biol. 291, 329-345 (1999). |
| 8. |
Z.
Wang, W. Fast, A.M. Valentine, and S.J. Benkovic
"Metallo-ß-lactamase: Structure and Mechanism,"
Curr. Opin. in Chem. Biol. 3, 614-622 (1999). |
| 9. |
S.J. Benkovic
and C.T. Walsh
"Mechanisms Research Highlights at the Chemistry-biology
Interface," Curr. Opin. in Chem. Biol. 3, 571-572 (1999).
|
| 10. |
M.
Wall, J.H. Shim, and S.J. Benkovic
"A Multisubstrate Adduct Inhibitor of AICAR Transformylase,"
J. Med. Chem. 42, 3421-3424 (1999). |
| 11. |
S.C.
Alley, A.D. Jones, P. Soumillion, and S.J. Benkovic
"The Carboxyl Terminus of the Bacteriophage T4 DNA Polymerse
Contacts Its Sliding Clamp at the Subunit Interface," J.
Biol. Chem. 274, 24485-24489 (1999). |
| 12. |
J.H.
Shim and S.J. Benkovic
"Catalytic Mechanism of Escherichia coli Glycinamide Ribonucleotide
Transformylase Probed by Site-Directed Mutagenesis and pH-Dependent
Studies," Biochemistry 38, 10024-10031 (1999). |
| 13. |
Z.
Wang, W. Fast, and S.J. Benkovic
"On the Mechanism of the Metallo-beta-lactamase from Bacteroides
fragilis," Biochemistry 38, 10013-10023 (1999). |
| 14. |
M.
Ostermeier and S.J. Benkovic
"Finding Cinderellaís SlipperóProteins That
Fit," Nature Biotechnology 17, 639-640 (1999). |
| 15. |
S.C.
Alley, V.K. Shier, E. Abel-Santos, D.J. Sexton, P. Soumillion,
and S.J. Benkovic
"Sliding Clamp of the Bacteriophage T4 Polymerase Has Open
and Closed
Subunit Interfaces in Solution," Biochemistry 38, 7686-7709
(1999). |
| 16. |
A.E.
Nixon, S.M. Firestine, F.G. Salinas, and S.J. Benkovic
"Rational Design of a Scytalone Dehydratase-like Enzyme
Using a Structurally Homologous Protein Scaffold," Proc.
Natl. Acad. Sci. USA 3568-3571 (1999). |
| 17. |
M.
Ostermeier, A.E. Nixon, J.-H. Shim, and S.J. Benkovic
"Combinatorial Protein Engineering by Incremental Truncation,"
Proc. Natl. Acad. Sci. USA 3562-3567 (1999). |
| |
1998 |
| 1. |
S.J. Benkovic
"A Perspective On Biological Catalysis," J. Phys.
Org. Chem. 11, 508-511 (1998). |
| 2. |
S.
De Lauzon, R. Quilez, L. Lion, B. Desfosses, B. Desfosses, I.
Lee, M.A. Sari, S.J. Benkovic, D. Mansuy, and J.P. Mahy, "Active
Site Topology of Artificial Peroxidase-like Hemoproteins Based
On Antibodies Constructed from a Specifically Designed Ortho-carboxy-substituted
Tetraarylporphyrin," Eur. J. Biochem. 257, 121-130
(1998). |
| 3. |
Y.
Su, M.M. Yamashita, S.E. Greasley, C.A. Mullen, J.H. Shim, P.A.
Jennings, S.J. Benkovic, and I.A. Wilson
"A Ph-dependent Stabilization of an Active Site Loop Observed
from Low and High Ph Crystal Structures of Mutant Monomeric
Glycinamide Ribonucleotide Transformylase at 1.8 to 1.9 A",
J. Mol. Biol. 281, 485-499 (1998). |
| 4. |
W.R.
Cannon and S.J. Benkovic
"Solvation, Reorganization Energy, and Biological Catalysis,"
J. Biol. Chem. 273, 26257-26260 (1998). |
| 5. |
P.
Wu, N. Nossal, and S.J. Benkovic
"Kinetic Characterization of a Bacteriophage T4 Antimutator
DNA Polymerase," Biochemistry 37, 14748-14755 (1998). |
| 6. |
Z. Wang, W.
Fast, and S.J. Benkovic
"Direct Observation of an Enzyme-Bound Intermediate in
the Catalytic Cycle of the Metallo-B-Lactamase from Bacteroides
fragilis," J. Am. Chem. Soc. 120, 10788-10789 (1998). |
| 7. |
A.J.
Berdis and S.J. Benkovic
"Simultaneous Formation of Functional Leading and Lagging
Strand Holoenzyme Complexes on a Small, Defined DNA Substrate,"
Proc. Natl. Acad. Sci. USA 95, 11128-11133 (1998). |
| 8. |
I. Lee and S.J.
Benkovic
"Catalytic Antibodies,"in Encyclopedia of Immunology
(2nd ed.) (P.J. Delves and I.M. Roitt Eds.) Academic Press Ltd,
London pp. 438-444 (1998). |
| 9. |
Z.
Wang and S.J. Benkovic
"Purification, Characterization, and Kinetic Studies of
a Soluble Bacteroides fragilis Metallo-?-lactamase That Provides
Multiple Antiobiotic Resistance," J. Biol. Chem. 273, 22402-22408
(1998). |
| 10. |
D.L.
Boger, M.J. Kochanny, H. Cai, D. Wyatt, P.A. Kitos, M.S. Warren,
J. Ramcharan, L.T. Gooljarsingh, and S.J. Benkovic
"Design, Synthesis, and Evaluation of Potential GAR and
AICAR Transformylase Inhibitors," Bioorg. Med. Chem. 6,
643-659 (1998). |
| 11. |
J.
H. Shim and S.J. Benkovic
"Evaluation of the Kinetic Mechanism of Escherichia coli
Glycinamide Ribonucleotide Transformylase," Biochemistry
37, 8776-8782 (1998). |
| 12. |
D.J.
Sexton, B.F. Kaboord, A.J. Berdis, T.E. Carver, and S.J. Benkovic
"Dissecting the Order of Bacteriophage T4 DNA Polymerase
Holoenzyme Assembly,"
Biochemistry 37, 7749-7756 (1998). |
| 13. |
G.P.
Miller and S.J. Benkovic
"Stretching Exercises-Flexibility in Dihydrofolate Reductase
Catalysis," Chemistry & Biology 5, R105-R113 (1998).
|
| 14. |
A.E.
Nixon, M. Ostermeier, and S.J. Benkovic
"Hybrid Enzymes: Manipulating Enzyme Design," Trends
Biotechnol. 16, 258-264 (1998). |
| 15. |
G.P.
Miller and S.J. Benkovic
"Strength of an Interloop Hydrogen Bond Determines the
Kinetic Pathway in Catalysis by Escherichia coli Dihydrofolate
Reductase," Biochemistry 37, 6336-6342 (1998). |
| 16. |
G.P.
Miller and S.J. Benkovic
"Deletion of a Highly Motional Residue Affects Formation
of the Michaelis Complex for Escherichia coli Dihydrofolate
Reductase," Biochemistry 37, 6327-6335 (1998). |
| 17. |
L.C.
Kroutil, M.W. Frey, B.F. Kaboord, T.A. Kunkel, and S.J. Benkovic
"Effect of Accessory Proteins on T4 DNA Polymerase Replication
Fidelity," J. Mol. Biol. 278, 135-146 (1998). |
| 18. |
A.J.
Berdis, I. Lee, J.K. Coward, C. Stephens, R. Wright, L. Shapiro,
and S.J. Benkovic
"A Cell Cycle-Regulated Adenine DNA Methyltransferase from
Caulobacter crescentus Processively Methylates GANTC Sites on
Hemimethylated DNA," Proc. Natl. Acad. Sci. U.S.A. 95,
2874-2879 (1998). |
| 19. |
P.
Soumillion, D.J. Sexton, and S.J. Benkovic
"Clamp Subunit Dissociation Dictates Bacteriophage T4 DNA
Polymerase Holoenzyme Disassembly," Biochemistry 37, 1819-1827
(1998). |
| 20. |
W.
Zhong and S.J. Benkovic
"Development of an Internally Quenched Fluorescent Substrate
for Escherichia coli Leader Peptidase," Anal. Biochem.
255, 66-73 (1998). |
| |
1997 |
| 1. |
C.E.
Cameron and S.J. Benkovic
"Evidence for a Functional Role of the Dynamics of Glycine-121
of Escherichia coli Dihydrofolate Reductase Obtained from Kinetic
Analysis of a Site-Directed Mutant," Biochemistry 36, 15792-15800
(1997). |
| 2. |
T.E.
Carver, Jr., D.J. Sexton, and S.J. Benkovic
"Dissociation of Bacteriophage T4 DNA Polymerase and Its
Processivity Clamp after Completion of Okazaki Fragment Synthesis,"
Biochemistry 36, 14409-14417 (1997). |
| 3. |
D.L.
Boger, N.-E. Haynes, M.S. Warren, J. Ramcharan, P.A. Kitos,
and S.J. Benkovic
"Multisubstrate Analogue Based on 5,8,10-Trideazafolate,"
Bioorg. Med. Chem. 5, 1853-1857 (1997). |
| 4. |
D.L.
Boger, N.-E. Haynes, M.S. Warren, J. Ramcharan, A.E. Marolewski,
P.A. Kitos, and S.J. Benkovic
"Abenzyl 10-Formyl-trideazafolic Acid (Abenzyl 10-Formyl-TDAF):
An Effective Inhibitor of Glycinamide Ribonucleotide Transformylase,"
Bioorg. Med. Chem. 5, 1847-1852 (1997). |
| 5. |
D.L.
Boger, N-E. Haynes, M.S. Warren, J. Ramcharan, P.A. Kitos, and
S.J. Benkovic
"Functionalized Analogues of 5,8,10-Trideazafolate: Development
of an Enzyme-Assembled Tight Binding Inhibitor of GAR Tfase
and a Potential Irreversible Inhibitor of AICAR Tfase,"
Bioorg. Med. Chem. 5, 1839-1846 (1997). |
| 6. |
D.L.
Boger, N.-E. Haynes, M.S. Warren, L.T. Gooljarsingh, J. Ramcharan,
P.A. Kitos, and S.J. Benkovic
"Functionalized Analogues of 5,8,10-Trideazafolate as Potential
Inhibitors of GAR Tfase or AICAR Tfase," Bioorg. Med. Chem.
5, 1831-1838 (1997). |
| 7. |
D.L.
Boger, N.-E. Haynes, P.A. Kitos, M.S. Warren, J. Ramcharan,
A.E. Marolewski, and S.J. Benkovic
"10-Formyl-5,8,10-trideazafolic Acid (10-Formyl-TDAF):
A Potent Inhibitor of Glycinamide Ribonucleotide Transformylase,"
Bioorg. Med. Chem. 5, 1817-1830 (1997). |
| 8. |
D.J.
Sexton, A.J. Berdis, and S.J. Benkovic
"Assembly and Disassembly of DNA Polymerase Holoenzyme,"
Curr. Opin. in Chem. Biol. 1, 316-322 (1997). |
| 9. |
D.B.
Smithrud and S.J. Benkovic
"The State of Antibody Catalysis," Curr. Opin. Biotechnol.
8, 459-466 (1997). |
| 10. |
W.R.
Cannon, B.J. Garrison, and S.J. Benkovic
"Consideration of the pH-dependent Inhibition of Dihydrofolate
Reductase by Methotrexate," J. Mol. Biol. 271, 656-668
(1997). |
| 11. |
C.E.
Cameron, M. Ghosh, S.F.J. Le Grice, and S.J. Benkovic
"Mutations in HIV Reverse Transcriptase which Alter RNase
H Activity and Decrease Strand Transfer
Efficiency are Suppressed by HIV Nucleocapsid Protein,"
Proc. Natl. Acad. Sci. USA 94, 6700-6705 (1997). |
| 12. |
A.E.
Marolewski, K.M. Mattia, M.S. Warren, and S.J. Benkovic
"Formyl Phosphate: A Proposed Intermediate in the Reaction
Catalyzed by Escherichia coli PurT GAR Transformylase,"
Biochemistry 36, 6709-6716 (1997). |
| 13. |
G.P.
Miller, B.A. Posner, and S.J. Benkovic
"Expanding the 43C9 Class of Catalytic Antibodies Using
a Chain-Shuffling Approach," Bioorganic & Medicinal
Chemistry 5, 581-590 (1997). |
| 14. |
G.P. Miller,
W. Zhong, J. Smiley, and S.J. Benkovic
"Combinatorial Libraries of Peptides, Proteins, and Antibodies
Using Biological Systems," in Combinatorial
Chemistry Synthesis and Application (S.R. Wilson and A.W. Czarnik
eds.) John Wiley & Sons, Inc., New York pp. 241-259 (1997).
|
| 15. |
W.R.
Cannon, B.J. Garrison, and S.J. Benkovic
"Electrostatic Characterization of Enzyme Complexes: Evaluation
of the Mechanism of Catalysis of Dihydrofolate Reductase",
J. Am. Chem. Soc. 119, 2386-2395 (1997). |
| 16. |
A.J.
Berdis and S.J. Benkovic
"Mechanism of Bacteriophage T4 DNA Holoenzyme Assembly:
The 44/62 Protein Acts as a Molecular Motor", Biochemistry
36, 2733-2743 (1997). |
| 17. |
M.S.
Warren and S.J. Benkovic
"Combinatorial Manipulation of Three Key Active Site Residues
in Glycinbamide Ribonucleotide Transformylase", Protein
Engineering 10, 63-68 (1997). |
| 18. |
A.E.
Nixon and S.J. Benkovic
"Assembly of An Active Enzyme by the Linkage of Two Protein
Modules", Proc. Natl. Acad. Sci. USA 94, 1069-1073 (1997).
|
| 19. |
D.B. Smithrud,
P.A. Benkovic, S.J. Benkovic, C.M. Taylor, K.M. Yager, J. Witherington,
B.W. Philips, P.A. Sprengeler, A.B. Smith, III, and R. Hirschmann.
"Investigations of an Antibody Ligase", J. Am. Chem.
Soc. 119, 278-282 (1997). |
| 20. |
S.J. Benkovic
and A. Ballesteros (organizers) conference entitled: Novel Biocatalysts,
Instituto Juan March de Estudios e Investigacions, Centre for
International Meetings on Biology, March 10-12, 1997, Madrid,
Spain. |
| |
1996 |
| 1. |
D.J.
Sexton, T.E. Carver, A.J. Berdis, and S.J. Benkovic
"Protein-Protein and Protein-DNA Interactions at the Bacteriophage
T4 DNA Replication Fork", J. Biol. Chem. 271, 28045-28051
(1996). |
| 2. |
A.J.
Berdis, P. Soumillion, and S.J. Benkovic
"The Carboxyl Terminus of the Bacteriophage T4 DNA Polymerase
is Required for Holoenzyme Complex Formation",
Proc. Natl. Acad. Sci. U.S.A. 93, 12822-12827 (1996). |
| 3. |
S.M.
Firestine, A.E. Nixon, and S.J. Benkovic
"Threading Your Way to Protein Function", Chemistry
& Biology 3, 779-783 (1996). |
| 4. |
M.S.
Warren, K.M. Mattia, A.E. Marolewski, and S.J. Benkovic
"The Transformylase Enzymes of de novo Purine Biosynthesis",
Pure & Appl. Chem. 68, 2029-2036 (1996). |
| 5. |
W.R.
Cannon, S.F. Singleton, and S.J. Benkovic
"A Perspective on Biological Catalysis", Nature Structural
Biology 3, 821-833 (1996). |
| 6. |
M.W.
Crowder, Z. Wang, S.L. Franklin, E.P. Zovinka, and S.J. Benkovic
"Characterization of the Metal-Binding Sites of the beta-Lactamase
from Bacterioides fragilis",
Biochemistry 35, 12126-12132 (1996). |
| 7. |
S.J.
Benkovic
"The Key is in the Pocket", Nature 383, 23-24 (1996).
|
| 8. |
M.S.
Warren, A.E. Marolewski, and S.J. Benkovic
"A Rapid Screen of Active Site Mutants in Glycinamide Ribonucleotide
Transformylase", Biochemistry 35, 8855-8862 (1996). |
| 9. |
A.J.
Berdis and S.J. Benkovic
"Role of Adenosine 5í-Triphosphate Hydrolysis in
the Assembly of the Bacteriophage T4 DNA Replication Holoenzyme
Complex", Biochemistry 35, 9253-9265 (1996). |
| 10. |
K.D.
Raney, T.E. Carver, and S.J. Benkovic
"Stoichiometry and DNA Unwinding by the Bacteriophage T4
41:59 Helicase", J. Biol. Chem. 271, 14074-14081 (1996).
|
| 11. |
M.W.
Frey, S.T. Frey, W.D. Horrocks, Jr., B.F. Kaboord, and S.J.
Benkovic
"Elucidation of the Metal-binding Properties of the Klenow
Fragment of E.coli Polymerase I and Bacteriophage T4 DNA Polymerase
by Lanthanide(III) Luminescence Spectroscopy", Chemistry
& Biology 3, 393-403 (1996). |
| 12. |
C.L.
Brummel, J.C. Vickerman, S.A. Carr, M.E. Hemling, G.D. Roberts,
W. Johnson, J. Weinstock, D. Gaintanopoulos, S.J. Benkovic,
and N. Winograd.
"Evaluation of Mass Spectrometric Methods Applicable to
the Direct Analysis of Non-Peptide Bead-Bound Combinatorial
Libraries", Analytical Biochemistry 68, 237-242 (1996).
|
| 13. |
G.T.
Anderson, M.D. Alexander, S.D. Taylor, D.B. Smithrud, S.J. Benkovic,
and S.M. Weinreb
"Catalytic Antibodies in Synthesis: Design and Synthesis
of a Hapten for Application to the Preparation of a Scalemic
Pyrrolidine Ring Synthon for Ptilomycalin A", J. Org. Chem.
61, 125-132 (1996). |
| 14. |
B.A.
Posner, L. Li, R. Bethell, T. Tsuji, and S.J. Benkovic
" Engineering Specificity for Folate into Dihydrofolate
Reductase from Escherichia coli", Biochemistry 35, 1653-1663
(1996). |
| 15. |
B.F.
Kaboord and S.J. Benkovic
"Dual Role of the 44/62 Protein as a Matchmaker Protein
and DNA Polymerase Chaperone During Assembly of the Bacteriophage
T4 Holoenzyme Complex", Biochemistry 35, 1084-1092 (1996).
|
| |
1995 |
| 1. |
C.R.
Wagner, Z. Huang, S.F. Singleton, and S.J. Benkovic
"Molecular Basis for Nonadditive Mutational Effects in
Escherichia coli Dihydrofolate Reductase",
Biochemistry 34, 15671-15680 (1995). |
| 2. |
T.L.
Capson, S.J. Benkovic, and N.G. Nossal
"Photochemical Cross-Linking of DNA Replication Proteins
at Primer Terminus", in Methods of Enzymology Vol. 249,
DNA Replication, Section V. Polymerase Accessory Functions,
Replication Proteins, Multienzyme Replication Complexes (J.L.
Campbell, ed.) Academic Press, San Diego, pp 449-456 (1995).
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