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Items: 1 to 50 of 494

1.

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps.

Perumal SK, Xu X, Yan C, Ivanov I, Benkovic SJ.

J Mol Biol. 2019 Jun 28;431(14):2493-2510. doi: 10.1016/j.jmb.2019.04.035. Epub 2019 Apr 30.

PMID:
31051173
2.

Mapping Post-Translational Modifications of de Novo Purine Biosynthetic Enzymes: Implications for Pathway Regulation.

Liu C, Knudsen GM, Pedley AM, He J, Johnson JL, Yaron TM, Cantley LC, Benkovic SJ.

J Proteome Res. 2019 May 3;18(5):2078-2087. doi: 10.1021/acs.jproteome.8b00969. Epub 2019 Apr 18.

PMID:
30964683
3.

Replication protein A dynamically regulates monoubiquitination of proliferating cell nuclear antigen.

Hedglin M, Aitha M, Pedley A, Benkovic SJ.

J Biol Chem. 2019 Mar 29;294(13):5157-5168. doi: 10.1074/jbc.RA118.005297. Epub 2019 Jan 30.

PMID:
30700555
4.

Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria.

Chan CY, Pedley AM, Kim D, Xia C, Zhuang X, Benkovic SJ.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):13009-13014. doi: 10.1073/pnas.1814042115. Epub 2018 Dec 3.

5.

Detecting Purinosome Metabolon Formation with Fluorescence Microscopy.

Pedley AM, Benkovic SJ.

Methods Mol Biol. 2018;1764:279-289. doi: 10.1007/978-1-4939-7759-8_17.

6.

Role of HSP90 in the Regulation of de Novo Purine Biosynthesis.

Pedley AM, Karras GI, Zhang X, Lindquist S, Benkovic SJ.

Biochemistry. 2018 Jun 12;57(23):3217-3221. doi: 10.1021/acs.biochem.8b00140. Epub 2018 Mar 23.

7.

Substrate-driven chemotactic assembly in an enzyme cascade.

Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A.

Nat Chem. 2018 Mar;10(3):311-317. doi: 10.1038/nchem.2905. Epub 2017 Dec 18.

PMID:
29461522
8.

Expression of the purine biosynthetic enzyme phosphoribosyl formylglycinamidine synthase in neurons.

Mangold CA, Yao PJ, Du M, Freeman WM, Benkovic SJ, Szpara ML.

J Neurochem. 2018 Mar;144(6):723-735. doi: 10.1111/jnc.14304. Epub 2018 Mar 26.

9.

Understanding DNA replication by the bacteriophage T4 replisome.

Benkovic SJ, Spiering MM.

J Biol Chem. 2017 Nov 10;292(45):18434-18442. doi: 10.1074/jbc.R117.811208. Epub 2017 Sep 25. Review.

10.

Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA.

Hedglin M, Aitha M, Benkovic SJ.

Biochemistry. 2017 Jul 11;56(27):3415-3421. doi: 10.1021/acs.biochem.7b00386. Epub 2017 Jun 27.

11.

RNA primer-primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication.

Spiering MM, Hanoian P, Gannavaram S, Benkovic SJ.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):5635-5640. doi: 10.1073/pnas.1620459114. Epub 2017 May 15.

12.

Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle.

Hedglin M, Benkovic SJ.

Chem Rev. 2017 Jun 28;117(12):7857-7877. doi: 10.1021/acs.chemrev.7b00046. Epub 2017 May 12. Review.

13.

Replication Protein A Prohibits Diffusion of the PCNA Sliding Clamp along Single-Stranded DNA.

Hedglin M, Benkovic SJ.

Biochemistry. 2017 Apr 4;56(13):1824-1835. doi: 10.1021/acs.biochem.6b01213. Epub 2017 Feb 28.

14.

A New View into the Regulation of Purine Metabolism: The Purinosome.

Pedley AM, Benkovic SJ.

Trends Biochem Sci. 2017 Feb;42(2):141-154. doi: 10.1016/j.tibs.2016.09.009. Epub 2016 Oct 28. Review.

15.

Characterization of human translesion DNA synthesis across a UV-induced DNA lesion.

Hedglin M, Pandey B, Benkovic SJ.

Elife. 2016 Oct 22;5. pii: e19788. doi: 10.7554/eLife.19788.

16.

Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis.

Hedglin M, Pandey B, Benkovic SJ.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1777-86. doi: 10.1073/pnas.1523653113. Epub 2016 Mar 14.

17.

Spatial colocalization and functional link of purinosomes with mitochondria.

French JB, Jones SA, Deng H, Pedley AM, Kim D, Chan CY, Hu H, Pugh RJ, Zhao H, Zhang Y, Huang TJ, Fang Y, Zhuang X, Benkovic SJ.

Science. 2016 Feb 12;351(6274):733-7. doi: 10.1126/science.aac6054.

18.

The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta.

Choi JS, Dasari A, Hu P, Benkovic SJ, Berdis AJ.

Nucleic Acids Res. 2016 Feb 18;44(3):1022-35. doi: 10.1093/nar/gkv1509. Epub 2015 Dec 29.

19.

Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA-Protein Interaction.

Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM.

Biochemistry. 2015 Dec 29;54(51):7457-69. doi: 10.1021/acs.biochem.5b01085. Epub 2015 Dec 16.

PMID:
26618501
20.

Protein Conformational Changes Are Detected and Resolved Site Specifically by Second-Harmonic Generation.

Moree B, Connell K, Mortensen RB, Liu CT, Benkovic SJ, Salafsky J.

Biophys J. 2015 Aug 18;109(4):806-15. doi: 10.1016/j.bpj.2015.07.016.

21.

Coordinated DNA Replication by the Bacteriophage T4 Replisome.

Noble E, Spiering MM, Benkovic SJ.

Viruses. 2015 Jun 19;7(6):3186-200. doi: 10.3390/v7062766. Review.

22.

Regulation of Rad6/Rad18 Activity During DNA Damage Tolerance.

Hedglin M, Benkovic SJ.

Annu Rev Biophys. 2015;44:207-28. doi: 10.1146/annurev-biophys-060414-033841. Review.

23.

Purinosome formation as a function of the cell cycle.

Chan CY, Zhao H, Pugh RJ, Pedley AM, French J, Jones SA, Zhuang X, Jinnah H, Huang TJ, Benkovic SJ.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1368-73. doi: 10.1073/pnas.1423009112. Epub 2015 Jan 20.

24.

Quantitative analysis of purine nucleotides indicates that purinosomes increase de novo purine biosynthesis.

Zhao H, Chiaro CR, Zhang L, Smith PB, Chan CY, Pedley AM, Pugh RJ, French JB, Patterson AD, Benkovic SJ.

J Biol Chem. 2015 Mar 13;290(11):6705-13. doi: 10.1074/jbc.M114.628701. Epub 2015 Jan 20.

25.

Controlling cell-cell interactions using surface acoustic waves.

Guo F, Li P, French JB, Mao Z, Zhao H, Li S, Nama N, Fick JR, Benkovic SJ, Huang TJ.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):43-8. doi: 10.1073/pnas.1422068112. Epub 2014 Dec 22.

26.

Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100.

Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ.

Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18231-6. doi: 10.1073/pnas.1415940111. Epub 2014 Dec 1.

27.

Acoustofluidic chemical waveform generator and switch.

Ahmed D, Muddana HS, Lu M, French JB, Ozcelik A, Fang Y, Butler PJ, Benkovic SJ, Manz A, Huang TJ.

Anal Chem. 2014 Dec 2;86(23):11803-10. doi: 10.1021/ac5033676. Epub 2014 Nov 18.

28.

Tryptophan-based fluorophores for studying protein conformational changes.

Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM.

Bioorg Med Chem. 2014 Nov 1;22(21):5924-34. doi: 10.1016/j.bmc.2014.09.015. Epub 2014 Sep 16.

29.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

Liu CT, Layfield JP, Stewart RJ 3rd, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ.

J Am Chem Soc. 2014 Jul 23;136(29):10349-60. doi: 10.1021/ja5038947. Epub 2014 Jul 11.

30.

The unique chemistry of benzoxaboroles: current and emerging applications in biotechnology and therapeutic treatments.

Liu CT, Tomsho JW, Benkovic SJ.

Bioorg Med Chem. 2014 Aug 15;22(16):4462-73. doi: 10.1016/j.bmc.2014.04.065. Epub 2014 May 10. Review. Erratum in: Bioorg Med Chem. 2015 Jul 1;23(13):3869.

PMID:
24864040
31.

Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions.

Zhao Y, Chen D, Yue H, Spiering MM, Zhao C, Benkovic SJ, Huang TJ.

Nano Lett. 2014;14(4):1952-60. doi: 10.1021/nl404802f. Epub 2014 Mar 24.

32.

DNA polymerase as a molecular motor and pump.

Sengupta S, Spiering MM, Dey KK, Duan W, Patra D, Butler PJ, Astumian RD, Benkovic SJ, Sen A.

ACS Nano. 2014 Mar 25;8(3):2410-8. doi: 10.1021/nn405963x. Epub 2014 Mar 6.

PMID:
24601532
33.

A clamp-like biohybrid catalyst for DNA oxidation.

van Dongen SF, Clerx J, Nørgaard K, Bloemberg TG, Cornelissen JJ, Trakselis MA, Nelson SW, Benkovic SJ, Rowan AE, Nolte RJ.

Nat Chem. 2013 Nov;5(11):945-51. doi: 10.1038/nchem.1752. Epub 2013 Sep 22.

PMID:
24153373
34.

Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification.

Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM.

Biochemistry. 2013 Nov 26;52(47):8580-9. doi: 10.1021/bi401275v. Epub 2013 Nov 11.

35.

Capturing a sulfenic acid with arylboronic acids and benzoxaborole.

Liu CT, Benkovic SJ.

J Am Chem Soc. 2013 Oct 2;135(39):14544-7. doi: 10.1021/ja407628a. Epub 2013 Sep 19.

PMID:
24050501
36.

RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue.

Manosas M, Perumal SK, Bianco PR, Ritort F, Benkovic SJ, Croquette V.

Nat Commun. 2013;4:2368. doi: 10.1038/ncomms3368. Erratum in: Nat Commun. 2014;5:4210. Bianco, Piero [corrected to Bianco, Piero R].

37.

Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids.

Chen S, Fahmi NE, Wang L, Bhattacharya C, Benkovic SJ, Hecht SM.

J Am Chem Soc. 2013 Sep 4;135(35):12924-7. doi: 10.1021/ja403007r. Epub 2013 Aug 22.

38.

Temporally overlapped but uncoupled motions in dihydrofolate reductase catalysis.

Liu CT, Wang L, Goodey NM, Hanoian P, Benkovic SJ.

Biochemistry. 2013 Aug 13;52(32):5332-4. doi: 10.1021/bi400858m. Epub 2013 Jul 29.

39.

Probing cell-cell communication with microfluidic devices.

Guo F, French JB, Li P, Zhao H, Chan CY, Fick JR, Benkovic SJ, Huang TJ.

Lab Chip. 2013 Aug 21;13(16):3152-62. doi: 10.1039/c3lc90067c. Epub 2013 Jul 10. Review.

40.

Probing DNA clamps with single-molecule force spectroscopy.

Wang L, Xu X, Kumar R, Maiti B, Liu CT, Ivanov I, Lee TH, Benkovic SJ.

Nucleic Acids Res. 2013 Sep;41(16):7804-14. doi: 10.1093/nar/gkt487. Epub 2013 Jun 19.

41.

A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase.

Boehr DD, Schnell JR, McElheny D, Bae SH, Duggan BM, Benkovic SJ, Dyson HJ, Wright PE.

Biochemistry. 2013 Jul 9;52(27):4605-19. doi: 10.1021/bi400563c. Epub 2013 Jun 24.

42.

Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans.

Liu CT, Hanoian P, French JB, Pringle TH, Hammes-Schiffer S, Benkovic SJ.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10159-64. doi: 10.1073/pnas.1307130110. Epub 2013 Jun 3.

43.

Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.

Perumal SK, Nelson SW, Benkovic SJ.

J Mol Biol. 2013 Aug 23;425(16):2823-39. doi: 10.1016/j.jmb.2013.05.012. Epub 2013 Jun 1.

44.

Insights into Okazaki fragment synthesis by the T4 replisome: the fate of lagging-strand holoenzyme components and their influence on Okazaki fragment size.

Chen D, Yue H, Spiering MM, Benkovic SJ.

J Biol Chem. 2013 Jul 19;288(29):20807-16. doi: 10.1074/jbc.M113.485961. Epub 2013 May 31.

45.

Lab-on-a-chip technologies for single-molecule studies.

Zhao Y, Chen D, Yue H, French JB, Rufo J, Benkovic SJ, Huang TJ.

Lab Chip. 2013 Jun 21;13(12):2183-98. doi: 10.1039/c3lc90042h. Epub 2013 May 14.

46.

The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans.

Zhao H, French JB, Fang Y, Benkovic SJ.

Chem Commun (Camb). 2013 May 18;49(40):4444-52. doi: 10.1039/c3cc41437j. Epub 2013 Apr 11.

47.

Replication clamps and clamp loaders.

Hedglin M, Kumar R, Benkovic SJ.

Cold Spring Harb Perspect Biol. 2013 Apr 1;5(4):a010165. doi: 10.1101/cshperspect.a010165. Review.

48.

Open questions - in brief: beyond -omics, missing motor proteins, and getting from molecules to organisms.

Benkovic SJ, Theriot J, Ringe D.

BMC Biol. 2013 Jan 31;11:8. doi: 10.1186/1741-7007-11-8. No abstract available.

49.

Hsp70/Hsp90 chaperone machinery is involved in the assembly of the purinosome.

French JB, Zhao H, An S, Niessen S, Deng Y, Cravatt BF, Benkovic SJ.

Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2528-33. doi: 10.1073/pnas.1300173110. Epub 2013 Jan 28.

50.

Tunable, pulsatile chemical gradient generation via acoustically driven oscillating bubbles.

Ahmed D, Chan CY, Lin SC, Muddana HS, Nama N, Benkovic SJ, Huang TJ.

Lab Chip. 2013 Feb 7;13(3):328-31. doi: 10.1039/c2lc40923b.

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