Publications

46. "Programming post-translational control over the metabolic labeling of cellular proteins with a non-canonical amino acid,” E.E. Thomas, N. Pandey, S.E. Knudsen, Z.T. Ball and J.J. Silberg, ACS Synth Biol., in press (2017). [journal]

45. “PERMutation Using Transposase Engineering (PERMUTE):  a simple approach for constructing circularly permuted protein libraries,” A.M. Jones, J.T. Atkinson, and J. J. Silberg, Methods in Molecular Biology, 1498: 295-308 (2017). [journal]

44. “Cellular assays for ferredoxins: a strategy to understand electron flow through protein carriers that link metabolic pathways,” J.T. Atkinson, I. Campbell, G.N. Bennett, and J. J. Silberg, Biochem., 55(51):7047-7064 (2016). [journal]

43. “Charcoal disrupts soil microbial communication through a combination of sorption and hydrolysis,” X. Gao, H.Y. Cheng, I Del Valle, S. Liu, C.A. Masiello, and J. J. Silberg, ACS Omega, 1(2): 226-233 (2016). [journal]

42. “Volatile gas production by methyl halide transferase:  an in situ reporter of microbial gene expression in soil,” H.S. Cheng, C.A. Masiello, G.N. Bennett, and J.J. Silberg, Environ. Sci. Technol., 50(16):8750-9 (2016). [journal]

41. “ Tolerance of a knotted near infrared fluorescent protein to random circular permutation,” N. Pandey, B. Kuypers, B. Nassif, E. E. Thomas, R. N. Alnahhas, L. Segatori, and J. J. Silberg,  Biochem., 55(27):3763-73 (2016). [journal]

40. “The structure of a thermophilic kinase shapes fitness upon random circular permutation,” A.M. Jones, M.M. Mehta, E.E. Thomas, J.T. Atkinson, T.H. Segall-Shapiro, S. Liu, and J. J. Silberg, ACS Synth. Biol.5(5):415-25 (2016). [journal]

39. "Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions," N. Pandey, C.L. Nobles, L. Zechiedrich, A.W. Maresso, and J.J. Silberg, ACS Synth. Biol., 4(5), 615-624 (2015). [journal] [NCB highlight]

38. “Tunable protease-activatable virus nanonodes,"  J. Judd, M.L. Ho, A. Tiwari, E.J. Gomez, C. Dempsey, K. Van Vliet, O. Igoshin, J.J. Silberg, M. Agbandje-McKenna, and J. Suh, ACS Nano8(5), 4740-4746. (2014). [journal] 

37. "Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit," W. Zhao, M. Bonem, C. White, J.J. Silberg, and L. SegatoriNature Communications5, 3612 (2014). [journal]

36. “SCHEMA computational design of virus capsid chimeras: calibrating how DNA packaging, protection, and transduction correlate with calculated disruption,” M.L. Ho, B. Adler, M. Torre, J.J. Silberg, and J. Suh. ACS Synth. Biol., 2, 724-733 (2013). [journal]

35. “Biochar and microbial signaling:  production conditions determine effects on microbial communication,” C.A. Masiello, C. Ye, X. Gao, S. Liu, H.Y. Cheng, M.R. Bennett, J.A. Rudgers, D.S. Wagner, K. Zygourakis, and J.J. Silberg, Environ. Sci. Technol., 47, 11496-11503 (2013). [journal]

34. “A genetic AND gate for cell-targeted metabolic labeling of proteins,” A. Mahdavi, T.H. Segall-Shapiro, S. Kou, G.A. Jindal, K.G. Hoff, S. Liu, M. Chitsaz, R.F. Ismagilov, J.J. SIlberg, and D.A. Tirrell, JACS 135, 2979-2982 (2013). [journal]

33. “Nitrogen, Biochar, and Mycorrhizae: Alteration of the Symbiosis and Oxidation of the Char Surface,” C. LeCroy, C.A. Masiello, J.A. Rudgers, W.C. Hockaday, and J.J. Silberg, Soil Biology & Biochemistry 58, 248-254 (2013). [journal]

32. “Random insertion of mCherry into the VP3 domain of adeno-associated virus (AAV) yields fluorescent capsids with no loss of infectivity,” J. Judd, F. Wei, P.Q. Nguyen, L.J. Tartaglia, M. Agbandje-McKenna, J.J. Silberg, and J. Suh, Molecular Therapy – Nucleic Acids, 1, e1 (2012). [journal

31. "A transposase strategy for creating libraries of circularly permuted proteins," M. M. Mehta, S. Liu, and J. J. Silberg, Nucleic Acids Res., 40(9): e71 (2012). [journal]

30. "The DNLZ/HEP zinc-binding subdomain supports the solubility of the mitochondrial chaperone HSPA9," M. Vu, P. Zhai, J. Lee, C. Guerra, S. Liu, M. C. Gustin, and J. J. Silberg, Protein Science 21, 258-267 (2012). [journal]

29. "Selective cell-surface labeling of the molecular motor prestin," R. M. McGuire, J. J. Silberg, F. R. Pereira, and R. M. Raphael, Biochem. Biophys. Res. Comm. 410, 134-139 (2011). [journal]

28. "A conserved histidine in human DNLZ/HEP is required for stimulation of HSPA9 ATPase activity," P. Zhai, M. Vu, K. G. Hoff, and J. J. Silberg, Biochem. Biophys. Res. Comm. 408, 589-594 (2011). [journal]

27. "Mesophilic and thermophilic adenylate kinases differ in their tolerance to random fragmentation," T. H. Segall-Shapiro, P. Q. Nguyen, E. Dos Santos, S. Subedi, J. Judd, J. Suh, and J. J. Silberg, J. Mol. Biol. 406, 135-148 (2011). [journal]

26. "A selection for protein-protein interactions within a thermophilic bacterium," P.Q. Nguyen and J. J. Silberg, Prot. Eng. Des. & Sel. 24, 529-536 (2010). [journal]

25. "Computational methods for directed protein evolution," J. J. Silberg and P. Q. Nguyen, Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo, Ed., 673, 175-188 (2010). [pubmed]

24. "In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2," K. G. Hoff, S. J. Culler, P.Q. Nguyen, R. McGuire, J. J. Silberg, C. D. Smolke, Chemistry & Biology 12, 1299-1308 (2009). [journal]

23. "Fluorescent detection of a protein-bound 2Fe2S cluster," K. G. Hoff, R. Liu, Goodlitt, R., Smolke, C. D., and J. J. Silberg, ChemBioChem 10, 667-670 (2009). [journal]

22. "Models predicting optimized strategies for protein evolution," J. J. Silberg and P. Q. Nguyen, The Metabolic Pathway Engineering Handbook, C. D. Smolke, Ed., 2, Chapter 5 (2009). [publisher]

21. "The human hsp70 escort protein Hep binds to the ATPase domain of mitochondrial Hsp70 and regulates nucleotide hydrolysis," P. Zhai, C. Stanworth, S. Liu, and J. J. Silberg, J. Biol. Chem. 283, 26098-26106 (2008). [journal]

20. "Thermostability promotes the cooperative function of split adenylate kinases," P. Q. Nguyen, J. Thompson, S. Liu, and J. J. Silberg, Prot. Eng. Des. & Sel. 21, 303-310 (2008). [journal]

19. "On the conservative nature of intragenic recombination," D. A. Drummond, J. J. Silberg, C. O. Wilke, M. M. Meyer, and F. H. Arnold, Proc. Nat'l. Acad. Sci. U.S.A. 102, 5380-5385 (2005). [pubmed]

18. "Thermodynamic prediction of protein neutrality," J. D. Bloom, J. J. Silberg, C. Wilke, D. A. Drummond, C. Adami, and F. H. Arnold, Proc. Nat'l. Acad. Sci. U.S.A. 102, 606-611 (2005). [pubmed]

17. "Site-directed protein recombination as a shortest-path problem," J. B. Endelman, J. J. Silberg, Z. G. Wang, and F. H. Arnold, Prot. Eng. Des. & Sel. 17, 589-594 (2004). [pubmed]

16. "Functional evolution and structural conservation in chimeric cytochromes P450: calibrating a structure-guided approach," C. Otey, J. J. Silberg, J. B. Endelman, G. Bandara, C. A. Voigt, and F. H. Arnold, Chemistry & Biology 11, 309-318 (2004). [pubmed]

15. "Regulation of the HscA ATPase reaction cycle by the J-type cochaperone HscB and the iron-sulfur escort protein IscU," J. J. Silberg, T. L. Tapley, K. G. Hoff, and L. E. Vickery, J. Biol. Chem. 279, 53924-53931 (2004). [pubmed]

14. "Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli," J. R. Cupp-Vickery, J. J. Silberg, D. T. Ta, and L. E. Vickery, J. Mol. Biol. 338, 127-137 (2004). [pubmed]

13. "SCHEMA-guided protein recombination," J. J. Silberg, J. B. Endelmen, and F. H. Arnold, Methods Enzymology, D. Robertson and J.P. Noel, Eds., 388 (2004). [pubmed]

12. "Library analysis of SCHEMA-guided recombination," M. M. Meyer, J. J. Silberg, C. A. Voigt, J. B. Endelman, S. L. Mayo, Z. G. Wang, and F. H. Arnold, Protein Science 12, 1686-1693 (2003). [pubmed]

11. "Sequence homology-independent protein recombination, SHIPREC," A.K. Udit, J. J. Silberg, and V. Sieber, Methods in Molecular Biology, F. H. Arnold and G. Georgiou, Eds., 231, 153-164 (2003). [pubmed]

10. "Analysis of shuffled libraries by oligonucleotide probe hybridization," P. Meinhold, J. Joern, and J.J. Silberg, Methods in Molecular Biology, F. H. Arnold and G. Georgiou, Eds., 231, 177-188 (2003). [pubmed]

9. "Hsc66 substrate specificity is directed towards a discrete region of the Fe/S template protein IscU," K. G. Hoff, D. T. Ta, T. L. Tapley, J. J. Silberg, and L. E. Vickery, J. Biol. Chem. 277, 27353-27359 (2002). [pubmed]

8. "Transfer of sulfur from IscS to IscU during iron-sulfur cluster assembly," H. D. Urbina, J. J. Silberg, K. G. Hoff, and L. E. Vickery, J. Biol. Chem. 276, 44521-44526 (2001). [pubmed]

7. "The Fe/S-escort protein IscU behaves as a substrate for the molecular chaperone Hsc66 from Escherichia coli," J. J. Silberg, K. G. Hoff, T. L. Tapley, and L. E. Vickery, J. Biol. Chem. 276, 1696-1700 (2001). [pubmed]

6. "Kinetic characterization of the ATPase cycle of the molecular chaperone Hsc66 from Escherichia coli," J. J. Silberg and L. E. Vickery, J. Biol. Chem. 275, 7779-7786 (2000). [pubmed]

5. "Interaction of the iron-sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system in Escherichia coli," K. G. Hoff, J. J. Silberg, and L. E. Vickery, Proc. Nat'l. Acad. Sci. U.S.A. 97, 7790-7795 (2000). [pubmed]

4. "The Hsc66-Hsc20 Chaperone System in Escherichia coli: Chaperone Activity and Interactions with the DnaK-DnaJ-GrpE System," J. J. Silberg, K. G. Hoff, and L. E. Vickery, J. Bacteriol. 180, 6617-6624 (1998). [pubmed]

3. "Hsc66 and Hsc20, a new heat shock cognate molecular chaperone system from Escherichia coli," L. E. Vickery, J. J. Silberg, and D. T. Ta, Protein Science 6, 1047-1056 (1997). [pubmed]

2. "Effect of thiocyanate on AMPA receptor mediated responses in excised patches and hippocampal slices," A. Arai, J. Silberg, M. Kessler, and G. Lynch, Neuroscience 66, 815-827 (1995). [pubmed]

1. "Differences in the refractory properties of two distinct inhibitory circuitries in field CA1 of the hippocampus," A. Arai, J. Silberg, and G. Lynch, Brain Res. 704, 298-306 (1995). [pubmed]

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