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Items: 48

1.

De novo design of symmetric ferredoxins that shuttle electrons in vivo.

Mutter AC, Tyryshkin AM, Campbell IJ, Poudel S, Bennett GN, Silberg JJ, Nanda V, Falkowski PG.

Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14557-14562. doi: 10.1073/pnas.1905643116. Epub 2019 Jul 1.

PMID:
31262814
2.

Overcoming component limitations in synthetic biology through transposon-mediated protein engineering.

Atkinson JT, Wu B, Segatori L, Silberg JJ.

Methods Enzymol. 2019;621:191-212. doi: 10.1016/bs.mie.2019.02.014. Epub 2019 Apr 2.

PMID:
31128779
3.

Metalloprotein switches that display chemical-dependent electron transfer in cells.

Atkinson JT, Campbell IJ, Thomas EE, Bonitatibus SC, Elliott SJ, Bennett GN, Silberg JJ.

Nat Chem Biol. 2019 Feb;15(2):189-195. doi: 10.1038/s41589-018-0192-3. Epub 2018 Dec 17.

PMID:
30559426
4.

A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit.

Zeng Y, Jones AM, Thomas EE, Nassif B, Silberg JJ, Segatori L.

ACS Synth Biol. 2018 Sep 21;7(9):2126-2138. doi: 10.1021/acssynbio.8b00129. Epub 2018 Aug 23.

PMID:
30089365
5.

Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis.

Atkinson JT, Jones AM, Zhou Q, Silberg JJ.

Nucleic Acids Res. 2018 Jul 27;46(13):e76. doi: 10.1093/nar/gky255.

6.

Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils.

Cheng HY, Masiello CA, Del Valle I, Gao X, Bennett GN, Silberg JJ.

ACS Synth Biol. 2018 Mar 16;7(3):903-911. doi: 10.1021/acssynbio.7b00405. Epub 2018 Feb 20.

PMID:
29366321
7.

Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid.

Thomas EE, Pandey N, Knudsen S, Ball ZT, Silberg JJ.

ACS Synth Biol. 2017 Aug 18;6(8):1572-1583. doi: 10.1021/acssynbio.7b00100. Epub 2017 May 17.

PMID:
28419802
8.

Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways.

Atkinson JT, Campbell I, Bennett GN, Silberg JJ.

Biochemistry. 2016 Dec 27;55(51):7047-7064. doi: 10.1021/acs.biochem.6b00831. Epub 2016 Dec 14.

PMID:
27966889
9.
10.

Charcoal Disrupts Soil Microbial Communication through a Combination of Signal Sorption and Hydrolysis.

Gao X, Cheng HY, Del Valle I, Liu S, Masiello CA, Silberg JJ.

ACS Omega. 2016 Aug 31;1(2):226-233. doi: 10.1021/acsomega.6b00085. Epub 2016 Aug 23.

11.

Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In Soil.

Cheng HY, Masiello CA, Bennett GN, Silberg JJ.

Environ Sci Technol. 2016 Aug 16;50(16):8750-9. doi: 10.1021/acs.est.6b01415. Epub 2016 Aug 1.

PMID:
27415416
12.

Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

Pandey N, Kuypers BE, Nassif B, Thomas EE, Alnahhas RN, Segatori L, Silberg JJ.

Biochemistry. 2016 Jul 12;55(27):3763-73. doi: 10.1021/acs.biochem.6b00258. Epub 2016 Jun 29.

13.

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation.

Jones AM, Mehta MM, Thomas EE, Atkinson JT, Segall-Shapiro TH, Liu S, Silberg JJ.

ACS Synth Biol. 2016 May 20;5(5):415-25. doi: 10.1021/acssynbio.5b00305. Epub 2016 Mar 25.

14.

Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions.

Pandey N, Nobles CL, Zechiedrich L, Maresso AW, Silberg JJ.

ACS Synth Biol. 2015 May 15;4(5):615-24. doi: 10.1021/sb5002938. Epub 2014 Oct 14.

15.

Tunable protease-activatable virus nanonodes.

Judd J, Ho ML, Tiwari A, Gomez EJ, Dempsey C, Van Vliet K, Igoshin OA, Silberg JJ, Agbandje-McKenna M, Suh J.

ACS Nano. 2014 May 27;8(5):4740-6. doi: 10.1021/nn500550q. Epub 2014 May 5.

16.

Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit.

Zhao W, Bonem M, McWhite C, Silberg JJ, Segatori L.

Nat Commun. 2014 Apr 8;5:3612. doi: 10.1038/ncomms4612.

PMID:
24710080
17.

Biochar and microbial signaling: production conditions determine effects on microbial communication.

Masiello CA, Chen Y, Gao X, Liu S, Cheng HY, Bennett MR, Rudgers JA, Wagner DS, Zygourakis K, Silberg JJ.

Environ Sci Technol. 2013 Oct 15;47(20):11496-503. doi: 10.1021/es401458s. Epub 2013 Sep 25.

18.

SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption.

Ho ML, Adler BA, Torre ML, Silberg JJ, Suh J.

ACS Synth Biol. 2013 Dec 20;2(12):724-33. doi: 10.1021/sb400076r. Epub 2013 Aug 22.

19.

A genetically encoded and gate for cell-targeted metabolic labeling of proteins.

Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA.

J Am Chem Soc. 2013 Feb 27;135(8):2979-82. doi: 10.1021/ja400448f. Epub 2013 Feb 18.

20.

A transposase strategy for creating libraries of circularly permuted proteins.

Mehta MM, Liu S, Silberg JJ.

Nucleic Acids Res. 2012 May;40(9):e71. doi: 10.1093/nar/gks060. Epub 2012 Feb 7.

21.

Random Insertion of mCherry Into VP3 Domain of Adeno-associated Virus Yields Fluorescent Capsids With no Loss of Infectivity.

Judd J, Wei F, Nguyen PQ, Tartaglia LJ, Agbandje-McKenna M, Silberg JJ, Suh J.

Mol Ther Nucleic Acids. 2012 Nov 13;1:e54. doi: 10.1038/mtna.2012.46.

22.

The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9.

Vu MT, Zhai P, Lee J, Guerra C, Liu S, Gustin MC, Silberg JJ.

Protein Sci. 2012 Feb;21(2):258-67. doi: 10.1002/pro.2012. Epub 2012 Jan 4.

23.

Selective cell-surface labeling of the molecular motor protein prestin.

McGuire RM, Silberg JJ, Pereira FA, Raphael RM.

Biochem Biophys Res Commun. 2011 Jun 24;410(1):134-9. doi: 10.1016/j.bbrc.2011.05.121. Epub 2011 May 27.

24.

A conserved histidine in human DNLZ/HEP is required for stimulation of HSPA9 ATPase activity.

Zhai P, Vu MT, Hoff KG, Silberg JJ.

Biochem Biophys Res Commun. 2011 May 20;408(4):589-94. doi: 10.1016/j.bbrc.2011.04.066. Epub 2011 Apr 21.

PMID:
21530495
25.

Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation.

Segall-Shapiro TH, Nguyen PQ, Dos Santos ED, Subedi S, Judd J, Suh J, Silberg JJ.

J Mol Biol. 2011 Feb 11;406(1):135-48. doi: 10.1016/j.jmb.2010.11.057. Epub 2010 Dec 8.

PMID:
21145325
26.

Computational design of chimeric protein libraries for directed evolution.

Silberg JJ, Nguyen PQ, Stevenson T.

Methods Mol Biol. 2010;673:175-88. doi: 10.1007/978-1-60761-842-3_10.

PMID:
20835798
27.

A selection that reports on protein-protein interactions within a thermophilic bacterium.

Nguyen PQ, Silberg JJ.

Protein Eng Des Sel. 2010 Jul;23(7):529-36. doi: 10.1093/protein/gzq024. Epub 2010 Apr 23.

28.

In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2.

Hoff KG, Culler SJ, Nguyen PQ, McGuire RM, Silberg JJ, Smolke CD.

Chem Biol. 2009 Dec 24;16(12):1299-308. doi: 10.1016/j.chembiol.2009.11.011.

29.

Fluorescence detection of a protein-bound 2Fe2S cluster.

Hoff KG, Goodlitt R, Li R, Smolke CD, Silberg JJ.

Chembiochem. 2009 Mar 2;10(4):667-70. doi: 10.1002/cbic.200800747.

30.

The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis.

Zhai P, Stanworth C, Liu S, Silberg JJ.

J Biol Chem. 2008 Sep 19;283(38):26098-106. doi: 10.1074/jbc.M803475200. Epub 2008 Jul 16.

31.

Thermostability promotes the cooperative function of split adenylate kinases.

Nguyen PQ, Liu S, Thompson JC, Silberg JJ.

Protein Eng Des Sel. 2008 May;21(5):303-10. doi: 10.1093/protein/gzn005. Epub 2008 Feb 20.

PMID:
18287175
32.

On the conservative nature of intragenic recombination.

Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH.

Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5380-5. Epub 2005 Apr 4.

33.

Thermodynamic prediction of protein neutrality.

Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH.

Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):606-11. Epub 2005 Jan 11.

34.

Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU.

Silberg JJ, Tapley TL, Hoff KG, Vickery LE.

J Biol Chem. 2004 Dec 24;279(52):53924-31. Epub 2004 Oct 13.

35.

Site-directed protein recombination as a shortest-path problem.

Endelman JB, Silberg JJ, Wang ZG, Arnold FH.

Protein Eng Des Sel. 2004 Jul;17(7):589-94. Epub 2004 Aug 25.

PMID:
15331774
36.

SCHEMA-guided protein recombination.

Silberg JJ, Endelman JB, Arnold FH.

Methods Enzymol. 2004;388:35-42. No abstract available.

PMID:
15289059
37.

Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach.

Otey CR, Silberg JJ, Voigt CA, Endelman JB, Bandara G, Arnold FH.

Chem Biol. 2004 Mar;11(3):309-18.

38.

Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli.

Cupp-Vickery JR, Silberg JJ, Ta DT, Vickery LE.

J Mol Biol. 2004 Apr 16;338(1):127-37.

PMID:
15050828
39.

Library analysis of SCHEMA-guided protein recombination.

Meyer MM, Silberg JJ, Voigt CA, Endelman JB, Mayo SL, Wang ZG, Arnold FH.

Protein Sci. 2003 Aug;12(8):1686-93.

40.

Analysis of shuffled libraries by oligonucleotide probe hybridization.

Meinhold P, Joern JM, Silberg JJ.

Methods Mol Biol. 2003;231:177-87. No abstract available.

PMID:
12824614
41.

Sequence homology-independent protein recombination (SHIPREC).

Udit AK, Silberg JJ, Sieber V.

Methods Mol Biol. 2003;231:153-63. No abstract available.

PMID:
12824612
42.

Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU.

Hoff KG, Ta DT, Tapley TL, Silberg JJ, Vickery LE.

J Biol Chem. 2002 Jul 26;277(30):27353-9. Epub 2002 May 6.

43.

Transfer of sulfur from IscS to IscU during Fe/S cluster assembly.

Urbina HD, Silberg JJ, Hoff KG, Vickery LE.

J Biol Chem. 2001 Nov 30;276(48):44521-6. Epub 2001 Sep 27.

44.

The Fe/S assembly protein IscU behaves as a substrate for the molecular chaperone Hsc66 from Escherichia coli.

Silberg JJ, Hoff KG, Tapley TL, Vickery LE.

J Biol Chem. 2001 Jan 19;276(3):1696-700. Epub 2000 Oct 26.

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