Published Manuscripts

Tim Whitehead and others



32. Wang X, Stapleton JA, Klesmith JR, Hewlett E, Whitehead TA, Maynard J (2017) “Fine epitope mapping of two antibodies neutralizing the Bordetella adenylate cyclase toxin”, Biochemistry in press doi: 10.1021/acs.biochem.6b01163

31. Klesmith JR, Bacik JP, Wrenbeck EE, Michalczyk R, Whitehead TA (2017) “Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning”, PNAS in press doi: 10.1073/pnas.1614437114

30. Wrenbeck EE, Faber M, Whitehead TA (2017) “Deep sequencing methods for protein engineering and design”, Current Opinion in Structural Biology 45:36-44

29. Haarmeyer C, Smith MD, Chundawat S, Sammond D, Whitehead TA, (2016) “Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein”, Biotechnology & Bioengineering in press


28. Kowalsky CA, Whitehead TA, (2016) “Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing”, Proteins 84(12): 1914-1928 doi:10.1002/prot.25175

27. Wrenbeck EE, Klesmith JR, Adeniran A, Stapleton JA, Tyo KJ, Whitehead TA, (2016) “Plasmid-based single-pot saturation mutagenesis”, Nature Methods 13(11): 928-930 doi:10.1038/nmeth.4029

·      Documentation at Nature Protocols Exchange (doi:10.1038/protex.2016.061)

26. Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA* (2016) “Haplotype-phased synthetic long reads from short-read sequencing”, PLoS ONE 11(1):e0147229

25. Khare S, Whitehead TA (2015), “Introduction to RosettaCON Special Collection”, PLoS ONE 10(12):e0144326

24. Klesmith JR, Whitehead TA (2015), “High-throughput evaluation of synthetic metabolic pathways”, Technology 4(01):9-14

23. Klesmith JR, Bacik JP, Michalczyk R, Whitehead TA (2015) “High-resolution sequence function mapping of a levoglucosan utilization pathway in E. coli”, ACS Synthetic Biology 4 (11), 1235-1243 DOI: 10.1021/acssynbio.5b00131

·      Selected for ‘Introducing our Authors’ feature highlight.

22. Bacik JP, Klesmith JR, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL, Michalczyk R (2015) “Structural insights into bioconversion of the biomass pyrolysis product levoglucosan”, Journal of Biological Chemistry 290 (44), 26638-26648

21. Kowalsky CA, Faber M, Nath A, Dann H, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard J, Chan C, Whitehead TA (2015) “Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing”, Journal of Biological Chemistry 290 (44), 26457-26470 doi:10.1074/jbc.M115.676635

·      Top 5 accessed article for J. Biol. Chem., Oct. 2015.

20. Stapleton JA, Whitehead TA, Nanda V (2015) “Computational redesign of the lipid-facing surface of the outer membrane protein OmpA”, PNAS 112(31):9632-9637

19. Kowalsky CA, Klesmith JR, Stapleton JA, Kelly VW, Reichkitzer N, Whitehead TA (2015) “High-resolution sequence-function mapping of full proteins”, PLoS ONE, 10(3): e0118193. doi:10.1371/journal.pone.0118193

18. Tomek KJ, Saldarriaga CRC, Velasquez FPC, Liu T, Hodge DB, Whitehead TA, (2015) “Removal and upgrading of lignocellulosic fermentation inhibitors by in situ biocatalysis and liquid-liquid extraction”, Biotechnology & Bioengineering, 112(3):627-632.

·      Selected for B&B video highlight.

17. Gao D, Haarmeyer C, Balan V, Whitehead TA, Dale BE, Chundawat SPS (2014) “Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccarification”, Biotechnology for Biofuels, 7:175

16. Bienick MS, Young KW, Klesmith JR, Detwiler EE, Tomek KJ, Whitehead TA, (2014) “The interrelationship between promoter strength, gene expression, and growth rate”, PLoS ONE, DOI: 10.1371/journal.pone.0109105

15. Whitehead TA, Baker D, Fleishman SJ (2013) “Computational design of novel protein binders and experimental affinity maturation”, Methods Enzymology, 523:1-19.

doi: 10.1016/B978-0-12-394292-0.00001-1.

14. Whitehead TA+, Chevalier A+, Song Y et al. (2012) “Optimization of affinity, specificity, and function of designed Influenza inhibitors using deep sequencing”, Nature Biotechnology 30(6):543-8. doi: 10.1038/nbt.2214

+ authors contributed equally

·      Cover of Nature Biotechnology; Featured in numerous popular press articles and radio interviews, including NPR.

____________________________PREVIOUS PUBLICATIONS_________________________

13. Fleishman SJ, Whitehead TA, Strauch EM et al. (2011) “Community-wide assessment of protein-interface modeling suggests improvements to design methodology”, J Mol Biol 414(2):289

12. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D (2011) “Hotspot-centric de novo design of protein binders”, J Mol Biol 413(5):1047

11. Fleishman SJ+, Whitehead TA+, Ekiert D+, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D (2011) “Computational design of proteins targeting the conserved stem region of Influenza hemagglutinin”, Science 332(6031):816-21

+authors contributed equally

·      Featured in numerous popular press articles and radio interviews, including NPR.

10. Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D (2010), “Rosetta in CAPRI rounds 13-19” Proteins 78(15):3212

9. Whitehead TA, Bergeron LM, Clark DS (2009), “Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins” Protein Eng Des Sel 22 (10):607-13

8. Slocik JM, Kim SN, Whitehead TA, Clark DS, Naik RR (2009), “Biotemplated metal nanowires using hyperthermophilic protein filaments”, Small 5 (18):2038-42

7.  Bruns N, Pustelny K, Bergeron LM, Whitehead TA, Clark DS (2009), “Mechanical nanosensor based on FRET within a thermosome: damage-reporting polymeric materials”, Angew Chem Int Ed Engl 48 (31):5666-9

·      Inside cover of Angew Chem Int Ed Engl; feature story in Chemistry World:

6.  Whitehead TA, Je E, Clark DS (2009), “Rational shape engineering of the filamentous protein gamma prefoldin through incremental gene truncation”, Biopolymers 91 (6):496-503

5.  Bergeron LM, Gomez L, Whitehead TA, Clark DS (2009), “Self-renaturing enzymes: design of an enzyme-chaperone chimera as a new approach to enzyme stabilization”, Biotechnol Bioeng 102 (5):1316-22

·      Spotlight article in Biotechnol Bioeng.

4. Whitehead TA, Meadows AL, Clark DS (2008), “Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein”, Small 4 (7):956-60

3. Whitehead TA, Boonyaratanakornkit BB, Hoellrigl V, Clark DS (2007), “A filamentous molecular chaperone of the prefoldin family from the deep-sea hyperthermophile Methanocaldococcus jannaschii”, Protein Science 16 (4): 626-634

2. Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, El-Sayed NMA, Clark DS (2005), “Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock”, Environmental Microbiology 7 (6): 789-797

1. Laksanalamai P, Whitehead TA, Robb FT (2004), “Minimal protein-folding systems in hyperthermophilic archaea”, Nature Reviews Microbiology 2 (4): 315-324

Manuscripts on bioRxiv


1. Klesmith JR^, Thorwall S&, Whitehead TA* “Interpreting deep mutational scanning data resulting from plate-based selections”, bioRxiv 087072