Computational design of proteins targeting the conserved stem region of influenza hemagglutinin

We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.

Previous Publications

14. Whitehead TA*, Chevalier A*, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. (2012) "Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.", Nat Biotechnol. 2012 May 27;30(6):543-8. doi: 10.1038/nbt.2214
*Authors contributed equally

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):1047-62

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

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, in press

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

15. Computational design of novel protein binders and experimental affinity maturation

Computational design of novel protein binders and experimental affinity maturation.Whitehead TA, Baker D, Fleishman SJ.Methods Enzymol. 2013;523:1-19. doi: 10.1016/B978-0-12-394292-0.00001-1.PMID: 23422423Computational design of novel protein binders has recently emerged as a useful technique to study biomolecular recognition and generate molecules for use in biotechnology, research, and biomedicine. Current limitations in computational design methodology have led to the adoption of high-throughput screening and affinity maturation techniques to diagnose modeling inaccuracies and generate high activity binders. Here, we scrutinize this combination of computational and experimental aspects and propose areas for future methodological improvements.A PDF reprint of this article is available upon request.

The interrelationship between promoter strength, gene expression, and growth rate

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