Biochemistry and Molecular Biophysics
Publications (PubMed / NIH)
Research
The Havranek lab studies specificity in protein-DNA and protein-peptide interactions using computational and experimental approaches. We develop and apply computational protein design alogrithms to generate useful molecular tools. Current projects include the development of protein probes for single molecule peptide sequencing and engineering Cre recombinase for genome editing applications.
Select Publications
Bodmer N.K. & Havranek J.J. (2018). “Efficient minimization of multipole electrostatic potentials in torsion space.” PLoS One. 2018 Apr 11;13(4):e0195578. doi: 10.1371/journal.pone.0195578. eCollection 2018. (Abstract)
Adam P. Joyce & James J. Havranek (2018). “Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors” Quantitative Biology, March 2018, Volume 6, Issue 1, pp 68–84 (Abstract)
Chang Y.K., Srivastava Y., Hu C., Joyce A., Yang X., Zuo Z., Havranek J.J., Stormo G.D., and Jauch R. (2017) “Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.” Nucleic Acids Res. 2017 Jan 25;45(2):832-845. doi: 10.1093/nar/gkw1198. Epub 2016 Dec 2. (Abstract)
Zhang C., Myers C.A., Qi Z., Mitra R.D., Corbo J.C., and Havranek J.J. (2015) “Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex.” Nucleic Acids Res. 2015 Oct 15;43(18):9076-85. doi: 10.1093/nar/gkv901. Epub 2015 Sep 13. (Abstract)
Sasaki Y., Margolin Z., Borgo B., Havranek J.J., & Milbrandt J. (2015). “Characterization of Leber Congenital Amaurosis-associated NMNAT1 Mutants.” J Biol Chem. 2015 Jul 10;290(28):17228-38. doi: 10.1074/jbc.M115.637850. Epub 2015 May 27. (Abstract)
Joyce A.P., Zhang C., Bradley P., & Havranek J.J. (2015). “Structure-based modeling of protein: DNA specificity.” Brief Funct Genomics. 2015 Jan;14(1):39-49. doi: 10.1093/bfgp/elu044. Epub 2014 Nov 19. (Abstract)
Borgo B. and Havranek J.J. (2014) “Motif-directed redesign of enzyme specificity.” Protein Sci. 2014 Mar;23(3):312-20. doi: 10.1002/pro.2417. Epub 2014 Feb 4. (Abstract)
Lyskov S., Chou F.C., Conchúir S.Ó., Der B.S., Drew K., Kuroda D., Xu J., Weitzner B.D., Renfrew P.D., Sripakdeevong P., Borgo B., Havranek J.J., Kuhlman B., Kortemme T., Bonneau R., Gray J.J., and Das R. (2013) “Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).” PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. (Abstract)
Leaver-Fay A., O’Meara M.J., Tyka M., Jacak R., Song Y., Kellogg E.H., Thompson J., Davis I.W., Pache R.A., Lyskov S., Gray J.J., Kortemme T., Richardson J.S, Havranek J.J., Snoeyink J., Baker D., and Kuhlman B. (2013) “Scientific benchmarks for guiding macromolecular energy function improvement.” Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0. (Abstract)
Tang Y.T., Gao R., Havranek J.J., Groisman E.A., Stock A.M., and Marshall G.R. (2012) “Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator.” Chem Biol Drug Des. 2012 Jun;79(6):1007-17. doi: 10.1111/j.1747-0285.2012.01362.x. Epub 2012 Mar 21. (Abstract)
Borgo B. and Havranek J.J. (2012) “Automated selection of stabilizing mutations in designed and natural proteins.” Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1494-9. doi: 10.1073/pnas.1115172109. Epub 2012 Jan 17. (Abstract)
Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., Kaufman K., Renfrew P.D., Smith C.A., Sheffler W., Davis I.W., Cooper S., Treuille A., Mandell D.J., Richter F., Ban Y.E., Fleishman S.J., Corn J.E., Kim D.E., Lyskov S., Berrondo M., Mentzer S., Popović Z., Havranek J.J., Karanicolas J., Das R., Meiler J., Kortemme T., Gray J.J., Kuhlman B., Baker D., and Bradley P. (2011) “ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.” Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6. (Abstract)