 Homme W. HellingaJames B. Duke Professor of BiochemistryCombined theoretical and experimental approaches to protein and drug design; molecular simulation; protein engineering. Contact InformationOffice Number: (919) 681-5885 Fax: (919) 684-8885 e-mail hwh@biochem.duke.edu Lab Location Room 413 Nanaline Duke Building Mailing Address Department of Biochemistry Nanaline H. Duke Box 3711, DUMC Durham, NC 27710 Education
Research InterestsThe Hellinga laboratory has developed and experimentally validated computational design methods for the design of proteins with novel ligand-binding sites and enzyme activities. This approach starts with a protein of known structure, and uses design algorithms to predict the set of mutations necessary to alter or introduce ligand binding or enzyme activity in that structure. These designs are then produced by oligo-nucleotide-directed mutagenesis (typically 10-20 mutations) and heterologous protein expression. Using this approach we have engineered various members of the periplasmic binding protein (PBP) superfamily to alter radically their ligand-binding specificity. These engineered receptors can be further engineered to function as reagentless fluorescent or electrochemical sensors by constructing appropriate conjugates with reporter groups. In this way we have constructed biosensors for a wide variety of ligands including TNT, nerve agent surrogates, and metabolites. Furthermore, the designed receptors can be re-introduced into E. coli where they drive two-component signal transduction pathways. In this way we have constructed synthetic circuits that control gene expression in response to xenobiotics (such as TNT). The design methodology has also been used successfully to introduce triose phosphate isomerase (TIM) activity into one of the PBP members, ribose-binding protein. The resulting “novoTIM” complements E. coli deletion mutants that lack wild-type TIM under gluconeogenic conditions. Current research includes further development and experimental testing of the computational design techniques to tackle more complex enzyme reactions, protein-protein, and protein-DNA interactions. Recent Publications1. Rizk, SS, Cuneo, MJ & Hellinga, HW (2006) Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. Protein Science 15(7):1745-51. More… 2. De Lorimier, RM, Tian, Y & Hellinga, HW (2006) Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins. Protein Science 15(8):1936-44. More… 3. Cuneo, MJ, Changela, A, Warren, JJ, Beese, LS & Hellinga, HW (2006) The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccaride binding sites. J Mol Biol 362(2):259-70. More… 4. Dattelbaum, JD, Looger, LL, Benson, DE, Sali, KM, Thompson, RB & Hellinga, HW (2005) Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. Protein Science 14(2):284-291. More… 5. Smith, JJ, Conrad, DW, Cuneo, MJ, & Hellinga HW (2005) Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms. Protein Science 14(1):64-73. More… 6. Yang, W, et al., Hellinga, HW, Kearney, A, van der Merwe, PA, Yang, JJ. (2005) Design of a calcium-binding protein with desired structure in a cell adhesion molecule. J Am Chem Soc, 127(7):2085-93. More… 7. Allert, M. Rizk, S Looger, LL & Hellinga, HW (2004) Computational design of receptors for an organophosphate surrogate of the nerve agent soman. PNAS, 101(21):7907-7912. More… 8. Dwyer, MA & Hellinga, HW (2004) Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Op. Struct. Biol., 14:495-504. More… 9. Yang, W, Jones, LM, Isley, L, Ye, Y, Lee, H-W, Wilkins, A, Liu, ZR , Hellinga, HW, Malchow, R, Ghazi, M & Yang, JJ (2003) Rational design of a calcium-binding protein. J. Am. Chem. Soc., 125:6165-6171. More… 10. Looger, LL, Dwyer, MW, Smith, JJ & Hellinga, HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature, 423:185-190. More… 11. Dwyer, MA, Looger, LL & Hellinga, HW (2003). Computational design of a Zn2+ receptor that controls bacterial gene expression. PNAS 100(20):11255-11260. More… 12. Benson, DE, Haddy, AE & Hellinga, HW (2002). Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry, 41:3262-3269. More… 13. de Lorimier, RM, Smith, JJ, Dwyer, MA, Looger, LL, Sali, KM, Paavola, CD, Rizk, SS, Sadigov, S, Conrad, DW, Loew, L, & Hellinga, HW (2002) Construction of a fluorescent biosensor family. Protein Science, 11:2655-2675. More… 14. Liu, H, Schmidt, JJ, Bachand, GD. Rizk, SS, Looger, LL, Hellinga, HW, & Montemagno, CD (2002) Control of a biomolecular motor-powered nanodevice with an engineered chemical switch. Nature Materials, 1:173-177. More… 15. Yang, W, Lee, H-W, Hellinga, HW & Yang, JJ (2002). Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins: Struct. Func. Genet., 47:344-356. More… 16. Wisz, MS & Hellinga, HW (2002) An empirical model for electrostatic interactions in proteins incorporating multiple, geometry-dependent dielectric constants. Proteins Struct. Func. Genet., 51:360-377. More… 17. Benson, DE, Conrad, DW, de Lorimier, RM, Trammell, SA & Hellinga, HW (2001). Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins. Science, 293(5535):1641-4. More… 18. Long, SB, Hancock, PJ, Kral, AM, Hellinga, HW & Beese, LS (2001). The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics. PNAS, 8(23), 12948-12953. More… 19. Looger, LL & Hellinga, HW (2001). Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. Journal of Molecular Biology, 307(1):429-445. More… 20. Marvin, JS & Hellinga, HW (2001). Conversion of a maltose receptor into a zinc biosensor by computational design. PNAS, 98(9):4955-4960. More… 21. Marvin, JS & Hellinga, HW (2001). Manipulation of ligand binding affinity by exploitation of conformational coupling. Nature Structural Biology, 8(9):795-798. More… 22. Trammell, SA, Goldston, Jr., HM, Tran, PT, Tender, L,. Conrad, DW, Benson, DE & Hellinga, HW (2001). Synthesis and characterization of a ruthenium(II)-based redox conjugate for reagentless biosensing. Bioconjugate Chemistry, 12(4):643-647. More… 23. Benson, DE, Wisz, MS & Hellinga, HW (2000). Rational design of nascent metalloenzymes. PNAS. 97(12):6292-7, 200. More… |
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