Contact Information Email: Click to Mail Phone: (805) 893-2610 Fax: (805) 893-4731 Office Location: 3341 Engineering II Address: Chemical Engineering, Mail Code 5080, Engineering II, Room 3357, University of California, Santa Barbara, CA 93106-5080 USA Lab Phone: (805) 893-3477

Assistant Information Name: Debbie Watts Email: Click to Mail Phone: (805) 893-8692 Fax: (805) 893-4731

Web Pages Research Group Home Page

Course Pages ChE 132A Analytical Methods in Chemical Engineering ChE 171 Introduction to Biochemical Engineering ChE 172 Cell Biology for Engineers BMSE 251 Introduction to Biopharmaceutical Engineering ChE 180A & B, Undergraduate Chemical Engineering Laboratory

Education & Honors

BS: Chemical Engr. (Honors), University of Minnesota, Minneapolis-St. Paul (1993)

PhD: Chemical Engineering, The University of Texas at Austin (1999)

Honors:
2007 ACS Young Investigator Award, Biochemical Technology Division
2006 Camille Dreyfus Teacher Scholar Award
2005 National Science Foundation CAREER Award
2005 Keynote Lecturer, FOSBE Meeting
2003 Santa Barbara Cottage Hospital Research Award

Research

Precision molecular recognition underlies the circuitry of complex biological systems. Current research in my laboratory aims to elucidate protein interaction principles in biological systems, and to develop and apply methods and technologies for the diagnosis and treatment of human disease. We have developed several new technologies that enable i) isolation and engineering of protein-binding ligands with improved affinity and specificity, ii) semi-automated affinity ligand isolation using micro-fluidic cell sorters, iii) intracellular sensing and screening for enzyme activity and protein interactions, and iv) engineering and characterization of peptidases. These new biotechnologies create significant opportunities to apply molecular and cellular engineering to improve human health. In particular, we are applying these tools to develop advanced medical diagnostic technologies, and novel therapeutic approaches that rely upon engineered molecular machines and artificial signal transduction systems. Our work is highly interdisciplinary and benefits from several active collaborations with academic and industrial laboratories, and physicians.

Publications

Dane K.Y., Gottstein C., Daugherty P.S. (2009) "Cell surface profiling with peptide libraries yields ligand arrays that classify breast tumor subtypes." Mol Cancer Ther. 2009 May 5. [Epub ahead of print]

Stec-Niemczyk J., Pustelny K., Kisielewska M., Bista M., Boulware K.T., Stennicke H.R., Thogersen I.B., Daugherty P.S., Enghild J.J., Baczynski K., Popowicz G.M., Dubin A., Potempa J., Dubin G. (2009) "Structural and functional characterization of SplA, an exclusively specific protease of Staphylococcus aureus." Biochem J. 2009 May 1; 419(3),555-64.

Kim U., Qian, J., Kenrick S.A., Daugherty, P.S., Soh H.T. (2008) "Multitarget dielectrophoresis activated cell sorter." Anal Chem. 80(22), 8656-61. Epub 2008 Oct 22.

Rice, J.J. and Daugherty, P.S. (2008) "Directed Evolution of a Biterminal Bacterial Display Scaffold Improves the Display of Diverse Peptides," Protein Eng. Des Sel. 2008, 21(7), 435-42.

Dubin, G., Stec-Niemczyk, J., Kisielewska, M., Pustelny, K., Popowicz, G.M., Bista, M., Kantyka, T., Boulware KT, Stennicke HR, Czarna A, Phopaisarn M, Daugherty, P.S., Thoegersen, I.B., Enghild, J.J., Thornberry, N., Dubin, A., Potempa, J. (2008) "Enzymatic activity of the Staphylococcus aureus SplB serine protease is induced by substrates containing the sequence Trp-Glu-Leu-Gln." J. Mol. Biol., 379(2), 343-56.

Kenrick, S., Rice, J., Daugherty, P. "Flow cytometric sorting of bacterial surface-displayed libraries." Curr Protoc Cytom. 2007 Chapter 4, Unit 4.6.

Kim, U., Shu, C.W., Dane, K.Y., Daugherty P.S., Wang J.Y., Soh, H.T. (2007) Selection of mammalian cells based on their cell-cycle phase using dielectrophoresis. Proc. Natl. Acad. Sci. USA 104(52) 20708.

Daugherty, P.S. (2007) "Protein engineering with bacterial display," Curr Opin Struct Biol. 17(4), 474-80.

Hall, S.S., Mitragotri, S., Daugherty, P.S.(2007) "Identification of peptide ligands facilitating nanoparticle attachment to erythrocytes," Biotechnol Prog. 23(3),749-54.

Bessette, P.H., Hu, X., Soh, H.T., Daugherty, P.S. (2007) Microfluidic Library Screening for Mapping Antibody Epitopes. Analytical Chemistry, 79(5), 2174-8.

You, X. Nguyen, A.W., Jabaiah, A., Sheff, M.A., Thorn, K.S., Daugherty, P.S. (2006) Intracellular Protein Interaction Mapping with FRET Hybrids, Proc. Natl. Acad. Sci. USA, 103 (48).

Mena, M.A., Treynor, T. Mayo, S.L. Daugherty, P.S. (2006) "Blue Fluorescent Proteins with Enhanced Brightness and Photostability from a Structurally Targeted Library," Nature Biotechnology, 24(12), 1569-71.

Oh, S.H., Kenrick, S., Daugherty, P.S., Soh, H.T. (2006) "Microfluidic Protein Detection Using Genetically Engineered Bacteria," J. Proteome Res., 5(12), 3433-7.

Dane, K.Y., Zhu, Y. Nguyen, A.W., Daugherty, P.S. (2006) "Detection of Caspase-3 Activity using Intracellular Fluorescent Protein FRET," Meth. Mol. Biol. Humana Press, In Press.

Nguyen, A.W., You, X. Jabaiah, A.M., Daugherty, P.S.(2006) Fluorescent Protein FRET Applications: Protein Engineering, Intracellular Sensing, and Interaction Screening, Principles of Fluorescence Spectroscopy, Fluorescent Proteins and Their Uses. Vol. 12; In Press.

Boulware, K.T. Daugherty, P.S. (2006) Protease Specificity Determination Using Cellular Libraries of Peptide Substrates (CLiPS), Proc. Natl. Acad. Sci. USA, 103(20), 7583-88.

Rice, J.J., Schohn, A., Bessette, P.H., Boulware, K.T., Daugherty, P.S. (2006) "Bacterial Display Using Circularly Permuted Outer Membrane Protein OmpX Yields High Affinity Peptide Ligands," Protein Science, 10(3), 825-36.

Curnow, P. Bessette, P.H., Kisalilus, D. Murr, M.M., Daugherty, P.S. Morse, D.E. (2005) "Enzymatic Synthesis of Layered Titanium Phosphates at Low Temperature and Neutral pH by Cell-Surface Display of Silicatein-alpha" J. Am. Chem. Soc., 127(45), 15749-55.

Dane, K.Y., Chan, L., Rice, J.R., Daugherty, P.S. (2006) "Isolation of Cell Specific Peptide Ligands using Fluorescent Bacterial Display Libraries," J. Immunol. Methods, 309(1-2), 120-9.

Hu, X. Bessette, P.H., Qian, J. Meinhart, C.D., Daugherty, P.S., Soh, H.T. (2005) Marker Specific Sorting of Rare Cells Using Dielectrophoresis, Proc. Natl. Acad. Sci. USA, 102(44) 15757-15761.

Mena, M.A., Daugherty P.S. (2005) "Computational Design of Degenerate Codon Libraries," Protein Engineering, Design & Selection, 18(12), 559-61.

Nguyen, A.W. Daugherty, P.S. (2005) "Evolutionary Optimization of Fluorescent Proteins for Intracellular FRET," Nature Biotechnology, 23(3), 355-60.