2nd Annual Advances in Biomolecular Engineering

On June 30, 2008, The City University of New York, in conjunction with Polytechnic University and The New York Academy of Sciences' Physical Sciences and Engineering Program, will host a day-long symposium focusing on protein design, a subject that lies at the interface of chemistry, biology, engineering and computer science.

The symposium will highlight the recent advances in proteins, specifically focusing on innovative approaches to tailor proteins with unique functions and architectures. This symposium is highly interdisciplinary and will bring together recognized scientists and engineers who are performing cutting-edge research with core knowledge in physical sciences and engineering. An important goal of this symposium is to highlight the research advances in protein design from academic, government, and industrial institutions by convening and promoting the exchange of ideas. Thus, there will be a poster session at the symposium. This session will provide individuals the opportunity to present their research and interact with meeting attendees.

Agenda

8:30 - 9:00
Registration Check-In, Set up Posters

9:00 - 9:10
Welcome and Introduction

9:10 - 9:55
Structure, Function and Folding of Designed Repeat Proteins
Lynne Regan, Department of Molecular Biophysics and Biochemistry and Chemistry, Yale University

9:55 - 10:40
Design of Protein Kinase-Inducible Domains
Neal Zondlo, Department of Chemistry, University of Delaware

10:40 - 11:00
Refreshments and View Posters

11:00 - 11:45
Domain Mapping and Structural Studies of the Chromosomal Passenger Complex
Andrea Cochran, Genentech

11:45 - 12:30
Redesigning the Ubiquitin Pathway to Identify the Substrates of E3 Ubiquitin Ligases
Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill

12:30 - 2:00
Lunch Break and Poster Session

2:00 - 2:45
Protein Switches and Bacteria as Band-Pass Filters
Marc Ostermeier, Department of Chemical and Biomolecular Engineering, Johns Hopkins University

2:45 - 3:30
D-Peptide Inhibitors of HIV Entry
Michael Kay, Department of Biochemistry, University of Utah

3:30 - 3:50
Refreshments and View Posters

3:50 - 4:35
Analysis and Design of Membrane Proteins
William DeGrado, Department of Biochemistry and Molecular Biophysics, University of Pennsylvania

4:35-4:45
Closing Remarks

Abstracts

Structure, Function and Folding of Designed Repeat Proteins
Lynne Regan, Yale University

Repeat proteins are comprised of tandem arrays of a small structural motif. Our research focuses on all-helical TPR repeats. I will present data showing the extent to which the stability and folding of such proteins can be understood and also rationally modified. Repeat proteins are non-globular extended structures. They are therefore particularly well-suited to mediate protein-protein interactions and to organize multiple proteins into functional complexes. Moreover, the modular structure allows for different sets of repeats to be used to bind to different ligands. I will present data showing examples of the design and engineering of TPR modules that display novel ligand-binding properties. I will also discuss possible applications of such versatile modules.

Design of Protein Kinase-Inducible Domains
Neal Zondlo, University of Delaware

Protein phosphorylation is a ubiquitous cellular signaling mechanism. We have used protein design to develop novel protein motifs, termed protein kinase-inducible domains (pKIDs). The basis of the design is the use of phosphoserine to mimic of a structurally important Glu residue in a protein. Non-phosphorylated pKIDs are disordered and exhibit weak fluorescence, whereas phosphorylated pKIDs fold, bind terbium and exhibit strong fluorescence. pKIDs may exhibit essentially complete phosphorylation-dependent switching. Protein kinase-inducible domains are compatible with complex solution environments, including cell extracts, and may be used as in vitro fluorescent sensors of protein kinase activity and protein phosphatase activity.

Domain Mapping and Structural Studies of the Chromosomal Passenger Complex
Andrea Cochran, Genentech

The chromosomal passenger complex (CPC) regulates numerous essential mitotic functions. It is named for its distinctive pattern of localization within the mitotic cell, and the complex moves to different structures as mitosis progresses. Known functions of the complex require that all four passenger proteins be present. However, it has been possible to learn a great deal about the CPC through mapping of subdomains within the individual proteins and through structural studies of subcomplexes. I will discuss recent work from our lab to characterize functional subdomains within the CPC protein Borealin.

Redesigning the Ubiquitin Pathway to Identify the Substrates of E3 Ubiquitin Ligases
Brian Kuhlman, University of North Carolina

Ubiquitin is attached to proteins by a cascade of enzymatic reactions involving the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzymes, and the E3 ubiquitin ligases. Substrate specificity of the pathway is conveyed by the E3s, of which there are hundreds in the human genome. Identifying E3 substrates is a difficult problem because substrate-ligase interactions are transient, ubiquitination is often a signal for degradation, and at any given time hundreds of proteins are ubiquitinated in the cell. To get around these problems we are redesigning the ubiquitin pathway so that specific E3's tag their substrates with the ubiquitin-like protein Nedd8, instead of ubiquitin. Like ubiquitin, Nedd8 is attached on proteins by an E1 and E2. Unlike ubiquitin, Nedd8 is not a signal for protein degradation and there are few proteins that are normally modified with Nedd8 in the cell. Using computer-based protein design in combination with high-throughput screening, we have redesigned the E2 enzyme for the Nedd8 pathway and the E3 enzyme E6AP so that they bind specifically with each other. Encouragingly, the redesigned E3 can pass Nedd8 to a known substrate of E6AP, p53. Currently we are focused on increasing the rate of Nedd8 transfer so that it will be a useful tool in living cells.

Protein Switches and Bacteria as Band-Pass Filters
Marc Ostermeier, Johns Hopkins University

We have developed combinatorial methods for engineering protein switches from natural proteins that exhibit the prerequisite input and output functions of the desired switch. In addition to the intended function, some switches have emergent allosteric properties not predictable based on the properties of the parental proteins. In order to facilitate identification of proteins switches that have regulated beta-lactamase activity, we have engineered a strain of E. coli to behave as a tunable band-pass filter for beta-lactamase activity. Unlike the paradigm in synthetic biology of tuning by modification of system components, our band-pass filter's band-width and position can be tuned externally.

D-Peptide Inhibitors of HIV Entry
Michael Kay, University of Utah

During HIV-1 entry, the highly conserved gp41 N-trimer pocket region is transiently exposed and vulnerable to inhibition. Using mirror-image phage display and structure-assisted design, we have discovered protease-resistant D-amino acid peptides (D-peptides) that bind the N-trimer pocket with high affinity and potently inhibit HIV entry. One of these peptides is the most potent pocket-specific entry inhibitor yet reported by three orders of magnitude (IC50 = 150 pM). The D-peptides described here address limitations associated with current L-peptide entry inhibitors and are promising leads for the prevention and treatment of HIV/AIDS.