Logo: University of Southern California

Richard Roberts

Chair, Chemical Engineering & Materials Science

Professor of Chemistry and Biology
 


Research Images


   
   


 

Research Overview

The Chemical Biology of Protein Synthesis.

Research in the Roberts lab focuses on the protein synthesis machinery both as a tool for polypeptide design and as a target that can be probed using chemical means. A key aspect of my lab's work is peptide and protein design using in vitro selection experiments. Toward this end, we use mRNA display, a technique the PI conceived and implemented to enable polypeptide design (see figure below). This approach allows the lab to create and sieve more than 10 trillion independent peptide or protein sequences for function, the most of any technique currently available. In applying any design approach, it is optimal if key issues, including affinity, specificity, diversity, structure, dynamics, and biological activity can be addressed in a principled way. The lab desires to execute a research program that tackles all of these issues.

Our passion is using the tools of chemistry to understand and control biological processes. We have applied our design approach to address biological control, molecular recognition, stability, and dynamics in RNA-peptide complexes, G proteins and G protein coupled receptors (GPCRs). In the future, our efforts should provide new tools for systems biology and leads for therapeutic development.

We are also very interested to re-engineer the protein synthesis machinery to create unnatural mRNA display libraries. This project, a nanoscale engineering effort, works to merge the power of display selections with the flexibility of combinatorial chemistry. To do this, the lab has worked to extend mRNA display beyond the natural genetic code, in an effort to create new and richly diverse compositions of matter for ligand design, drug discovery, and beyond.

In conjunction with our re-engineering efforts, we have become intensely interested in thinking about the ribosome as a target for puromycin analogues. Our work began with efforts to understand the ribosome's substrate specificity. These efforts have also yielded unexpected and exciting new reagents that have enabled us to visualize protein synthesis in vivo in T-cells and neurons with spatial and temporal resolution.

Selected Publications


Takahashi, T; Millward, S; Roberts, Richard, "Natural and Unnatural Display Libraries," Trends in Biochemical Science, Jan 2008

Ryan J. Austin, William Ja, and Richard W. Roberts,* "Evolution of Class-Specific Peptides Targeting a Hot Spot of the Gαs Subunit" J. Mol. Biol. (2008) 377, 1406–1418. (PDF)
Steven W. Millward†, Stephen Fiacco‡, Ryan J. Austin‡, and Richard W. Roberts‡,* "Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity " ACS Chem. Bio. 2007 Vol. 2 No. 9 (625-634). (PDF)

William Ja, Anthony West, Silvia Delker, Pamela Bjorkman, Seymour Benzer, Richard Roberts, "Extension of Drosophilia melanogaster life span with a GPCR peptide inhibitor." Nat. Chem. Bio. 2007 Vol 3 No. 7 (415-419). (PDF)

C. Anders Olson, Richard W. Roberts.* " Design, expression, and stability of a diverse protein library based on the human fibronectin type III domain." Protein Science 2007 Mar;16(3):476-84. (PDF)

William W. Ja, Ofer Wiser, Ryan J. Austin, Lily Y. Jan, Richard W. Roberts.* "Turning G Proteins On and Off Using Peptide Ligands." ACS Chem. Biol. 1 (9), 570–574, 2006 (PDF)

Ofer Wiser, Xiang Qian, Melissa Ehlers, William W. Ja, Richard W. Roberts, Eitan Reuveny, Yuh Nung Jan, and Lily Yeh Jan "Modulation of Basal and Receptor-Induced GIRK Potassium Channel Activity and Neuronal Excitability by the Mammalian PINS Homolog LGN" Neuron 50, 561–573, May 18, 2006 (PDF)

Steven W. Millward, Terry T. Takahashi, Richard W. Roberts.* "A General Route for Post-Translational Cyclization of mRNA Display Libraries." J. Am. Chem. Soc., 127 (41), 14142 -14143, 2005. (PDF)

Tianbing Xia, Chaozhi Wan, Richard W. Roberts,* Ahmed H. Zewail.* RNA-Protein Recognition: Single-Residue Ultrafast Dynamical Control of Structural Specifcity and Function. Proc Natl Acad Sci 102 13013-18 (2005). (PDF)

William W. Ja, Richard W. Roberts.* "G Protein-Directed Ligand Discovery with Peptide Combinatorial Libraries." TiBS 30 318-324 (2005).(PDF)
William W. Ja, Anirban Adhikari, Ryan J. Austin, Stephen R. Sprang, and Richard W. Roberts.* "A Peptide Core Motif for Binding Heterotrimeric G protein ± Subunits" Journal of Biological Chemistry 280 32057-60 (2005).(PDF)
William W. Ja and Richard W. Roberts.* "Epitope Mapping Using mRNA Display and a Unidirectional Nested Deletion Library" Protein Engineering, Design, and Selection 18 309-19 (2005).(PDF)
W. Bryan Smith, Shelley R. Starck, Richard W. Roberts, and Erin M. Schuman.* "Dopaminergic Stimulation of Local Protein Synthesis Enhances Surface Expression of GluR1 and Synaptic Transmission" Neuron 45 765-779 (2005).(PDF)
Richard W. Roberts.* Engineering Switches, Genetically" Chemistry & Biology 11 1475-1476 (2004); this article is a preview of G. Guntas, S. F. Mitchell, M. Ostermeier "A Molecular Switch Created by In Vitro Recombination of Non-Homologous Genes" Chemistry & Biology 11 1483-87 (2004).(PDF)
Irene A. Chen, Richard W. Roberts, and Jack W. Szostak.* "Systems-Level Properties of Model Protocells and the Emergence of Darwinian Evolution" Science 305 1474-1476 (2004).(PDF)
William W. Ja and Richard W. Roberts.* "In Vitro Selection of State-Specific Modulators of G Protein Signaling Using mRNA Display" Biochemistry, 43, 9265-9275 (2004).(PDF)
Shelley R. Starck, Harry M. Green, Jose Alberola-Ila, and Richard W. Roberts.* "A General Approach to Detect Protein Expression in Vivo Using Fluorescent Puromycin Conjugates" Chemistry & Biology, 11, 999-1008 (2004). (PDF)

Christine T. Ueda and Richard W. Roberts.* " Analysis of a Long Range Interaction Between Conserved Domains of Human Telomerase RNA," RNA, 10, 139-147 (2004).(PDF)
Adam Frankel, Steven W. Millward, and Richard W. Roberts.* "Encodamers: Unnatural Peptide Oligomers Encoded in RNA," Chemistry & Biology, 10, 1043-1050 (2003).(PDF)
Ryan J. Austin, Tianbing Xia, Jinsong Ren, Terry T. Takahashi, and Richard W. Roberts.* "Differential Modes of Recognition in N-peptide/BoxB RNA Complexes" Biochemistry, 42, 14957-14967 (2003).(PDF)
Jeffrey E. Barrick and Richard W. Roberts.* "Achieving Specificity in Selected and Wild-Type N Peptide-RNA complexes," Biochemistry, 42, 12298-13007 (PDF), and supporting information. (PDF)

Adam Frankel, Shuwei Li, Shelley R. Starck, and Richard W. Roberts .* "Unnatural RNA Display Libraries," Current Opinion in Structural Biology, 13, 506-512 (2003). (PDF)
Tianbing Xia, Adam Frankel, Jinsong Ren, Terry T. Takahashi, and Richard W. Roberts.* "Context and Conformation Dictate Function of a Transcription Antitermination Switch," Nature Structural Biology, 10, 812-819 (2003) .(PDF)
Tianbing Xia, Chaozhi Wan, Hans-Christian Becker, Adam Frankel, Richard W. Roberts*, and Ahmed H. Zewail.* "The RNA-Protein Complex: Direct Probing of the Interfacial Recognition Dynamics and its Correlation with Biological Functions," Proc. Natl. Acad. Sci. USA, 100, 8119-8123 (2003).

Shelley R. Starck, Xin Qi, Brett N. Olsen, and Richard W. Roberts.* "The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes," J. Am. Chem. Soc., 125, 8090-8091 (2003). (PDF)

Adam Frankel and Richard W. Roberts.* "In Vitro Selection for Sense Codon Suppression," RNA, 9, 780-786 (2003). (PDF)

Terry T. Takahashi, Ryan Austin, and Richard W. Roberts.* "mRNA Display: Ligand Discovery, Interaction Analysis and Beyond," Trends in Biochemical Sciences, 28, 159-165 (2003). (PDF)

Shuwei Li and Richard W. Roberts.* "A Novel Strategy for In Vitro Selection of Peptide-Drug Conjugates," Chemistry & Biology, 10, 233-239 (2003). (PDF)

Shuwei Li, Steven W. Millward, Richard W. Roberts.* "In Vitro Selection of mRNA Display Libraries Containing an Unnatural Amino Acid," J. Am Chem. Soc. 124, 9972-9973 (2002). (PDF)

Ryan J. Austin, Tianbing Xia, Jinsong Ren, Terry T. Takahashi, Richard W. Roberts.* "Designed Arginine Rich RNA-Binding Peptides with Picomolar Affinity," J. Am. Chem. Soc., 124, 10966-10967 (2002). (PDF)

Jeffrey E. Barrick and Richard W. Roberts.* "Sequence Analysis of an Artificial Family of RNA-Binding Peptides," Protein Science, 11, 2688-2696 (2002). (PDF)

Shelley R. Starck and Richard W. Roberts.* "Puromycin Oligonucleotides Reveal Steric Restrictions for Ribosome Entry and Multiple Modes of Translation Inhibition," RNA, 8, 890-903 (2002). (PDF)

Rick Baggio, Petra Burgstaller, Steve Hale, Andrew Putney, Meghan Lane, Dasa Lipovsek, Martin C. Wright, Richard W. Roberts, Rihe Liu, Jack W. Szostak and Richard W. Wagner.* "Identification of Epitope-like Consensus Motifs Using mRNA Display," J. Molec. Recog. 15, 126-134 (2002). (PDF)

Todd Thorsen, Richard W. Roberts, Frances H. Arnold, and Stephen R. Quake.* "Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device," Physical Review Letters, 86, 4163-4166 (2001). (PDF)

Jeffrey E. Barrick, Terry T. Takahashi, Jinsong Ren, Tianbing Xia and Richard W. Roberts.* "Large Libraries Reveal Diverse Solutions to an RNA Recognition Problem," Proc. Natl. Acad. Sci (USA), 98, 12374-12378 (2001). (PDF)

Jeffrey E. Barrick, Terry T. Takahashi, Andrey Balakin, and Richard W. Roberts.* "Selection of RNA-Binding Peptides Using mRNA-Peptide Fusions," Methods 23,287-293 (2001). (PDF)

Rihe Liu, Jeffrey Barrick, Jack W. Szostak* and Richard W. Roberts.* "Optimized Synthesis of RNA-Protein Fusions for In Vitro Protein Selection," Methods in Enzymology, 318, 268-293 (2000). (PDF)

Richard W. Roberts* and William W. Ja. "In Vitro Selection of Nucleic Acids and Proteins: What Are We Learning?" Current Opinion in Structural Biology, 9, 521-529 (1999). (PDF)

Richard W. Roberts.* "Totally In Vitro Protein Selection Using mRNA-Protein Fusions and Ribosome Display," Current Opinion in Chemical Biology, 3, 268-273 (1999). (PDF)

Richard W. Roberts and Jack W. Szostak.* "RNA-Peptide Fusions: A Novel System for the In Vitro Selection of Peptides and Proteins," Proc. Natl Acad. Sci. (USA), 94 12297-12302 (1997). (PDF)

G. Eric Plum, Richard W. Roberts, and Kenneth J. Breslauer.* "Thermodynamics and Kinetics of Nucleic Acid Association/Dissociation and Folding Processes," in Comprehensive Natural Products Chemistry, 1st ed. (Barton, D. & Nakanishi, K., eds.), Vol. 1. Elsevier, New York (1998).
Richard W. Roberts* and Donald M. Crothers.* "Prediction of Stability of DNA Triplexes," Proc. Natl Acad. Sci. (USA), 93, 4320-4325 (1996). (PDF)

Richard W. Roberts and Donald M. Crothers.* "Kinetic Discrimination in the Formation of Intramolecular Triple Helices," J. Mol. Biol., 260, 135-146 (1996). (PDF)

Richard W. Roberts and Donald M. Crothers.* "Stability and Properties of Double and Triple Helices: Dramatic Effects of RNA or DNA Backbone Composition," Science, 258, 1463-1466 (1992). (PDF)

Richard W. Roberts and Donald M. Crothers.* "Specificity and Stringency in DNA Triplex Formation," Proc. Natl Acad. Sci. (USA), 88, 9397-9401 (1991). (PDF)