Ph.D., University of California, Riverside , 2000
HHMI Fellow, Harvard Medical School
Office: BDA 224B
Phone: (480) 727-0392 Lab Phone: (480)727-0463
Fax: (480) 727-0396
Dr. JOHN CHAPUT's Lab or Group Website
Research and Teaching Interests
We apply the principles of Darwinian evolution to evolve peptides, proteins, and nucleic acids with desired functional properties. Starting from large pools of sequences, functional molecules are isolated through iterative cycles of selection and amplification. Using this methodology, we are creating novel tools for molecular medicine, exploring the functional landscape of the human genome, and examining the magnitude of the protein universe. This research combines traditional synthetic organic chemistry and molecular biology with functional genomics, structural biology, and biotechnology. Specific projects in my laboratory include:
Evolution of an Artificial Genetic System: Creating an artificial genetic system capable of Darwinian evolution is one of the grand challenges in synthetic biology, and an important step in the chemical path to synthetic life. While natural nucleic acids are widely used molecules in molecular evolution, extending this methodology to artificial genetic systems requires chemical synthesis to build substrates that are not otherwise available and engineered polymerases that can make unnatural polymers with high efficiency and fidelity. Of the possible genetic systems related to RNA, threose nucleic acid (TNA) is an attractive progenitor candidate of RNA due to its chemical simplicity and unusual ability to exchange genetic information with itself and with complementary strands of RNA. To determine the fitness of TNA as an alternative genetic system, we are evolving TNA receptors and enzymes in vitro and comparing the functional properties of these molecules to similar molecules constructed of RNA.
In Vitro Evolution of Novel Protein Folds: Does nature use all possible protein folds or just a subset of protein folds? Current databases estimate that all biological proteins derived from one of about a thousand different protein folds. Whether additional folds exist beyond the set found in nature remains an interesting question with important fundamental and practical implications. To investigate this question, we use mRNA display to select polypeptides that bind to desired small molecule targets with high affinity and specificity. We then optimize these sequences by directed evolution, and solve their three-dimensional structures by NMR and X-ray crystallography. This approach provides a unique opportunity to explore the structural and functional diversity available in the protein universe.
Exploring the Translational Landscape of the Human Genome: Gene expression is the coupled process of transcribing DNA information into messenger RNA (mRNA), which is then translated via the genetic code into amino acid sequences called proteins. While many large-scale genomics efforts reveal that the human genome is routinely and pervasively transcribed into RNA, it is unclear how much of this RNA codes for proteins. To explore this question, we have developed a genome-wide experimental method to survey the human genome for RNA sequences that enhance protein translation. Using a combination of bioinformatics and functional assays, we are examining the preponderance of RNA elements that function via cap-independent translation enhancing mechanisms. Many of the sequences discovered thus far appear to function as strong internal ribosomal entry sites when assayed in vitro and in human cells.
Developing Synthetic Antibodies to Human Proteins: Antibodies are proteins made by the immune system that bind and neutralize foreign objects. While antibodies have become valuable tools in biological research, only a small number of all human proteins have antibodies that are commercially available. This shortfall, coupled with the cost and time required to produce traditional monoclonal antibodies has begun to impact many large-scale proteomics projects. To overcome this limitation, new technologies are needed to rapidly manufacture protein affinity reagents to large numbers of protein targets. We have developed one such class of molecules, called NuPromers that function with antibody-like properties, but do not require recursive rounds of selection or animal immunization as their primary means of discovery. We are currently developing a pipeline for constructing NuPromers to large numbers of human proteins.
"Genome-wide profiling of human cap-independent translation-enhancing elements," Wellensiek, B.P., et al. , Nature Methods In Press (2013)
"Synthetic genetic polymers capable of heredity and evolution," Pinheiro, V.B. et al., Science 336 341-344 (2012)
"Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor," H. Yu, S. Zhang, and J.C. Chaput, Nature Chemistry 4 183-187 (2012)
"The emerging world of synthetic genetics," J.C. Chaput, H. Yu, and S. Zhang, Chemistry & Biology 19 1360-1371 (2012)
"Aptamers can Discriminate Alkaline Proteins with High Specificity," H. Yu, B. Jiang, and J. C. Chaput, ChemBioChem 12 2659-2666 (2011)