Chaput Lab: Research

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 nanobiotechnology. Specific projects in my laboratory include:

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 chemical diversity available in the protein universe.

Histone Post-Translational Modifications and the Epigenome: The histone code postulates that post-translational modifications found on histone proteins constitute an elaborate epigenetic code that regulates access to the human genome. Learning how to read this code is now a major goal of epigenetics research, as these modifications are believed to play a significant role in gene activation and silencing. Because traditional antibodies are often unable to distinguish subtle post-translational modifications, we are evolving DNA aptamers that bind to important histone modifications with ultrahigh specificity. We envision these reagents being used to study histone post-translational modification and the epigenome.

Exploring the Translational Landscape of the Human Genome: Gene expression is the coupled process of transcribing DNA 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 are developing a combined experimental-bioinformatics approach that will allow us to discover novel translation enhancing elements in the human genome.

Developing Synthetic Antibodies to Human Proteins: Antibodies are proteins made by the immune system that bind and neutralize foreign objects. While antibodies have become invaluable tools in biological research, only a small number of human proteins have antibodies that are commercially available. This shortfall, coupled with the cost and time associated with the production of traditional antibodies is beginning to impact many large-scale proteomics efforts. 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 synbodies, that function with antibody-like properties, but do not require in vitro selection or animal immunization as their primary means of discovery.