Dr. Choma obtained a Ph.D. in Biochemistry in 1990 from the University of Ottawa/National Research Council of Canada; on a Natural Sciences and Engineering Research Fellowship from the Canadian government, did postdoctoral research in protein design with William DeGrado at DuPont Pharmaceuticals in Wilmington, Delaware. Prior to joining the faculty at RPI, was principal scientist of the Protein Engineering Facility, University of Groningen, the Netherlands, and research associate at the University of Pennsylvania.

de novo Protein design

De novo protein design is the generation from first principles of a protein sequence that will fold into a predicted and defined three-dimensional structure. In de novo design, the designed sequence bears no intentional resemblance to the sequence of a natural protein. The guiding principle behind de novo design is that, if we can design from scratch a simple protein whose physical characteristics mirror that of the design, then we can hope to fully understand protein structure, stability, specificity and, ultimately, function. Thus, the approach of designing proteins from first principles may permit the incremental synthesis of a system that mimics the complexity and subtlety of a natural protein. We are focussing on the design of two types of proteins: synthetic membrane proteins, and synthetic water-soluble peroxidases. Both projects require the extensive use of computer modeling, chemical synthesis and physical-chemical characterization of the designed proteins.

Membrane Proteins

Membrane proteins are of critical importance to most biological processes, but because of their low solubility and the very limited amount of detailed structural information available, we know relatively little about how these proteins fold and are stabilized in the membrane. Consequently, the design of synthetic membrane proteins is virtually untouched territory, and yet the exercise of designing and characterizing simple, model protein structures could be a powerful approach to help us understand more complex, natural membrane proteins. Recent studies into the energetics governing the folding and function of membrane proteins, together with novel approaches to the chemical synthesis of very hydrophobic long peptides, are now making the rational design of synthetic membrane proteins a realistic possibility. In our laboratory, we are focussing on the design of four-helix bundle membrane proteins with the intent of learning more about how specific amino acids in transmembrane helix sequences direct the orientation and packing of multi-helix membrane proteins.

Synthetic Peroxidase

A major goal of protein design is the generation of synthetic enzymes. To work towards this goal, it would be advantageous to develop a simple model system that can be systematically studied and evolved in tandem with our increasing understanding of protein-based catalysis. In this project, we are designing a peroxidase mimic by incorporating an oxidizing catalyst with a unique three-dimensional geometry into designed protein structures. We will use these model systems to appraise the effect of sequence modifications on the structure of the designed protein and the environment of the catalytic site, and to develop approaches for designing substrate selectivity into our enzyme mimics. Our results will hopefully be applicable to the design of other functional proteins where activity can be tuned by means of subtle amino acid changes in the vicinity of the functional group. Further, once we have a better grasp of how to optimize a given function, other methods such as automated procedures for structure and sequence prediction, repacking programs, genetic approaches and methods of combinatorial synthesis, can be rationally employed to allow rapid optimization of the initial design. The melding of de novo protein design with these other powerful tools will make the design of novel proteins with practical applications increasingly achievable.

Protein Microsequencing Techniques

The human genome database has enormous potential to help us identify abnormal, disease-causing genes, and has lead to greatly increased activity in the field of genomics and proteomics. However, only a small number of these genes are expressed in any given cell type. Identifying which genes are expressed in which cell types is critical if we are to use the information in the genome to diagnose and treat genetic diseases. My laboratory is working on developing ultra-sensitive, rapid and universally-applicable techniques for sequencing segments of all the proteins in a cell. This information, together with the genomic data bank, could be used to identify all the proteins, normal or abnormal, in a cell type.

Van den Heuvel, M., T. van den Berg, R. M. Kellogg, C. T. Choma and B. L. Feringa (2004). Synthesis of a non-heme template for attaching four peptides: an approach to artificial iron(II)-containing peroxidases. J. Org. Chem., 69, 250-262.

Stewart, N.A., V.T. Pham, C.T. Choma and H. Kaplan (2002) Improved peptide detection with matrix-assisted laser desorption mass spectrometry by trimethylation of amino groups. Rapid Commun. Mass Spectrom. 16, 1448-1453.

Choma, C. T., P. Tieleman, L. Serrano, D. Cregut and H. Berendsen (2001). Towards the design and computational characterization of a membrane protein. J. Mol. Graphics & Modelling 20, 219-234.

Changemet-Barret, P., Choma, C. T., Gooding, E. F., DeGrado, W. F. and R. M. Hochstrasser. (2000). Ultrafast dielectric response of proteins from dynamics stokes shifting of coumarin in calmodulin. J. Phys. Chem. B 104, 9322-9329.

Choma, C. T., H. Gratkowski, J. Lear and W. F. DeGrado (2000). Asparagine-mediated self-assembly of a model transmembrane helix. Nature Structural Biology 7, 161-166.

Englebretsen, D. R., C. T. Choma and G. T. Robillard (1998). Synthesis of a designed transmembrane protein by thioether ligation of solubilised segments: N-haloacetylated peptides survived resin cleavage using TFA and EDTA as scavenger. Tetrahedron Lett. 39, 4929-4932.

Choma, C. T., G. T. Robillard and D. R. Englebretsen (1998). Synthesis of hydrophobic peptides: an Fmoc 'solubilizing tail' method. Tetrahedron Lett. 39, 2417-2420.

Choma, C. T., E. Schudde, R. Kellogg, G. T. Robillard and B. L. Feringa (1998). A functional mimic of natural peroxidases: synthesis and catalytic activity of a non-heme iron/peptide hydroperoxide complex. J. Chem. Soc., Perkin Trans. 1, 1998, 769-773.

Choma, C. T., K. Kaestle, K. Akerfeldt, R. Kim, J. Groves and W. DeGrado (1994). A general method for coupling unprotected peptides to bromoacetamido porphyrin templates. Tetrahedron Lett. 34, 6191-6194.

Choma, C. T., J. Lear, M. Nelson, D. Robertson, L. Dutton and W. DeGrado (1994). Design of a heme-binding four helix bundle J. Am. Chem. Soc. 116, 856-865.