I will first reiterate the functions of the NMR facility of the LMC: The first is as a resource for the entire chemist community of the LMC and NCI Frederick to use as a routine use facility to walk up and collect NMR data on synthetic compounds prepared for projects under the auspices of other PIs and 2) It is used to tackle more challenging problems related to the structure and 2-dimensional conformations of drug molecules or other biopolymers (peptide, glycopeptides, oligonucleotides and oligosaccharides) studied in the various sections of the lab. This project relates to number (2) in that I use part of my time to do NMR-based conformational analysis that is a critical part of my work and of the entire LMC. Thus the creation of this new project is to define the effort dedicated to original research in the area of conformational analysis of molecules of biological significance to the LMC and NCI as a whole. In the past fiscal year, we have completed a study related to the DNA containing locked nucleosides which we have already spent considerable effort in the past. This culminated with a publication in the Nucleic Acids Research concerning a comprehensive biophysical study of six DNA molecules that contained sugar pucker-locked nucleotide analogues. Our main effort has been in defining the solution conformation of peptides and glycopeptides as described in the last report. Our solution conformation of an integrin binding peptide of thrombospondin-1, an important extracellular matrix protein with a wealth of biological functions, was published in Journal of Medicinal Chemistry. We have defined the conformation of this motif in water and in dodecylphosphocholine micelles and this work is now a prelude to performing similar studies with the highly interesting glycopeptide Antiproliferative Factor (APF), a molecule that will become a useful tool in the design of bladder cancer therapeutics. The peptide is virtually unstructured in water solution but assumes some structure in membrane mimicking environments (trifluoroethanol). This work has progressed where nearly 50 analogues of the glycopeptide were synthesized and an SAR study is near complettion for submission to J. Med. Chem. Due to the untimely death of Christopher Michejda, the leader of this SAR, I have taken over the responsibility of supervising his former post doc who will continue this work into 2009. A separate project that was started in mid 2007 is to explore the binding site of a Single Chain Variable Fragment (scFV) of an immunoglobulin to hen eggwhite lysozyme (HEL) that was designed, cloned and comprehensively analyzed by Sandra Smith-Gill and her colleagues. Due to difficulties in obtaining crystal or NMR structures of the scFV-HEL complex, they undertook the expression of a series of mutants that contained 5-fluoro tryptophan in place of other aromatic amino acids and we are examining the 19F NMR spectra in collaboration with this group. To this point, we have collected spectra of the free proteins (six mutants), and have performed several titration studies with HEL at various temperatures according to the stability profile of each protein. We have shown that the spectra are completely resolved only in the presence of the enzyme at specific concentrations, and we have begun to map the binding site by observing changes in chemical shift of the 19F signals: Only 3 of 6 show marked changes with addition of enzyme, suggesting they are involved in binding. In addditionb, we are assigning then tryptophan residues by collecting spectra of deletion mutants prepared by the Smith-Gill lab. This is evolving to be a very interesting and very relevant project in the optimization of antibody fragment design, thermodynamic evaluation and binding site mapping of structurally recalcitrant proteins
