CAMRA - CHEMICAL-SHIFT BASED COMPUTER-AIDED PROTEIN NMR ASSIGNMENTS

A suite of programs called CAMRA (Computer Aided Magnetic Resonance As signment) has been developed for computer assisted residue-specific as signments of proteins. CAMRA consists of three units: ORE, CAPTURE and PROCESS. ORE predicts NMR chemical shifts for unassigned proteins usi ng a chemical shift database of previously assigned homologous protein s supplemented by a statistically derived chemical shift database in w hich the shifts are categorized according to their residue, atom and s econdary structure type. CAPTURE generates a List of valid peaks from NMR spectra by filtering out noise peaks and other artifacts and then separating the derived peak list into distinct spin systems. PROCESS c ombines the chemical shift predictions from ORE with the spin systems identified by CAPTURE to obtain residue specific assignments. PROCESS ranks the top choices for an assignment along with scores and confiden ce values. In contrast to other auto-assignment programs, CAMRA does n ot use any connectivity information but instead is based solely on mat ching predicted shifts with observed spin systems. As such, CAMRA repr esents a new and unique approach for the assignment of protein NMR spe ctra. CAMRA will be particularly useful in conjunction with other assi gnment methods and under special circumstances, such as the assignment of flexible regions in proteins where sufficient NOE information is g enerally not available. CAMRA was tested on two medium-sized proteins belonging to the chemokine family. It was found to be effective in pre dicting the assignment providing a database of previously assigned pro teins with at least 30% sequence identity is available. CAMRA is versa tile and can be used to include and evaluate heteronuclear and three-d imensional experiments.