CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43050/1/10858_2005_Article_4079.pd

Improved detection of long-range residual dipolar couplings in weakly aligned samples by Lee-Goldburg decoupling of homonuclear dipolar truncation

Homonuclear (1)H residual dipolar couplings (RDCs) truncate the evolution of transverse (1)H magnetization of weakly aligned molecules in high-resolution NMR experiments. This leads to losses in sensitivity or resolution in experiments that require extended (1)H evolution times. Lee-Goldburg decoupling schemes have been shown to remove the effects of homonuclear dipolar couplings, while preserving chemical shift evolution in a number of solid-state NMR applications. Here, it is shown that the Lee-Goldburg sequence can be effectively incorporated into INEPT- or HMQC-type transfer schemes in liquid state weak alignment experiments in order to increase the efficiency of the magnetization transfer. The method is applied to the sensitive detection of (1)H(N)-(13)C long-range RDCs in a three-dimensional HCN experiment. As compared to a conventional HCN experiment, an average sensitivity increase by a factor of 2.4 is obtained for a sample of weakly aligned protein G. This makes it possible to detect 170 long-range (1)H(N)-(13)C RDCs for distances up to 4.9 angstroms