Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

Abstract

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2

“…the Sparky program (T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco). The backbone assignment was manually performed, assisted by the COM-PASS software (64).…”

Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3

“…Backbone resonances were assigned using the software COMPASS [27]. Peaks were integrated and relaxation rate constants were fitted using PINT [28].…”

Backbone Assignment of the MALT1 Paracaspase by Solution NMR

“…To estimate the secondary structure in MALT1 Casp-Ig3 (338–719), random coil chemical shifts corrected for nearest-neighbour effects[ 25 ] were subtracted from 13 C’, 13 Cα and 13 Cβ chemical shifts corrected for deuterium isotope shifts[ 26 ] and plotted against the amino acid sequence of MALT1 Casp-Ig3 (338–719). The chemical shift index (CSI) for each carbon type was calculated using a cut-off at ± 0.7 and averaged over all three carbon types to a “consensus” CSI.…”