ARTIST: an automatic residue type assignment program for multidimensional NMR spectra

Abstract

We describe a general algorithm for accurate residue type assignments of multidimensional NMR spectra of biomolecules. It exploits identical chemical shifts of the same nuclear site across spectra, to match resonances to known residue type assignments. Thus, congested spectra can be automatically assigned, so long as resonances positions can be resolved. The algorithm is coded into program ARTIST in Python and tested by 3D ncacx and ncocx spectra of the tubular assembly formed by 237-residue Rous sarcoma virus capsid protein. The script can easily be modified to assist residue type assignments of other multidimensional NMR spectra to alleviate the challenge from spectral congestion, and to accelerate the workflow.

ASAP: an automatic sequential assignment program for solid state multidimensional NMR spectra

“…First of all, it eliminates the workload and challenges to make accurate assignment of congested spectra, with all possible combinations considered. As shown by our prior work, when tested by the unassigned ncocx peak list of 237-residue RSV CA, 24 8 residue type assignments in ncacx were reported to find more than 10 possible matched pairs in ncocx. In addition, it is possible for a particular resonance 𝐵 𝑠 to be engaged in multiple matches to pair with different 𝐴 𝑝 , which we refer to as resonance entanglements.…”

“…The algorithm of ARTIST was introduced in our prior publication. 24 Briefly, given a reference residue type assignment 𝐴 𝑝 (𝑛 𝑝 ) from spectrum A, ARTIST executes an exhaustive screening over all individual resonances 𝐵 𝑠 in spectrum B to find its matched pair. Here superscript 𝑝 and 𝑠 specify the position index of the reference residue type assignment in input 1, and the position index of the resonance in input 3.…”

“…Recently, we created a novel algorithm called ARTIST to automatically determine residue type assignments of congested NMR spectra, based on assignments of the well resolved spectra of the same sample. 24 In this work, we introduce an automatic sequential assignment program (ASAP) based on ARTIST and Monte Carlo simulated annealing (MCSA) algorithms. Exploiting ARTIST, all possible combinations to group resonances in unassigned spectra into matched residue type assignments are exhaustively considered for sequential assignments, in agreement with provided reference assignments from the well-resolved spectrum.…”

“…The script will automatically parse them into individual resonance signals, as described in ARTIST. 24…”