BaMORC: A Software Package for Accurate and Robust C Reference Correction of Protein NMR Spectra

Overview

Journal Nat Prod Commun

Publisher Sage Publications

Date 2021 May 3

PMID 33936358

Authors

Xi Chen

Andrey Smelter

Hunter N B Moseley

Affiliations

Soon will be listed here.

Abstract

We describe BaMORC, a software package that performs C chemical shifts reference correction for either assigned or unassigned peak lists derived from protein NMR spectra. BaMORC provides an intuitive command line interface that allows non-NMR experts to detect and correct C chemical shift referencing errors of unassigned peak lists at the very beginning of NMR data analysis, further lowering the bar of expertise required for effective protein NMR analysis. Furthermore, BaMORC provides an application programming interface for integration into sophisticated protein NMR data analysis pipelines, both before and after the protein resonance assignment step.

References

Ulrich E, Akutsu H, Doreleijers J, Harano Y, Ioannidis Y, Lin J . BioMagResBank. Nucleic Acids Res. 2007; 36(Database issue):D402-8. PMC: 2238925. DOI: 10.1093/nar/gkm957. View

Moseley H, Curto E, Krishna N . Complete relaxation and conformational exchange matrix (CORCEMA) analysis of NOESY spectra of interacting systems; two-dimensional transferred NOESY. J Magn Reson B. 1995; 108(3):243-61. DOI: 10.1006/jmrb.1995.1129. View

Zhang H, Neal S, Wishart D . RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR. 2003; 25(3):173-95. DOI: 10.1023/a:1022836027055. View

Williamson M . Using chemical shift perturbation to characterise ligand binding. Prog Nucl Magn Reson Spectrosc. 2013; 73:1-16. DOI: 10.1016/j.pnmrs.2013.02.001. View

Smelter A, Astra M, Moseley H . A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. BMC Bioinformatics. 2017; 18(1):175. PMC: 5356280. DOI: 10.1186/s12859-017-1580-5. View

Wang L, Eghbalnia H, Bahrami A, Markley J . Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR. 2005; 32(1):13-22. DOI: 10.1007/s10858-005-1717-0. View

Shuker S, Hajduk P, Meadows R, Fesik S . Discovering high-affinity ligands for proteins: SAR by NMR. Science. 1996; 274(5292):1531-4. DOI: 10.1126/science.274.5292.1531. View

Jayalakshmi V, Krishna N . CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. J Magn Reson. 2004; 168(1):36-45. DOI: 10.1016/j.jmr.2004.01.017. View

Markley J, Bax A, Arata Y, Hilbers C, Kaptein R, Sykes B . Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. J Biomol NMR. 1998; 12(1):1-23. DOI: 10.1023/a:1008290618449. View

10.

Chen X, Smelter A, Moseley H . Automatic C chemical shift reference correction for unassigned protein NMR spectra. J Biomol NMR. 2018; 72(1-2):11-28. PMC: 6209040. DOI: 10.1007/s10858-018-0202-5. View

11.

Shen Y, Lange O, Delaglio F, Rossi P, Aramini J, Liu G . Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A. 2008; 105(12):4685-90. PMC: 2290745. DOI: 10.1073/pnas.0800256105. View

12.

Anderson A . The process of structure-based drug design. Chem Biol. 2003; 10(9):787-97. DOI: 10.1016/j.chembiol.2003.09.002. View

13.

Nowick J, Khakshoor O, Hashemzadeh M, Brower J . DSA: a new internal standard for NMR studies in aqueous solution. Org Lett. 2003; 5(19):3511-3. DOI: 10.1021/ol035347w. View

14.

Drozdetskiy A, Cole C, Procter J, Barton G . JPred4: a protein secondary structure prediction server. Nucleic Acids Res. 2015; 43(W1):W389-94. PMC: 4489285. DOI: 10.1093/nar/gkv332. View

15.

Smelter A, Rouchka E, Moseley H . Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping. J Biomol NMR. 2017; 68(4):281-296. PMC: 5587626. DOI: 10.1007/s10858-017-0126-5. View

16.

Han B, Liu Y, Ginzinger S, Wishart D . SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR. 2011; 50(1):43-57. PMC: 3085061. DOI: 10.1007/s10858-011-9478-4. View

17.

Wishart D, Bigam C, Yao J, Abildgaard F, Dyson H, Oldfield E . 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR. 1995; 6(2):135-40. DOI: 10.1007/BF00211777. View