POKY Software Tools Encapsulating Assignment Strategies for Solution and Solid-state Protein NMR Data

Overview

Journal J Struct Biol X

Specialty Cell Biology

Date 2022 Sep 9

PMID 36081577

Authors

Ira Manthey

Marco Tonelli

Lawrence Clos Ii

Mehdi Rahimi

John L Markley

Woonghee Lee

Affiliations

Soon will be listed here.

Abstract

NMR spectroscopy provides structural and functional information about biomolecules and their complexes. The complexity of these systems can make the NMR data difficult to interpret, particularly for newer users of NMR technology, who may have limited understanding of the tools available and how they are used. To alleviate this problem, we have created software based on standardized workflows for both solution and solid-state NMR spectroscopy of proteins. These tools assist with manual and automated peak picking and with chemical shift assignment and validation. They provide users with an optimized path through spectral analysis that can help them perform the necessary tasks more efficiently.

Citing Articles

The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A.

Olivieri C, Wang Y, Walker C, Veliparambil Subrahmanian M, Ha K, Bernlohr D Elife. 2024; 12.

PMID: 38913408 PMC: 11196109. DOI: 10.7554/eLife.91506.

Predicting multiple conformations via sequence clustering and AlphaFold2.

Wayment-Steele H, Ojoawo A, Otten R, Apitz J, Pitsawong W, Homberger M Nature. 2023; 625(7996):832-839.

PMID: 37956700 PMC: 10808063. DOI: 10.1038/s41586-023-06832-9.

Observation of pH-Dependent Residual Structure in the Pmel17 Repeat Domain and the Implication for Its Amyloid Formation.

Morris D, Nyenhuis D, Dean D, Strub M, Tjandra N Biochemistry. 2023; 62(22):3222-3233.

PMID: 37917797 PMC: 11822675. DOI: 10.1021/acs.biochem.3c00445.

References

Weber D, Wang S, Markley J, Veglia G, Lee W . PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020; 36(9):2915-2916. PMC: 7203746. DOI: 10.1093/bioinformatics/btaa019. View

Lee W, Rahimi M, Lee Y, Chiu A . POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics. 2021; 37(18):3041-3042. PMC: 8479676. DOI: 10.1093/bioinformatics/btab180. View

Lee W, Markley J . PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2017; 34(9):1586-1588. PMC: 5925765. DOI: 10.1093/bioinformatics/btx785. View

Moseley H, Sperling L, Rienstra C . Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR. 2010; 48(3):123-8. PMC: 2962796. DOI: 10.1007/s10858-010-9448-2. View

Schmidt E, Gath J, Habenstein B, Ravotti F, Szekely K, Huber M . Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J Biomol NMR. 2013; 56(3):243-54. DOI: 10.1007/s10858-013-9742-x. 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

Lee W, Westler W, Bahrami A, Eghbalnia H, Markley J . PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009; 25(16):2085-7. PMC: 2723000. DOI: 10.1093/bioinformatics/btp345. View

Opella S, Marassi F . Structure determination of membrane proteins by NMR spectroscopy. Chem Rev. 2004; 104(8):3587-606. PMC: 3270942. DOI: 10.1021/cr0304121. View

Dashti H, Tonelli M, Lee W, Westler W, Cornilescu G, Ulrich E . Probabilistic validation of protein NMR chemical shift assignments. J Biomol NMR. 2016; 64(1):17-25. PMC: 4744101. DOI: 10.1007/s10858-015-0007-8. View

10.

Berman H, Henrick K, Nakamura H, Markley J . The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2006; 35(Database issue):D301-3. PMC: 1669775. DOI: 10.1093/nar/gkl971. View

11.

Lee W, Petit C, Cornilescu G, Stark J, Markley J . The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR. 2016; 65(2):51-7. PMC: 4921114. DOI: 10.1007/s10858-016-0036-y. View

12.

Lee W, Stark J, Markley J . PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR. 2014; 60(2-3):73-5. PMC: 4207954. DOI: 10.1007/s10858-014-9855-x. View

13.

Fritzsching K, Hong M, Schmidt-Rohr K . Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria. J Biomol NMR. 2016; 64(2):115-30. PMC: 4933674. DOI: 10.1007/s10858-016-0013-5. View

14.

Lee W, Bahrami A, Dashti H, Eghbalnia H, Tonelli M, Westler W . I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR. 2019; 73(5):213-222. PMC: 6579641. DOI: 10.1007/s10858-019-00255-3. View

15.

Wang J, Denny J, Tian C, Kim S, Mo Y, Kovacs F . Imaging membrane protein helical wheels. J Magn Reson. 2000; 144(1):162-7. DOI: 10.1006/jmre.2000.2037. View

16.

Polenova T, Gupta R, Goldbourt A . Magic angle spinning NMR spectroscopy: a versatile technique for structural and dynamic analysis of solid-phase systems. Anal Chem. 2015; 87(11):5458-69. PMC: 4890703. DOI: 10.1021/ac504288u. View

17.

Lee W, Tonelli M, Markley J . NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2014; 31(8):1325-7. PMC: 4393527. DOI: 10.1093/bioinformatics/btu830. View

18.

Fritzsching K, Yang Y, Schmidt-Rohr K, Hong M . Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. J Biomol NMR. 2013; 56(2):155-67. PMC: 4048757. DOI: 10.1007/s10858-013-9732-z. View

19.

Markley J, Ulrich E, Berman H, Henrick K, Nakamura H, Akutsu H . BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR. 2008; 40(3):153-5. PMC: 2268728. DOI: 10.1007/s10858-008-9221-y. View

20.

Lee W, Cornilescu G, Dashti H, Eghbalnia H, Tonelli M, Westler W . Integrative NMR for biomolecular research. J Biomol NMR. 2016; 64(4):307-32. PMC: 4861749. DOI: 10.1007/s10858-016-0029-x. View