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MAP-XSII: an improved program for the automatic assignment of methyl resonances in large proteins

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Abstract

NMR studies of large proteins have gathered much interest in recent years, especially after methyl-transverse relaxation optimized spectroscopy was successfully applied to systems as large as ~1 MDa in molecular weight. However, to fully take advantage of these spectra, there is a need for convenient and robust methods for making resonance assignments rapidly. Here, we present an improved version of our program MAP-XS (methyl assignment prediction from X-ray structure) for the automatic assignment of methyl peaks, based on nuclear Overhauser effects (NOE) correlations and chemical shifts together with available structures. No manual analysis of the NOE data is needed in this new version, which helps to further accelerate the assignment process. A refined algorithm as well as more efficient sampling produces results from single runs of MAP-XSII using unanalyzed NOE data are comparable to those achieved by the old version using manually curated data with every NOE peak correctly attributed to the two related methyl peaks; in addition, checking the results from multiple parallel runs against each other provides an effective mechanism for getting rid of the wrong assignments while keeping the correct ones, which significantly improves the reliability of final assignments. The new program is tested against three different proteins and delivers ~95 % correct assignments; positive results are also achieved for tests using different cut-off distances for NOEs, structures of lower resolutions, and ambiguous residue types.

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Abbreviations

TROSY:

Transverse relaxation optimized spectroscopy

NOE:

Nuclear overhauser effect

PRE:

Paramagnetic relaxation enhancement

MBP:

Maltose binding protein

EIN:

N-terminal domain of E. coli Enzyme I

RDC:

Residual dipolar coupling

PCS:

Pseudocontact shift

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Acknowledgments

The research is supported by grants from the Wellcome Trust and BBSRC. We are grateful to Dr. Sprangers and Prof. Kay, Dr. Venditti and Prof. Clore, Dr. Wen and Prof. Wu for sharing their data on proteasome, EIN, and MBP respectively. The program can be downloaded from nmr.bc.ic.ac.uk/map-xs/.

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Authors and Affiliations

  1. Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK

    Yingqi Xu & Stephen Matthews

  2. Cross Faculty NMR Centre, Imperial College London, South Kensington, London, SW7 2AZ, UK

    Yingqi Xu & Stephen Matthews

  3. Centre for Structural Biology, Imperial College London, South Kensington, London, SW7 2AZ, UK

    Yingqi Xu & Stephen Matthews

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  1. Yingqi Xu
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  2. Stephen Matthews
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Correspondence to Stephen Matthews.

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Xu, Y., Matthews, S. MAP-XSII: an improved program for the automatic assignment of methyl resonances in large proteins. J Biomol NMR 55, 179–187 (2013). https://doi.org/10.1007/s10858-012-9700-z

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