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Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: Application to the lac repressor headpiece

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Summary

A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the 15N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.

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Abbreviations

2D, 3D:

two-, three-dimensional

NOESY:

nuclear Overhauser enhancement spectroscopy

HMQC:

heteronuclear multiple quantum coherence

SSE:

secondary structure element

SERENDIPITY:

SEcondary structuRE ideNtification in multiDImensional ProteIn specTra analYsis

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Authors and Affiliations

  1. Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

    Elizabeth C. van Geerestein-Ujah, Monique Slijper, Rolf Boelens & Robert Kaptein

Authors
  1. Elizabeth C. van Geerestein-Ujah
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  2. Monique Slijper
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  3. Rolf Boelens
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  4. Robert Kaptein
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Additional information

Supplementary Material available from the authors: Two tables containing the total number of mappings resulting from the graph search procedure for simulated and experimental NOE data.

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van Geerestein-Ujah, E.C., Slijper, M., Boelens, R. et al. Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: Application to the lac repressor headpiece. J Biomol NMR 6, 67–78 (1995). https://doi.org/10.1007/BF00417493

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  • DOI: https://doi.org/10.1007/BF00417493

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