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Correlation to Protein Conformation of Wide-Angle X-ray Scatter Parameters

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Abstract

In the last decade, several studies have reported that Wide-Angle X-ray Scattering (WAXS) from protein in solution contains valuable information about protein secondary and tertiary structures. Nevertheless, the use of such information will remain limited until a clear understanding of the correlation between protein structural elements and WAXS profile regions is established. In this work, large number of possible protein conformations is generated using comparative modeling (LOOPP & PHYRE servers) of nine different proteins representing six main protein classes (SCOP database). After model validation (SAVES server), protein structural elements of the selected models are retrieved (Swiss PDB Viewer & VORONOIA) and their corresponding WAXS profiles are generated (CRYSOL). The correlations between seven elements of protein structure (alpha helix, beta sheet and random coil content, alpha to beta ratio, alpha to random coil ratio, average packing density and number of residues) and seven WAXS profile parameters (Full Width at Half Maximum of two main scattering peaks of interest, their areas, positions and ratio of intensities) are investigated. Results revealed high (up to 0.75) and moderate (0.30–0.50) correlations between some of the suggested profile parameters and investigated protein structural elements indicating that these parameters represent a useful probe of protein conformation. Moreover, a high observed correlation between the degree of fitting of model to reference structures and the degree of fitting of their corresponding WAXS profiles suggests that the latter can be used in experimental model validation.

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Abbreviations

WAXS:

Wide-angle X-ray scattering

SAXS:

Small angle X-ray scattering

FWHM:

Full width at half maximum

LOOPP:

Learning, observing and outputting protein patterns

PHYRE:

Protein homology/analogy recognition engine

SCOP:

Structure classification of proteins

SAVES:

Structural analysis and verification server

PDB:

Protein data bank

RMSD:

Root mean square difference

AUC:

Area under curve

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Acknowledgments

This work was supported by the Graduate Research Challenge Fund (GRCF) from the Faculty of Science, Cairo University.

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Authors and Affiliations

  1. Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt

    Wael M. Elshemey, Abdo A. Elfiky & Wissam A. Gawad

Authors
  1. Wael M. Elshemey
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  2. Abdo A. Elfiky
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  3. Wissam A. Gawad
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Correspondence to Wael M. Elshemey.

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Elshemey, W.M., Elfiky, A.A. & Gawad, W.A. Correlation to Protein Conformation of Wide-Angle X-ray Scatter Parameters. Protein J 29, 545–550 (2010). https://doi.org/10.1007/s10930-010-9291-z

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