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Bioinformatics Advance Access originally published online on December 18, 2007
Bioinformatics 2008 24(4):521-528; doi:10.1093/bioinformatics/btm625
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structural flexibility in proteins: impact of the crystal environment

Konrad Hinsen 1,2

1Centre de Biophysique Moléculaire (CNRS), Rue Charles Sadron, 45071 Orléans Cedex 2, France and 2Synchrotron Soleil, Saint Aubin, B.P. 48, 91192 Gif sur Yvette Cedex, France


  Abstract

Motivation: In the study of the structural flexibility of proteins, crystallographic Debye-Waller factors are the most important experimental information used in the calibration and validation of computational models, such as the very successful elastic network models (ENMs). However, these models are applied to single protein molecules, whereas the experiments are performed on crystals. Moreover, the energy scale in standard ENMs is undefined and must be obtained by fitting to the same data that the ENM is trying to predict, reducing the predictive power of the model.

Results: We develop an elastic network model for the whole protein crystal in order to study the influence of crystal packing and lattice vibrations on the thermal fluctuations of the atom positions. We use experimental values for the compressibility of the crystal to establish the energy scale of our model. We predict the elastic constants of the crystal and compare with experimental data. Our main findings are (1) crystal packing modifies the atomic fluctuations considerably and (2) thermal fluctuations are not the dominant contribution to crystallographic Debye-Waller factors.

Availability: The programs developed for this work are available as supplementary material at Bioinformatics Online.

Contact: hinsen{at}cnrs-orleans.fr

Supplementary information: (1) A full derivation of the normal mode equations in a crystal and in a continuous medium. (2) A movie illustrating the lattice vibrations. Both supplements are available at Bioinformatics Online.

Associate Editor: Anna Tramontano

Received on October 4, 2007; revised on November 19, 2007; accepted on December 15, 2007

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