A new perspective on the analysis of helix-helix packing preferences in globular proteins

Details A new perspective on the analysis of helix-helix packing preferences in globular proteins A new perspective on the analysis of helix-helix packing preferences in globular proteins

2003-04-18

arxiv.org/abs/cond-mat/0304429v1

Physics

Condensed Matter

Soft Condensed Matter

23 pages, 5 figures

Scientific paper

For many years it had been believed that steric compatibility of helix interfaces could be the source of the observed preference for particular angles between neighbouring helices as emerging from statistical analysis of protein databanks. Several elegant models describing how side chains on helices can interdigitate without steric clashes were able to account quite reasonably for the observed distributions. However, it was later recognized (Bowie, 1997 and Walther, 1998) that the ``bare'' measured angle distribution should be corrected to avoid statistical bias. Disappointingly, the rescaled distributions dramatically lost their similarity with theoretical predictions casting many doubts on the validity of the geometrical assumptions and models. In this report we elucidate a few points concerning the proper choice of the random reference distribution. In particular we show the existence of crucial corrections due to the correct implementation of the approach used to discriminate whether two helices are in contact or not and to measure their relative orientations. By using this new rescaling, the ``true'' packing angle preferences are well described, even more than with the original ``bare'' distribution, by regular packing models.

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