Efficient characterization of protein secondary structure in terms of screw motions

Acta Crystallographica. Section D, Biological Crystallography
G R Kneller, Paolo A Calligari

Abstract

A simple and efficient method is presented to describe the secondary structure of proteins in terms of orientational distances between consecutive peptide planes and local helix parameters. The method uses quaternion-based superposition fits of the protein peptide planes in conjunction with Chasles' theorem, which states that any rigid-body displacement can be described by a screw motion. The helix parameters are derived from the best superposition of consecutive peptide planes and the ;worst' fit is used to define the orientational distance. Applications are shown for standard secondary-structure motifs of peptide chains for several proteins belonging to different fold classes and for a description of structural changes in lysozyme under hydrostatic pressure. In the latter case, published reference data obtained by X-ray crystallography and by structural NMR measurements are used.

Citations

Aug 5, 2006·Proceedings of the National Academy of Sciences of the United States of America·Janet E DeaneSusan M Lea
May 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ariel J BlockerSusan M Lea
Nov 16, 2012·Acta Crystallographica. Section D, Biological Crystallography·Paolo A Calligari, Gerald R Kneller
Oct 5, 2013·The Journal of Chemical Physics·Konrad HinsenAntti J Niemi
Jun 11, 2009·The Journal of Chemical Physics·Seungho Choe, Michael Grabe
Sep 4, 2009·The Journal of Chemical Physics·Joel Ireta, Matthias Scheffler
Oct 27, 2012·Journal of Molecular Graphics & Modelling·Andrew J Hanson, Sidharth Thakur
Jul 7, 2015·Acta Crystallographica. Section D, Biological Crystallography·Gerald R Kneller, Konrad Hinsen
May 23, 2015·The Journal of Physical Chemistry. B·Paolo A CalligariGerald R Kneller
Nov 2, 2015·The Journal of Chemical Physics·Sridhar NeelamrajuRoy L Johnston
Mar 27, 2021·Journal of Chemical Information and Modeling·Francisco Adasme-CarreñoJoel Ireta
Aug 9, 2011·Journal of Chemical Theory and Computation·Joel Ireta
Aug 14, 2012·Journal of Chemical Theory and Computation·Julia RomanowskaJoanna Trylska

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