Computational simulations of the conformational behaviour of the adhesive proteins RGDS fragment |
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Authors: | M Cotrait M Kreissler J Hoflack J-M Lehn B Maigret |
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Institution: | (1) Laboratoire de Cristallographie et Physique Cristalline, URA CNRS No. 144, Université de Bordeaux I, 351, Cours de la Libération, 33405 Talence Cedex, France;(2) Laboratoire de Physicochimie Théorique, URA CNRS No. 503, Chimie Physique A, 351, Cours de la Libération, 33405 Talence Cedex, France;(3) Marion-Merrell Dow Research Center, 16, Rue d'Ankara, BP 447 R/9, 67009 Strasbourg Cedex, France;(4) Laboratoire de Chimie Organique Physique, URA CNRS No. 422, Institut Lebel-Université L. Pasteur, 4, rue Blaise Pascal, 67000 Strasbourg, France |
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Abstract: | Summary Many adhesive proteins present in extracellular matrices and in blood contain the tetrapeptide sequence -Arg-Gly-Asp-Ser- (or RGDS) at their cell recognition site. Since this sequence, or similar ones, was found in many proteins involved in major biological mechanisms, conformational investigations were performed on the RGDS fragment. A preliminary review of available crystal structures indicates that the RxDy sequences exhibit 3 well-defined structural patterns: one corresponding to a strong interaction between the Arg and Asp ionic side chains which are only about 4 Å apart, one with the ions separated by about 8 Å, and another in which the side chains are further apart (about 11 Å).The conformational behaviour of the isolated RGDS fragment was next tackled using sequential building, Monte Carlo and molecular dynamics computational techniques. Analysis of the RGDS sequence conformational possibilities, as simulated in vacuum and in water solution, indicates that they can be classified into several conformational classes, which correspond roughly to the behaviour of the RGDS fragment as observed in protein matrices. This suggests the possibility of understanding the biological role of the RGDS or parent sequences in recognition processes. |
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Keywords: | Adhesive proteins RGDS fragment Adhesins Integrins |
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