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A Review of the Morph Server and the Macromolecular Motions Database: A Standardized System for Analyzing and Visualizing Macromolecular Motions in a Database Framework

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Polymer and Cell Dynamics

Part of the book series: Mathematics and Biosciences in Interaction ((MBI))

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Summary

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a ‘front-end’ server to our database of macromolecular motions, a database that classifies proteins into a limited number of categories, first on the basis of size (distinguishing among fragment, domain, and subunit motions) and then on the basis of packing. Our system attempts to describe a protein motion as a rigid-body rotation of a small ‘core’ relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and, as a byproduct, results in a ‘morph movie.’ We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an ‘evolutionary morph.’ Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of 10 degrees and a maximum C-alpha displacement of 17 Å. Almost all involve at least one large torsion angle charge of >140 degrees. The server is accessible at http://bioinfo.mbb.yale.edu/MolMovDB.

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Authors and Affiliations

  1. San Diego Supercomputer Center, Dept. 505, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0505, USA

    Werner G. Krebs

  2. Department of Molecular Biophysics & Biochemistry, Yale University, P.O. Box 208114, New Haven, CT, 06520-8114, USA

    Mark Gerstein

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  1. Werner G. Krebs
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  2. Mark Gerstein
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Editors and Affiliations

  1. Abteilung Theoretische Biologie Botanisches Institut, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany

    Wolfgang Alt

  2. Department of Mathematics, University of Dundee, 23 Perth Road, Dundee, DDI 4HN, UK

    Mark Chaplain

  3. Institut für Angewandte Mathematik (IAM) Abteilung Wissenschaftliches Rechnen und Numerische Simulation, Universität Bonn, Wegeier Str. 6, D-53115, Bonn, Germany

    Michael Griebel

  4. Bioreact GmbH, Botanisches Institut, Kirschallee 1, 53115, Bonn, Germany

    Jürgen Lenz

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Krebs, W.G., Gerstein, M. (2003). A Review of the Morph Server and the Macromolecular Motions Database: A Standardized System for Analyzing and Visualizing Macromolecular Motions in a Database Framework. In: Alt, W., Chaplain, M., Griebel, M., Lenz, J. (eds) Polymer and Cell Dynamics. Mathematics and Biosciences in Interaction. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8043-5_4

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  • DOI: https://doi.org/10.1007/978-3-0348-8043-5_4

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-0348-9417-3

  • Online ISBN: 978-3-0348-8043-5

  • eBook Packages: Springer Book Archive

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