Database of protein complexes with multivalent binding ability: Bival-bind

Authors

  • Tim Meyer,

    1. Fachbereich Biologie Chemie, Pharmazie/Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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  • Ernst-Walter Knapp

    Corresponding author
    1. Fachbereich Biologie Chemie, Pharmazie/Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
    • Correspondence to: E.-W. Knapp, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Fabeckstrasse 36A, 14195 Berlin, Germany. E-mail: knapp@chemie.fu-berlin.de

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ABSTRACT

Phenomena of multivalent binding of ligands with receptors are ubiquitous in biology and of growing interest in material sciences. Multivalency can enhance binding affinity dramatically. To understand the mechanism of multivalent binding in more detail model systems of bi- and multivalent receptors are needed, but are difficult to find. Furthermore it is useful to know about multivalent receptors, which can serve as targets to design multivalent drugs. The present contribution tries to close this gap. The Bival-Bind database (http://agknapp.chemie.fu-berlin.de/bivalbind) provides a relatively complete list – 2073 protein complexes with less than 90% sequence identity – out of the protein database, which can serve as bi- or multivalent receptors. Steric clashes of molecular spacers – necessary to connect the monomeric ligand units – with the receptor surface can diminish binding affinity dramatically and, thus, abolish the expected enhancement of binding affinity due to the multivalency. The potential multivalent receptors in the Bival-Bind database are characterized with respect to the receptor surface topography. A height profile between the receptor binding pockets is provided, which is an important information to estimate the influence of unfavorable spacer receptor interaction. Proteins 2014; 82:744–751. © 2013 Wiley Periodicals, Inc.

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