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Protein Flexibility and Ligand Rigidity: A Thermodynamic and Kinetic Study of ITAM-Based Ligand Binding to Syk Tandem SH2

Authors

  • Nico J. de Mol Dr.,

    1. Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University (UIPS), Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Fax: (+31) 30-253-6655
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  • M. Isabel Catalina Dr.,

    1. Department of Biomolecular Mass Spectrometry, UIPS and Bijvoet Center for Molecular Sciences, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    2. Current address: Department of Parasitology, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden
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  • Frank J. Dekker Dr.,

    1. Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University (UIPS), Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Fax: (+31) 30-253-6655
    2. Current address: Max Planck Institute for Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
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  • Marcel J. E. Fischer Dr.,

    1. Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University (UIPS), Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Fax: (+31) 30-253-6655
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  • Albert J. R. Heck Prof. Dr.,

    1. Department of Biomolecular Mass Spectrometry, UIPS and Bijvoet Center for Molecular Sciences, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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  • Rob M. J. Liskamp Prof. Dr.

    1. Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University (UIPS), Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Fax: (+31) 30-253-6655
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Abstract

The Syk tandem Src homology 2 domain (Syk tSH2) constitutes a flexible protein module involved in the regulation of Syk kinase activity. The Syk tSH2 domain is assumed to function by adapting the distance between its two SH2 domains upon bivalent binding to diphosphotyrosine ligands. A thermodynamic and kinetic analysis of ligand binding was performed by using surface plasmon resonance (SPR). Furthermore, the effect of binding on the Syk tSH2 structural dynamics was probed by hydrogen/deuterium exchange and electrospray mass spectrometry (ESI-MS). Two ligands were studied: 1, a flexible peptide derived from the tSH2 recognition ITAM sequence at the γ chain of the FcεRI-receptor, and 2, a ligand in which the amino acids between the two SH2 binding motifs in ligand 1 have been replaced by a rigid linker of comparable length. Both ligands display comparable affinity for Syk tSH2 at 25 °C, yet a major difference in thermodynamics is observed. Upon binding of the rigid ligand, 2, the expected entropy advantage is not realized. On the contrary, 2 binds with a considerably higher entropy price of ∼9 kcal mol−1, which is attributed to a further decrease in protein flexibility upon binding to this rigid ligand. The significant reduction in deuterium incorporation in the Syk tSH2 protein upon binding of either 1 or 2, as monitored by ESI-MS, indicates a major reduction in protein dynamics upon binding. The results are consistent with a two-step binding model: after an initial binding step, a rapid structural change of the protein occurs, followed by a second binding step. Such a bivalent binding model allows high affinity and fast dissociation kinetics, which are very important in transient signal-transduction processes.

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