Grafting of functional motifs onto protein scaffolds identified by PDB screening – an efficient route to design optimizable protein binders

Authors

  • Rym Tlatli,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Hervé Nozach,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Guillaume Collet,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Fabrice Beau,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Laura Vera,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Enrico Stura,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Vincent Dive,

    1. Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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  • Philippe Cuniasse

    Corresponding author
    • Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, Gif-sur-Yvette, France
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Correspondence

P. Cuniasse, Service d'Ingénierie Moléculaire des Protéines, Institut de Biologie et Technologies de Saclay (IBITEC-S), Commissariat à l'Energie Atomique, F-91191 Gif-sur-Yvette, France

Fax: +33 1 69 08 90 71

Tel: +33 1 69 08 56 35

E-mail: philippe.cuniasse@cea.fr

Abstract

Artificial miniproteins that are able to target catalytic sites of matrix metalloproteinases (MMPs) were designed using a functional motif-grafting approach. The motif corresponded to the four N-terminal residues of TIMP-2, a broad-spectrum protein inhibitor of MMPs. Scaffolds that are able to reproduce the functional topology of this motif were obtained by exhaustive screening of the Protein Data Bank (PDB) using stamps software (search for three-dimensional atom motifs in protein structures). Ten artificial protein binders were produced. The designed proteins bind catalytic sites of MMPs with affinities ranging from 450 nm to 450 μm prior to optimization. The crystal structure of one artificial binder in complex with the catalytic domain of MMP-12 showed that the inter-molecular interactions established by the functional motif in the artificial binder corresponded to those found in the MMP-14–TIMP-2 complex, albeit with some differences in geometry. Molecular dynamics simulations of the ten binders in complex with MMP-14 suggested that these scaffolds may allow partial reproduction of native inter-molecular interactions, but differences in geometry and stability may contribute to the lower affinity of the artificial protein binders compared to the natural protein binder. Nevertheless, these results show that the in silico design method used provides sets of protein binders that target a specific binding site with a good rate of success. This approach may constitute the first step of an efficient hybrid computational/experimental approach to protein binder design.

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