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GH32 family activity: a topological approach through protein contact networks

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Abstract

Key message

The application of Protein Contact Networks methodology allowed to highlight a novel response of border region between the two domains to substrate binding.

Abstract

Glycoside hydrolases (GH) are enzymes that mainly hydrolyze the glycosidic bond between two carbohydrates or a carbohydrate and a non-carbohydrate moiety. These enzymes are involved in many fundamental and diverse biological processes in plants. We have focused on the GH32 family, including enzymes very similar in both sequence and structure, each having however clear specificities of substrate preferences and kinetic properties. Structural and topological differences among proteins of the GH32 family have been here identified by means of an emerging approach (Protein Contact network, PCN) based on the formalization of 3D structures as contact networks among amino-acid residues. The PCN approach proved successful in both reconstructing the already known functional domains and in identifying the structural counterpart of the properties of GH32 enzymes, which remain uncertain, like their allosteric character. The main outcome of the study was the discovery of the activation upon binding of the border (cleft) region between the two domains. This reveals the allosteric nature of the enzymatic activity for all the analyzed forms in the GH32 family, a character yet to be highlighted in biochemical studies. Furthermore, we have been able to recognize a topological signature (graph energy) of the different affinity of the enzymes towards small and large substrates.

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Authors and Affiliations

  1. Unit of Chemical-physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy

    Luisa Di Paola & Alessandra Ridolfi

  2. Unit of Food Science and Nutrition, Department of Medicine, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy

    Sara Cimini & Laura De Gara

  3. Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy

    Alessandro Giuliani

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  1. Sara Cimini
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  2. Luisa Di Paola
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  3. Alessandro Giuliani
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  4. Alessandra Ridolfi
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  5. Laura De Gara
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Correspondence to Luisa Di Paola.

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Cimini, S., Di Paola, L., Giuliani, A. et al. GH32 family activity: a topological approach through protein contact networks. Plant Mol Biol 92, 401–410 (2016). https://doi.org/10.1007/s11103-016-0515-2

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  • DOI: https://doi.org/10.1007/s11103-016-0515-2

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