Investigation of the impact of PTMs on the protein backbone conformation

Craveur, Pierrick; Narwani, Tarun J.; Rebehmed, Joseph; de Brevern, Alexandre G.

doi:10.1007/s00726-019-02747-w

Original Article
Published: 10 June 2019

Investigation of the impact of PTMs on the protein backbone conformation

Pierrick Craveur^1,2,3,4,5^na1^na2,
Tarun J. Narwani^1,2,3,4^na1^na2,
Joseph Rebehmed^1,2,3,4,6 &
Alexandre G. de Brevern ORCID: orcid.org/0000-0001-7112-5626^1,2,3,4

Amino Acids volume 51, pages 1065–1079 (2019)Cite this article

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Abstract

Post-translational modifications (PTMs) are known to play a critical role in the regulation of protein functions. Their impact on protein structures and their link to disorder regions have already been spotted in the past decade. Nonetheless, the high diversity of PTM types and the multiple schemes of protein modifications (multiple PTMs, of different types, at different time, etc.) make difficult the direct confrontation of PTM annotations and protein structure data. Therefore, we analyzed the impact of the residue modifications on the protein structures at the local level. Thanks to a dedicated structure database, namely PTM-SD, a large screen of PTMs have been done and analyzed at local protein conformation levels using the structural alphabet protein blocks (PBs). We investigated the relation between PTMs and the backbone conformation of modified residues, of their local environment, and at the level of the complete protein structure. The two main PTM types (N-glycosylation and phosphorylation) have been studied in non-redundant datasets, and then four different proteins were focused, covering three types of PTMs: N-glycosylation in renin endopeptidase and liver carboxylesterase, phosphorylation in cyclin-dependent kinase 2 (CDK2), and methylation in actin. We observed that PTMs could either stabilize or destabilize the backbone structure, at a local and global scale, and that these effects depend on the PTM types.

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Acknowledgements

This work was supported by grants from the Ministry of Research (France), University of Paris Diderot, Sorbonne Paris Cité, National Institute for Blood Transfusion (INTS, France), and Institute for Health and Medical Research (INSERM, France). PC acknowledges grant from the French Ministry of Research. Calculations were done on SGI cluster granted by Conseil Régional—Ile de France and INTS (SESAME Grant). The authors were granted access to high-performance computing (HPC) resources at the French National Computing Center CINES under Grant no. c2013037147 funded by the GENCI (Grand Equipement National de Calcul Intensif). TN and AdB acknowledge the Indo-French Centre for the Promotion of Advanced Research/CEFIPRA for collaborative Grant (Number 5302-2). This study was supported by a grant from the Laboratory of Excellence GR-Ex, reference ANR-11-LABX-0051. The labex GR-Ex is funded by the program Investissements d’avenir of the French National Research Agency, reference ANR-11-IDEX-0005-02. This work is supported by a grant from the French National Research Agency (ANR): NaturaDyRe (ANR-2010-CD2I-014-04) to JR and AdB.

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The funding bodies have no role in the design of the study and collection, analysis, interpretation of data, and in writing the manuscript.

Author information

Pierrick Craveur and Tarun J. Narwani contributed equally.
Joseph Rebehmed and Alexandre G. de Brevern contributed equally.

Affiliations

INSERM UMR_S 1134, BIGR, DSIMB, 75739, Paris, France
Pierrick Craveur, Tarun J. Narwani, Joseph Rebehmed & Alexandre G. de Brevern
Université de Paris, Université de la Réunion, l’Université des Antilles, UMR_S 1134, 6, rue Alexandre Cabanel, 75739, Paris Cedex 15, France
Pierrick Craveur, Tarun J. Narwani, Joseph Rebehmed & Alexandre G. de Brevern
Institut National de la Transfusion Sanguine (INTS), 75739, Paris, France
Pierrick Craveur, Tarun J. Narwani, Joseph Rebehmed & Alexandre G. de Brevern
Laboratoire d’Excellence GR-Ex, 75739, Paris, France
Pierrick Craveur, Tarun J. Narwani, Joseph Rebehmed & Alexandre G. de Brevern
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
Pierrick Craveur
Department of Computer Science and Mathematics, Lebanese American University, Byblos, 1h401 2010, Lebanon
Joseph Rebehmed

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Pierrick Craveur
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Tarun J. Narwani
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Alexandre G. de Brevern
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Craveur, P., Narwani, T.J., Rebehmed, J. et al. Investigation of the impact of PTMs on the protein backbone conformation. Amino Acids 51, 1065–1079 (2019). https://doi.org/10.1007/s00726-019-02747-w

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Received: 18 December 2018
Accepted: 18 May 2019
Published: 10 June 2019
Issue Date: 01 July 2019
DOI: https://doi.org/10.1007/s00726-019-02747-w

Keywords

Rigidity
Mobility
Deformability
N-Glycosylation
Phosphorylation
Methylation
Statistics
Renin endopeptidase
Liver carboxylesterase
Cyclin-dependent kinase 2 (CDK2)
Actin