Investigation of the impact of PTMs on the protein backbone conformation

TL;DR

This study analyzes how different post-translational modifications influence protein backbone conformation at a local level, revealing that PTMs can stabilize or destabilize structures depending on their type.

Contribution

The paper introduces a comprehensive analysis of PTM effects on protein structure using the PTM-SD database and structural alphabet Protein Blocks, focusing on key PTM types.

Findings

PTMs can stabilize or destabilize backbone conformation.

Effects depend on PTM type and local environment.

Specific PTMs like N-glycosylation and phosphorylation have distinct structural impacts.

Abstract

Post-Translational Modifications (PTMs) are known to play a critical role in the regulation of the protein functions. Their impact on protein structures, and their link to disorder regions have already been spotted on the past decade. Nonetheless, the high diversity of PTMs 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 structures data.We so analyzed the impact of the residue modifications on the protein structures at local level. Thanks to a dedicated structure database, namely PTM-SD, a large screen of PTMs have been done and analyze at a 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, 4 different proteins were focused, covering 3 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.