Post-translational modifications in proteins: resources, tools and prediction methods

Abstract

Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

“…Additionally, they describe glycosylation as one of the most complex PTMs, but they assert that the process is crucial in excretory proteins' folding. This assertion is confirmed by Ramazi and Zahiri [142], who remarkably linked glycosylation, or the lack thereof, to the onset of conditions such as cancer and diabetes in humans. Previously, Goto et al [145] had reviewed structures and functions of O-glycosylation in fungi, providing a dossier of its cellular usefulness.…”

“…Such protein functionality imbues in fungi, for example, virulence and pathogenicity [ 141 ]. Other examples of PTMs can be observed in proteins found in the cell membrane responsible for cell-to-cell interactions or secretory functions, which is extracellularly useful [ 142 ]. PTMs may be reversible or irreversible; however, external factors may cause irreversible changes to already modified proteins, which inevitably affects their ability to function as well.…”

“…Most fungal secretory proteins are glycosylated through the action of O-mannosyltransferase and several other glycosyltransferases as they move from the endoplasmic reticulum to the golgi apparatus before reaching the cell exterior. These modifications have been reported to add stability and solubility to extracellular proteins [ 142 , 145 , 146 ]. PTMs therefore play an important role in enzyme production strategies, especially when the research progression strategies may involve cloning and/or artificial synthesis.…”

The Pivotal Immunomodulatory and Anti-Inflammatory Effect of Histone-Lysine N-Methyltransferase in the Glioma Microenvironment: Its Biomarker and Therapy Potentials

“…Posttranslational modifications (PTMs) are covalent processing actions that transform the structure and function of a protein via the proteolytic cleavage as well as addition of a modifying group, like acetyl, glycosyl, methyl, and phosphoryl, to one or more amino acids [ 16 , 34 , 35 ]. PTMs are often revisable or irreversible, and they participate in several critical biological processes by expressively affecting the structure as well as dynamics of proteins [ 16 , 35 ].…”

“…Posttranslational modifications (PTMs) are covalent processing actions that transform the structure and function of a protein via the proteolytic cleavage as well as addition of a modifying group, like acetyl, glycosyl, methyl, and phosphoryl, to one or more amino acids [ 16 , 34 , 35 ]. PTMs are often revisable or irreversible, and they participate in several critical biological processes by expressively affecting the structure as well as dynamics of proteins [ 16 , 35 ]. PTMs often influence several protein behaviors as well as characteristics such as enzyme function and assembly, protein-protein interactions, protein lifespan, protein solubility, protein folding, protein localization, cell-cell as well as cell-matrix interactions, molecular trafficking, and receptor activation [ 16 , 35 ].…”