scholarly journals Posttranslational modifications in proteins: resources, tools and prediction methods

Database ◽  
2021 ◽  
Author(s):  
Shahin Ramazi ◽  
Javad Zahiri
Keyword(s):  
Computational Methods ◽  
Posttranslational Modifications ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Cellular Processes ◽  
Online Databases ◽  
Different Types ◽  
Protein Functions ◽  
And Function ◽  
Molecular Regulatory Mechanisms

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.

scholarly journals Knockout of the Golgi stacking proteins GRASP55 and GRASP65 impairs Golgi structure and function

2017 ◽  
Vol 28 (21) ◽  
pp. 2833-2842 ◽  
Author(s):  
Michael E. Bekier ◽  
Leibin Wang ◽  
Jie Li ◽  
Haoran Huang ◽  
Danming Tang ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Protein Trafficking ◽  
Critical Role ◽  
Hek293 Cells ◽  
Double Knockout ◽  
Knock Out ◽  
Golgi Stack ◽  
Cellular Processes ◽  
Golgi Structure ◽  
And Function

Golgi reassembly stacking protein of 65 kDa (GRASP65) and Golgi reassembly stacking protein of 55 kDa (GRASP55) were originally identified as Golgi stacking proteins; however, subsequent GRASP knockdown experiments yielded inconsistent results with respect to the Golgi structure, indicating a limitation of RNAi-based depletion. In this study, we have applied the recently developed clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology to knock out GRASP55 and GRASP65, individually or in combination, in HeLa and HEK293 cells. We show that double knockout of GRASP proteins disperses the Golgi stack into single cisternae and tubulovesicular structures, accelerates protein trafficking, and impairs accurate glycosylation of proteins and lipids. These results demonstrate a critical role for GRASPs in maintaining the stacked structure of the Golgi, which is required for accurate posttranslational modifications in the Golgi. Additionally, the GRASP knockout cell lines developed in this study will be useful tools for studying the role of GRASP proteins in other important cellular processes.

scholarly journals Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Bo Sun ◽  
Menghuan Zhang ◽  
Peng Cui ◽  
Hong Li ◽  
Jia Jia ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Single Nucleotide ◽  
Inherited Diseases ◽  
Cellular Processes ◽  
Protein Functions ◽  
Human Proteins ◽  
Working Together ◽  
Single Nucleotide Variations ◽  
Protein Posttranslational Modifications ◽  
Relationship Of

Protein posttranslational modifications (PTMs) play key roles in a variety of protein activities and cellular processes. Different PTMs show distinct impacts on protein functions, and normal protein activities are consequences of all kinds of PTMs working together. With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. The damaged PTMs could be the reason of the development of some human diseases. In this study, we elucidated the proteome wide relationship of eight damaged PTMs to human inherited diseases and cancers. Some human inherited diseases or cancers may be the consequences of the interactions of damaged PTMs, rather than the result of single damaged PTM site.

scholarly journals Microtubule Regulation and Function during Virus Infection

2017 ◽  
Vol 91 (16) ◽  
Author(s):  
Mojgan H. Naghavi ◽  
Derek Walsh
Keyword(s):  
Posttranslational Modifications ◽  
Intracellular Transport ◽  
Spatial Organization ◽  
Virus Particles ◽  
Cellular Processes ◽  
Wide Range ◽  
Associated Proteins ◽  
And Function ◽  
Induced Changes ◽  
Growth Pause

ABSTRACT Microtubules (MTs) form a rapidly adaptable network of filaments that radiate throughout the cell. These dynamic arrays facilitate a wide range of cellular processes, including the capture, transport, and spatial organization of cargos and organelles, as well as changes in cell shape, polarity, and motility. Nucleating from MT-organizing centers, including but by no means limited to the centrosome, MTs undergo rapid transitions through phases of growth, pause, and catastrophe, continuously exploring and adapting to the intracellular environment. Subsets of MTs can become stabilized in response to environmental cues, acquiring distinguishing posttranslational modifications and performing discrete functions as specialized tracks for cargo trafficking. The dynamic behavior and organization of the MT array is regulated by MT-associated proteins (MAPs), which include a subset of highly specialized plus-end-tracking proteins (+TIPs) that respond to signaling cues to alter MT behavior. As pathogenic cargos, viruses require MTs to transport to and from their intracellular sites of replication. While interactions with and functions for MT motor proteins are well characterized and extensively reviewed for many viruses, this review focuses on MT filaments themselves. Changes in the spatial organization and dynamics of the MT array, mediated by virus- or host-induced changes to MT regulatory proteins, not only play a central role in the intracellular transport of virus particles but also regulate a wider range of processes critical to the outcome of infection.

scholarly journals Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 472 ◽  
Author(s):  
Fernando Fontove ◽  
Gabriel Del Rio
Keyword(s):  
Protein Structure ◽  
Three Dimensional ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Computationally Efficient ◽  
Residue Contact ◽  
Contact Maps ◽  
Effective Models ◽  
And Function ◽  
Potential Use

Proteins are characterized by their structures and functions, and these two fundamental aspects of proteins are assumed to be related. To model such a relationship, a single representation to model both protein structure and function would be convenient, yet so far, the most effective models for protein structure or function classification do not rely on the same protein representation. Here we provide a computationally efficient implementation for large datasets to calculate residue cluster classes (RCCs) from protein three-dimensional structures and show that such representations enable a random forest algorithm to effectively learn the structural and functional classifications of proteins, according to the CATH and Gene Ontology criteria, respectively. RCCs are derived from residue contact maps built from different distance criteria, and we show that 7 or 8 Å with or without amino acid side-chain atoms rendered the best classification models. The potential use of a unified representation of proteins is discussed and possible future areas for improvement and exploration are presented.

scholarly journals FADD in Cancer: Mechanisms of Altered Expression and Function, and Clinical Implications

Cancers ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1462 ◽  
Author(s):  
José L Marín-Rubio ◽  
Laura Vela-Martín ◽  
José Fernández-Piqueras ◽  
María Villa-Morales
Keyword(s):  
Posttranslational Modifications ◽  
Cell Cycle Control ◽  
Regulation Of Gene Expression ◽  
Death Receptor ◽  
Clinical Implications ◽  
Altered Expression ◽  
Cellular Processes ◽  
Potential Biomarker ◽  
And Function ◽  
And Control

FADD was initially described as an adaptor molecule for death receptor-mediated apoptosis, but subsequently it has been implicated in nonapoptotic cellular processes such as proliferation and cell cycle control. During the last decade, FADD has been shown to play a pivotal role in most of the signalosome complexes, such as the necroptosome and the inflammasome. Interestingly, various mechanisms involved in regulating FADD functions have been identified, essentially posttranslational modifications and secretion. All these aspects have been thoroughly addressed in previous reviews. However, FADD implication in cancer is complex, due to pleiotropic effects. It has been reported either as anti- or protumorigenic, depending on the cell type. Regulation of FADD expression in cancer is a complex issue since both overexpression and downregulation have been reported, but the mechanisms underlying such alterations have not been fully unveiled. Posttranslational modifications also constitute a relevant mechanism controlling FADD levels and functions in tumor cells. In this review, we aim to provide detailed, updated information on alterations leading to changes in FADD expression and function in cancer. The participation of FADD in various biological processes is recapitulated, with a mention of interesting novel functions recently proposed for FADD, such as regulation of gene expression and control of metabolic pathways. Finally, we gather all the available evidence regarding the clinical implications of FADD alterations in cancer, especially as it has been proposed as a potential biomarker with prognostic value.

scholarly journals A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation

2019 ◽  
Author(s):  
Kotaro Tsuboyama ◽  
Tatsuya Osaki ◽  
Eriko Suzuki-Matsuura ◽  
Hiroko Kozuka-Hata ◽  
Yuki Okada ◽  
...  
Keyword(s):  
Heat Shock ◽  
High Salinity ◽  
Therapeutic Potential ◽  
Extreme Conditions ◽  
Heat Resistant ◽  
Different Types ◽  
Protein Functions ◽  
Client Proteins ◽  
Protein Instability ◽  
And Function

AbstractProteins are typically denatured and aggregated by heat. Exceptions to this principle include highly disordered and heat-resistant proteins found in extremophiles, which help these organisms tolerate extreme conditions such as drying, freezing, and high salinity. In contrast, the functions of heat-soluble proteins in non-extremophilic organisms including humans remain largely unexplored. Here we report that heat-resistant obscure (Hero) proteins, which remain soluble after boiling at 95°C, are widespread in Drosophila and humans. Hero proteins are hydrophilic and highly charged, and function to stabilize various “client” proteins, protecting them from denaturation even under stress conditions such as heat shock, desiccation, and exposure to organic solvents. Hero proteins can also block several different types of pathological protein aggregations in cells and in Drosophila strains that model neurodegenerative diseases. Moreover, Hero proteins can extend lifespan of Drosophila. Our study reveals that organisms naturally use Hero proteins as molecular shields to stabilize protein functions, highlighting their biotechnological and therapeutic potential.

Mutational studies of protein structures and their stabilities

1992 ◽  
Vol 25 (2) ◽  
pp. 205-250 ◽  
Author(s):  
David Shortle
Keyword(s):  
Amino Acid ◽  
Functional Role ◽  
Hydrophobic Interactions ◽  
Protein Structures ◽  
Three Dimensional ◽  
Rnase A ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
X Ray Crystallography ◽  
And Function

The fundamental relationship between structure and function has served to guide investigations into the workings of living systems at all levels - from the whole organism to individual cells on down to individual molecules. When X-ray crystallography began to reveal the three-dimensional structures of proteins like myoglobin, lysozyme and RNase A, protein chemists were well prepared to draw inferences about functional mechanisms from the precise positioning of amino acid residues they could see. The close proximity between an amino acid side chain and a chemical group on a bound ligand strongly suggests a functional role for that side chain in binding affinity and specificity. Likewise, the nearly universal finding of large clusters of hydrophobic side chains buried in the core of proteins strongly supports a major functional role of hydrophobic interactions in protein folding and stability. Even though eminently plausible hypotheses like these, grounded in the most fundamental principles of chemistry and the logic of structure–function relationships, become widely accepted and make their way into textbooks, protein chemists have felt compelled to search for ways to test them and put them on a more quantitative basis.

Research progress in protein posttranslational modification site prediction

2018 ◽  
Vol 18 (4) ◽  
pp. 220-229 ◽  
Author(s):  
Wenying He ◽  
Leyi Wei ◽  
Quan Zou
Keyword(s):  
Posttranslational Modifications ◽  
Cell Biology ◽  
Research Progress ◽  
Future Research ◽  
Cellular Processes ◽  
Machine Learning Methods ◽  
Bioinformatics Tools ◽  
Glycosylation Sites ◽  
Almost All ◽  
And Function

AbstractPosttranslational modifications (PTMs) play an important role in regulating protein folding, activity and function and are involved in almost all cellular processes. Identification of PTMs of proteins is the basis for elucidating the mechanisms of cell biology and disease treatments. Compared with the laboriousness of equivalent experimental work, PTM prediction using various machine-learning methods can provide accurate, simple and rapid research solutions and generate valuable information for further laboratory studies. In this review, we manually curate most of the bioinformatics tools published since 2008. We also summarize the approaches for predicting ubiquitination sites and glycosylation sites. Moreover, we discuss the challenges of current PTM bioinformatics tools and look forward to future research possibilities.

Chaperonin as the normal controls and pathological anti-stress response in the human reproductive system

2016 ◽  
pp. 126-129
Author(s):  
M. Makarenko ◽  
◽  
D. Hovsyeyev ◽  
L. Sydoryk ◽  
◽  
...  
Keyword(s):  
Reproductive System ◽  
Stress Proteins ◽  
Physiological Stress ◽  
Protein Complexes ◽  
Reproductive Function ◽  
Intercellular Signaling ◽  
Toll Like Receptors ◽  
Wide Range ◽  
Protein Functions ◽  
And Function

Different kinds of physiological stress cause mass changes in the cells, including the changes in the structure and function of the protein complexes and in separate molecules. The protein functions is determined by its folding (the spatial conclusion), which depends on the functioning of proteins of thermal shock- molecular chaperons (HSPs) or depends on the stress proteins, that are high-conservative; specialized proteins that are responsible for the correct proteinaceous folding. The family of the molecular chaperones/ chaperonins/ Hsp60 has a special place due to the its unique properties of activating the signaling cascades through the system of Toll-like receptors; it also stimulates the cells to produce anti- inflammatory cytokines, defensins, molecules of cell adhesion and the molecules of MHC; it functions as the intercellular signaling molecule. The pathological role of Hsp60 is established in a wide range of illnesses, from diabetes to atherosclerosis, where Hsp60 takes part in the regulation of both apoptosis and the autoimmune processes. The presence of the HSPs was found in different tissues that are related to the reproductive system. Key words: molecular chaperons (HSPs), Toll-like receptors, reproductive function, natural auto antibody.

Formation and Function of Formate in the Side-Chain Alkylation of Toluene with Methanol

2013 ◽  
Vol 33 (6) ◽  
pp. 1041-1047
Author(s):  
Dan LIN ◽  
Huimin ZHAO ◽  
Xiaoyue ZHANG ◽  
Dongxue LAN ◽  
Yuan CHUN
Keyword(s):  
Side Chain ◽  
And Function
Sign in / Sign up

Export Citation Format

Share Document