Exploring protein phosphorylation by combining computational approaches and biochemical methods

Pérez‐Mejías, Gonzalo; Velázquez‐Cruz, Alejandro; Guerra‐Castellano, Alejandra; Baños-Jaime, Blanca; Díaz‐Quintana, Antonio; González‐Arzola, Katiuska; Rosa, Miguel Á. De la; Dı́az-Moreno, Irene

doi:10.1016/j.csbj.2020.06.043

Cited by 40 publications

(31 citation statements)

References 165 publications

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“…The use of non-canonical amino acids aims at a better emulating the physical properties of the target residues—e.g., the volume and/or charge—as compared to canonical substitutions ( Table S1 ) [ 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. A good example is the non-natural residue p-carboxymethyl-L-phenylalanine (pCMF), which has been widely used to mimic tyrosine phosphorylation [ 77 ].…”

Section: Post-translational Modifications Of Cytochrome mentioning

confidence: 99%

Post-Translational Modifications of Cytochrome c in Cell Life and Disease

Guerra‐Castellano

Márquez

Pérez‐Mejías

et al. 2020

IJMS

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Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.

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Section: Post-translational Modifications Of Cytochrome mentioning

confidence: 99%

Post-Translational Modifications of Cytochrome c in Cell Life and Disease

Guerra‐Castellano

Márquez

Pérez‐Mejías

et al. 2020

IJMS

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“…A detailed knowledge of the molecular bases of disease-related dysregulation of PTMs on RBPs hold promise for helping to diagnosis, prognosis and treatment of many severe illnesses by revealing new biomarkers and therapeutic targets. Such a research task will indeed benefit from a multidisciplinary approach that allows investigators to keep pushing the boundaries in this field, through the combination of genomic and proteomic tools, cell-based assays, biophysical techniques and bioinformatic methods ( Foshag et al, 2018 ; Huang R. et al, 2019 ; Liu and Liu, 2020 ; Pérez-Mejías et al, 2020 ; Van Nostrand et al, 2020 ). Nonetheless, further technological and methodological advances will also be necessary to fully unravel the mechanisms behind the PTM control of RBPs.…”

Section: Discussionmentioning

confidence: 99%

Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation

Velázquez‐Cruz

Baños-Jaime

Díaz‐Quintana

et al. 2021

Front. Mol. Biosci.

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Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.

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“…Consensus sequences of SLiMs for protein kinases are characterized and suggested from structural studies on protein kinases in complex with their protein substrates or peptide substrates. In addition to structural approaches, mass spectrometry-based proteomics, phage display, peptide arrays, and computational approaches have been used as major tools for identifying the residues required for optimal substrate phosphorylation/dephosphorylation [ 72 , 73 , 74 , 75 , 76 ].…”

Section: Substrate Recognition With Short Linear Motifs (Slims)mentioning

confidence: 99%

Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases

Seok

2021

Life

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Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.

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Exploring protein phosphorylation by combining computational approaches and biochemical methods

Abstract: Graphical abstract

Cited by 40 publications

References 165 publications

Post-Translational Modifications of Cytochrome c in Cell Life and Disease

Post-Translational Modifications of Cytochrome c in Cell Life and Disease

Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation

Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases

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