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Cells
Special Issues
PTM Rewired Protein Network in Diseases
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PTM Rewired Protein Network in Diseases

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Pathology".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 7266

Special Issue Editors

Prof. Dr. Huadong Liu

E-Mail Website
Guest Editor
School of Life Science, Xian Jiaotong University, Xi’an 710049, China
Interests: proteomics
Prof. Dr. Shawn Li

E-Mail Website
Guest Editor
Department of Biochemistry, Western University, London, ON, Canada
Interests: proteomics

Special Issue Information

Dear Colleagues,

Protein–protein interactions (PPIs) play a central role in almost all cellular processes. However, protein interactions driven by posttranslational modifications (PTMs) such as phosphorylation, which comprises a significant part of the PPI network, have proven difficult to decipher systematically. Technological advances such as Apex, TurboID, and Pup-it were developed recently. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry. In combination with newly developed superbinders and prediction methods, PTM regulated dynamic protein networks were identified in depth, which enabled the elucidation of an incredibly complex PPI network within the cell.

This Special Issue on “PTM Rewired Protein Network in Diseases” aims to introduce new technologies used in protein network identification and to present a selection of their many important contributions to the molecular understanding of diseases.

We look forward to your contributions.

Prof. Dr. Huadong Liu
Prof. Dr. Shawn Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • protein network
  • post-translational modifications
  • proximity labeling

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Published Papers (2 papers)

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Review

17 pages, 2066 KiB  
Review
Mapping the Protein Kinome: Current Strategy and Future Direction
by Zhanwu Hou and Huadong Liu
Cells 2023, 12(6), 925; https://doi.org/10.3390/cells12060925 - 17 Mar 2023
Cited by 2 | Viewed by 2374
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular [...] Read more.
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored. Full article
(This article belongs to the Special Issue PTM Rewired Protein Network in Diseases)
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44 pages, 6654 KiB  
Review
Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review
by Igor Tvaroška, Stanislav Kozmon and Juraj Kóňa
Cells 2023, 12(2), 324; https://doi.org/10.3390/cells12020324 - 14 Jan 2023
Cited by 18 | Viewed by 4512
Abstract
Integrins are heterodimeric glycoproteins crucial to the physiology and pathology of many biological functions. As adhesion molecules, they mediate immune cell trafficking, migration, and immunological synapse formation during inflammation and cancer. The recognition of the vital roles of integrins in various diseases revealed [...] Read more.
Integrins are heterodimeric glycoproteins crucial to the physiology and pathology of many biological functions. As adhesion molecules, they mediate immune cell trafficking, migration, and immunological synapse formation during inflammation and cancer. The recognition of the vital roles of integrins in various diseases revealed their therapeutic potential. Despite the great effort in the last thirty years, up to now, only seven integrin-based drugs have entered the market. Recent progress in deciphering integrin functions, signaling, and interactions with ligands, along with advancement in rational drug design strategies, provide an opportunity to exploit their therapeutic potential and discover novel agents. This review will discuss the molecular modeling methods used in determining integrins’ dynamic properties and in providing information toward understanding their properties and function at the atomic level. Then, we will survey the relevant contributions and the current understanding of integrin structure, activation, the binding of essential ligands, and the role of molecular modeling methods in the rational design of antagonists. We will emphasize the role played by molecular modeling methods in progress in these areas and the designing of integrin antagonists. Full article
(This article belongs to the Special Issue PTM Rewired Protein Network in Diseases)
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