Special Issue "Probing the Dynamic Properties of the Kinome"

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (31 May 2015).

Special Issue Editor

Prof. Dr. Lee M. Graves
Website
Guest Editor
Department of Pharmacology, University of NC at Chapel Hill, Genetic Medicine Building, Room 4111, CB# 7365120 Mason Farm Road, Chapel Hill, NC, 27599-7365, USA
Interests: protein phosphorylation and protein kinase-mediated signaling pathways; application of proteomics; protein kinase inhibitors as therapeutics; regulation of metabolic enzymes by phosphorylation and interacting proteins
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Special Issue Information

Dear Colleagues,

The human kinome is a highly interconnected network of ~500 kinases that controls a myriad of cellular events through reversible phosphorylation. This network is regulated by multiple inputs including second messengers, activation loop phosphorylation, feedback and cross-talk phosphorylation events, transcriptional modulation, post-translational modifications, dimerization, targeted degradation and other mechanisms. Aberrant activation of kinases, by mutations or over-expression, and the importance of these events to cell growth regulation are well documented in cancer biology. Not surprisingly, a large number of kinase inhibitors are in clinical trials for treatment of a variety of cancers and other diseases. However, efforts to study the kinome through the study of isolated kinase pathways have resulted in limited knowledge regarding the function of the kinome as an entity. New technologies have emerged that allow better characterization of kinome behavior ‘en masse’. The application of these approaches has lead to the realization that the kinome is highly dynamic and is capable of responding or “reprogramming” to growth or inhibitory signals. Identifying these homeostatic mechanisms will be important to understanding the action of targeted kinase inhibitors, particularly those that fail in the clinic for unknown reasons. The objective of this special issue is to explore recent studies designed to study the kinome and to evaluate the insight gained from this research.

Prof. Dr. Lee M. Graves
Guest Editor

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 papers will be 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. Proteomes is an international peer-reviewed open access quarterly 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 1000 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

  • Phosphorylation
  • inhibitors (allosteric, competitive etc.)
  • Kinome
  • mutation
  • mass spectrometry
  • drug resistance
  • post-translational modification

Published Papers (2 papers)

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Research

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Open AccessArticle
Activation of SsoPK4, an Archaeal eIF2α Kinase Homolog, by Oxidized CoA
Proteomes 2015, 3(2), 89-116; https://doi.org/10.3390/proteomes3020089 - 15 May 2015
Cited by 5
Abstract
The eukaryotic protein kinase (ePK) paradigm provides integral components for signal transduction cascades throughout nature. However, while so-called typical ePKs permeate the Eucarya and Bacteria, atypical ePKs dominate the kinomes of the Archaea. Intriguingly, the catalytic domains of the handful of [...] Read more.
The eukaryotic protein kinase (ePK) paradigm provides integral components for signal transduction cascades throughout nature. However, while so-called typical ePKs permeate the Eucarya and Bacteria, atypical ePKs dominate the kinomes of the Archaea. Intriguingly, the catalytic domains of the handful of deduced typical ePKs from the archaeon Sulfolobus solfataricus P2 exhibit significant resemblance to the protein kinases that phosphorylate translation initiation factor 2α (eIF2α) in response to cellular stresses. We cloned and expressed one of these archaeal eIF2α protein kinases, SsoPK4. SsoPK4 exhibited protein-serine/threonine kinase activity toward several proteins, including the S. solfataricus homolog of eIF2α, aIF2α. The activity of SsoPK4 was inhibited in vitro by 3ʹ,5ʹ-cyclic AMP (Ki of ~23 µM) and was activated by oxidized Coenzyme A, an indicator of oxidative stress in the Archaea. Activation enhanced the apparent affinity for protein substrates, Km, but had little effect on Vmax. Autophosphorylation activated SsoPK4 and rendered it insensitive to oxidized Coenzyme A. Full article
(This article belongs to the Special Issue Probing the Dynamic Properties of the Kinome)
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Review

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Open AccessReview
Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases
Proteomes 2015, 3(4), 369-410; https://doi.org/10.3390/proteomes3040369 - 04 Nov 2015
Cited by 23
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means [...] Read more.
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes. Full article
(This article belongs to the Special Issue Probing the Dynamic Properties of the Kinome)
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