Techniques to examine nucleotide binding by pseudokinases

2013 ◽  
Vol 41 (4) ◽  
pp. 975-980 ◽  
Author(s):  
Isabelle S. Lucet ◽  
Jeffrey J. Babon ◽  
James M. Murphy
Keyword(s):  
Signal Transduction ◽  
Drug Targets ◽  
Nucleotide Binding ◽  
Biological Functions ◽  
Binding Properties ◽  
Catalytic Activities ◽  
Functional Studies ◽  
Signalling Molecules ◽  
Advantages And Disadvantages ◽  
Human Kinome

Approximately 10% of the human kinome has been classified as pseudokinases due to the absence of one or more of three motifs known to play key roles in the catalytic activities of protein kinases. Structural and functional studies are now emerging, reclassifying this ‘dead’ kinase family as essential signalling molecules that act as crucial modulators of signal transduction. This raises the prospect that pseudokinases may well represent an as-yet-unexplored class of drug targets. However, the extent to which nucleotide binding and catalytic activity contribute to the biological functions of pseudokinases remains an area of great controversy. In the present review, we discuss the advantages and disadvantages of the different methods employed to characterize the nucleotide-binding properties and activity of pseudokinases.

scholarly journals Human Herpesvirus 8 Interleukin-6 (vIL-6) Signals through gp130 but Has Structural and Receptor-Binding Properties Distinct from Those of Human IL-6

1999 ◽  
Vol 73 (10) ◽  
pp. 8268-8278 ◽  
Author(s):  
Xiaoyu Wan ◽  
Hailin Wang ◽  
John Nicholas
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Receptor Binding ◽  
Interleukin 6 ◽  
Human Herpesvirus ◽  
Body Cavity ◽  
Human Herpesvirus 8 ◽  
Binding Properties ◽  
Herpesvirus 8 ◽  
Functional Studies

ABSTRACT Human herpesvirus 8 (HHV-8) has been associated with classical, endemic (African), and AIDS-related Kaposi’s sarcoma (KS), body cavity-based primary effusion lymphomas, and multicentric Castleman’s disease (MCD). HHV-8 encodes a functional homologue of interleukin-6 (IL-6), a cytokine that promotes the growth of KS and myeloma cells and is found at elevated levels in MCD lesions and patient sera. We have previously reported that the viral IL-6 (vIL-6) gene product can support the growth of the IL-6-dependent murine hybridoma cell line, B9, and that the gp80 (IL-6 receptor [IL-6R]) component of the IL-6 receptor-signal transducer (gp180) complex plays a role in mediating this activity. However, it has been shown by others that vIL-6 can function in human cells independently of IL-6R. Here we have extended our functional studies of vIL-6 by identifying transcription factors and pathways used in human Hep3B cells, investigating the utilization of gp130 and IL-6R by vIL-6, and undertaking mutational analyses of vIL-6 and gp130. The data presented here establish that vIL-6, in common with its endogenous counterparts, can mediate signal transduction through gp130 and activate multiple transcription factors, map residues within the vIL-6 protein that are and are not important for vIL-6 signalling, and identify a gp130 mutant that is nonfunctional with respect to vIL-6 signalling in the absence of IL-6R but that retains the ability to mediate vIL-6 and human IL-6 (hIL-6) signal transduction when IL-6R is coexpressed. The data presented demonstrate functional and mechanistic similarities between vIL-6 and endogenous IL-6 proteins but also highlight differences in the structural and receptor-binding properties of vIL-6 relative to its human counterpart.

scholarly journals TRANSPATH®—A High Quality Database Focused on Signal Transduction

2004 ◽  
Vol 5 (2) ◽  
pp. 163-168 ◽  
Author(s):  
Claudia Choi ◽  
Mathias Krull ◽  
Alexander Kel ◽  
Olga Kel-Margoulis ◽  
Susanne Pistor ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Drug Targets ◽  
Data Extraction ◽  
General Information ◽  
Expression Array ◽  
Signalling Molecules ◽  
Experimental Systems ◽  
Pathway Reconstruction ◽  
Direct Reactions ◽  
Potential Drug Targets

TRANSPATH®can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyser. Therefore, three modules have been created: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder™, which provides several different types of network visualization and hence faciliates understanding; the third is ArrayAnalyzer™, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH®to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH®is the inclusion of transcription factor–gene relations, which are transferred from TRANSFAC®, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. More information is available at www.biobase.de/pages/products/databases.html.

scholarly journals Novel Roles for the Sirtuin Deacylase SIRT5 in Normal Physiology and in Cancer

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 741-741
Author(s):  
David Lombard
Keyword(s):  
Mitochondrial Matrix ◽  
Genomic Integrity ◽  
Biological Functions ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Catalytic Activities ◽  
Cellular Processes ◽  
Specific Cancer ◽  
Cancer Types ◽  
Chromatin Biology

Abstract Sirtuins are NAD+-dependent deacylases that regulate diverse cellular processes such as metabolic homeostasis and genomic integrity. Mammals possess seven sirtuin family members, SIRT1-SIRT7, that display diverse subcellular localization patterns, catalytic activities, protein targets, and biological functions. Three sirtuins, SIRT3, SIRT4, and SIRT5, are primarily located in the mitochondrial matrix. SIRT5 is a very inefficient deacetylase, instead removing negatively charged post-translational modifications (succinyl, glutaryl, and malonyl groups) from lysines of its target proteins, in mitochondria and throughout the cell. SIRT5 plays only modest known roles in normal physiology, with its major functions occurring in the heart under stress conditions. In contrast, in specific cancer types, including melanoma, we have identified a major pro-survival role for SIRT5. We have traced this function of SIRT5 to novel roles for this protein in regulating chromatin biology. New insights into mechanisms of SIRT5 action in cancer, and in normal myocardium, will be discussed.

scholarly journals Regulation of CAMP (cathelicidin antimicrobial peptide) expression in adipocytes by TLR 2 and 4

2021 ◽  
Vol 27 (2) ◽  
pp. 184-191
Author(s):  
Alexandra Höpfinger ◽  
Thomas Karrasch ◽  
Andreas Schäffler ◽  
Andreas Schmid
Keyword(s):  
Signal Transduction ◽  
Antimicrobial Peptide ◽  
Drug Targets ◽  
Specific Effect ◽  
Potent Inducer ◽  
Regulatory Circuits ◽  
Signal Transduction Inhibitors ◽  
Tlr4 Agonist ◽  
Future Drug ◽  
Regulatory Effects

Recent data argue for a pro-inflammatory role of CAMP (cathelicidin antimicrobial peptide) in adipocytes and adipose tissue (AT) and for regulatory circuits involving TLRs. In order to investigate regulatory effects of TLR2 and TLR4, 3T3-L1 adipocytes were stimulated with TLR2 agonistic lipopeptide MALP-2 and with TLR4 agonist LPS in presence or absence of signal transduction inhibitors. CAMP gene expression was analysed by quantitative real-time PCR in adipocytes and in murine AT compartments and cellular subfractions. CAMP expression was higher in gonadal than in subcutaneous AT and there was a gender-specific effect with higher levels in males. Adipocytes had higher CAMP expression than the stroma-vascular cell (SVC) fraction. MALP-2 up-regulated CAMP expression significantly, mediated by STAT3 and PI3K and potentially (non-significant trend) by NF-κB and MAPK, but not by raf-activated MEK-1/-2. Moreover, LPS proved to act as a potent inducer of CAMP via NF-κB, PI3K and STAT3, whereas specific inhibition of MAPK and MEK-1/-2 had no effect. In conclusion, activation of TLR2 and TLR4 by classical ligands up-regulates adipocyte CAMP expression involving classical signal transduction elements. These might represent future drug targets for pharmacological modulation of CAMP expression in adipocytes, especially in the context of metabolic and infectious diseases.

scholarly journals Characterization and nucleotide binding properties of a mutant dihydropteridine reductase containing an aspartate 37-isoleucine replacement.

1992 ◽  
Vol 267 (22) ◽  
pp. 15334-15339
Author(s):  
C.E. Grimshaw ◽  
D.A. Matthews ◽  
K.I. Varughese ◽  
M Skinner ◽  
N.H. Xuong ◽  
...  
Keyword(s):  
Nucleotide Binding ◽  
Dihydropteridine Reductase ◽  
Binding Properties

scholarly journals KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study

2021 ◽  
Vol 22 (1) ◽  
pp. 448
Author(s):  
Federica D’Aria ◽  
Bruno Pagano ◽  
Luigi Petraccone ◽  
Concetta Giancola
Keyword(s):  
Thermodynamic Stability ◽  
Drug Targets ◽  
Promoter Sequence ◽  
Physicochemical Study ◽  
Biological Processes ◽  
Scanning Calorimetry ◽  
Binding Properties ◽  
Anticancer Compounds ◽  
Nmr Structures ◽  
Genomic Regions

DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.

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