scholarly journals Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases

2014 ◽  
Vol 2014 ◽  
pp. 1-24 ◽  
Author(s):  
Anshuman Dixit ◽  
Gennady M. Verkhivker
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Prediction Models ◽  
Point Mutations ◽  
Structural Features ◽  
Protein Kinase Activity ◽  
Activating Mutations ◽  
Functional Dynamics ◽  
Cancer Mutations ◽  
Activity State

A central goal of cancer research is to discover and characterize the functional effects of mutated genes that contribute to tumorigenesis. In this study, we provide a detailed structural classification and analysis of functional dynamics for members of protein kinase families that are known to harbor cancer mutations. We also present a systematic computational analysis that combines sequence and structure-based prediction models to characterize the effect of cancer mutations in protein kinases. We focus on the differential effects of activating point mutations that increase protein kinase activity and kinase-inactivating mutations that decrease activity. Mapping of cancer mutations onto the conformational mobility profiles of known crystal structures demonstrated that activating mutations could reduce a steric barrier for the movement from the basal “low” activity state to the “active” state. According to our analysis, the mechanism of activating mutations reflects a combined effect of partial destabilization of the kinase in its inactive state and a concomitant stabilization of its active-like form, which is likely to drive tumorigenesis at some level. Ultimately, the analysis of the evolutionary and structural features of the major cancer-causing mutational hotspot in kinases can also aid in the correlation of kinase mutation effects with clinical outcomes.

scholarly journals S183. ABNORMALITIES IN SERINE/THREONINE SIGNALING NETWORKS IN SEVERE NEUROPSYCHIATRIC ILLNESS: DEVELOPMENT OF A PIPELINE TO EXPLORE ABNORMALITIES OF KINASE ACTIVITY AND IDENTIFY NOVEL TREATMENT STRATEGIES FOR SCHIZOPHRENIA

2020 ◽  
Vol 46 (Supplement_1) ◽  
pp. S107-S108
Author(s):  
Robert McCullumsmith ◽  
Khaled Alganem ◽  
Nicholas Henkel ◽  
Abdul Hammoud ◽  
Rammohan Shukla ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Biological Pathways ◽  
Signaling Networks ◽  
Protein Kinase Activity ◽  
Drug Candidates ◽  
Group 10 ◽  
Disease Signatures ◽  
Neuropsychiatric Illness

Abstract Background Abnormalities of cellular signaling are well characterized in neuropsychiatric illnesses, including schizophrenia. Changes in signaling pathways reflect the underlying genetic, environmental, and epigenetic perturbations driving disease phenotypes. A shortcoming of most signaling studies is a focus on one or a few protein kinases at a time, a limitation since protein kinases work in networks with other kinases, phosphatases, and regulatory molecules to effect signaling events. We addressed this challenge by employing a kinome array platform that simultaneously measures protein kinase activity at hundreds of reporter peptide substrates. We then developed a novel bioinformatics pipeline to identify protein kinase nodes, signaling networks, upstream biological pathways, and drug candidates that “reverse” kinomic disease signatures. Methods Postmortem DLPFC brain samples from subjects with schizophrenia (n = 20 per group, 10 males and 10 females per group), were compared to age, PMI and pH matched control subjects (n = 20 per group, 10 males and 10 females per group) using the Pamgene12 serine/threonine kinome array chip. Samples were pooled by diagnosis and gender, and run in triplicate. The R-shiny app KRSA was created to automate assignment of kinases, perform permutation analyses, identify biological pathways, and connect to iLINCs for identification of drugs that reverse kinomic disease signatures. We also performed targeted confirmation studies using specific kinase activity assays, QPCR, and western blot analyses. Results We identified unique and common kinase nodes for each diagnostic group. Several of the nodes (for example AKT) are well characterized in schizophrenia, while others have not previously been identified (such as AMPK). We used AMPK KD cultures and AMPK KO brain tissues to demonstrate the validity if the kinome array for this protein kinase. We used standard kinase activity assays for AMPK and found decreased activity for AMPK (P < 0.05). We also found decreased expression of transcripts for the regulatory subunits of AMPK (P < 0.05). We identified several unique biological pathways, as well as candidate drugs, associated with the disease signature in schizophrenia. Discussion Our results confirm well characterized signaling defects in severe neuropsychiatric illness, and identify novel signaling nodes for further study. Confirmation studies for AMPK kinase show significant changes in expression and activity of this kinase, suggesting perturbation of energy sensing and production pathways in schizophrenia. Bioenergetic pathways may be targeted by myriad mechanisms, and we identified several drug candidates that might help restore this pathway in afflicted persons. Overall our novel workflow and pipeline provides a promising new avenue for understanding the complex signaling perturbations found in brain diseases and may provide new leads for developing treatments for schizophrenia and other cognitive disorders.

Biochemical changes accompanying enhanced cardiac contractility by ionophore A23187

1985 ◽  
Vol 249 (6) ◽  
pp. H1204-H1210 ◽  
Author(s):  
J. J. Murray ◽  
P. W. Reed ◽  
J. G. Dobson
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Protein Kinase Activity ◽  
Ionophore A23187 ◽  
Phosphorylase Activity ◽  
Dependent Protein Kinase ◽  
Camp Content ◽  
Camp Dependent Protein Kinase ◽  
Dependent Protein

We have reported that the divalent cation ionophore A23187, like the beta-adrenergic agonist isoproterenol, increased the force of contraction and rate of relaxation and shortened the duration of contraction of papillary muscles isolated from guinea pigs. A23187 produced a fall in resting tension and decreased the contracture tension of K +/- depolarized muscles, as did isoproterenol. In the present studies, isoproterenol produced a concentration-dependent, rapid, and sustained increase in the cyclic AMP (cAMP) content of papillary muscle. In contrast, A23187 had no detectable effect on cAMP levels, even in the presence of the phosphodiesterase inhibitor, papaverine. Neither drug, at concentrations maximal for contractile effects, altered cyclic GMP (cGMP). Isoproterenol increased the cAMP-dependent protein kinase activity ratio, whereas A23187 did not change the activity of this enzyme. However, both A23187 and isoproterenol produced a concentration-dependent increase in phosphorylase activity. Concentrations of A23187 or isoproterenol that enhanced contractility maximally increased the alkali-labile phosphate (by ca. 35%) but were without effect on the acid-labile, alkali-stable phosphate in the total acid precipitable protein. Contractile effects of isoproterenol, which reflect activated Ca2+ uptake, and the increase in phosphorylase activity produced by this agent are believed to be due to an increase in cAMP with subsequent activation of cAMP-dependent protein kinases and phosphorylation of proteins. A23187 may produce similar contractile effects without an increase in cAMP or cAMP-dependent protein kinase activity by activating other protein kinases and/or inhibiting phosphoprotein phosphatases, most likely by its effects on intracellular calcium.

Introduction to the Kinases in Diabetes Biochemical Society focused meeting: are protein kinases good targets for antidiabetic drugs?

2005 ◽  
Vol 33 (2) ◽  
pp. 339-342 ◽  
Author(s):  
M.P. Coghlan ◽  
D.M. Smith
Keyword(s):  
Insulin Resistance ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Whole Body ◽  
Protein Kinase Activity ◽  
Pharmacological Agents ◽  
Insulin Resistant ◽  
Insulin Mimetic ◽  
Glucose Homoeostasis

Insulin regulates whole-body glucose homoeostasis by modulating the activities of protein kinases in its target tissues: muscle, liver and fat. Defects in insulin's ability to modulate protein kinase activity lead to ‘insulin resistance’ or impaired insulin action. Insulin resistance in combination with defective insulin secretion from the pancreas results in the elevated blood glucose levels that are characteristic of diabetes mellitus. Pharmacological agents that selectively modulate protein kinase activities in insulin-resistant tissues may act either as insulin-sensitizing or insulin-mimetic drugs. Consistent with this, small molecule modulators of a number of protein kinases have demonstrated efficacy in animal models of insulin resistance and diabetes. Moreover, emerging data in humans suggest that marketed anti-diabetic agents may also act in part through modulating protein kinase activities. This meeting was convened to consider the potential to treat insulin resistance and Type II diabetes by modulating protein kinase activity.

Relationship Between RNA Polymerase and Protein Kinase Activities in Rat Mammary Gland Nuclei

1975 ◽  
Vol 53 (5) ◽  
pp. 591-598 ◽  
Author(s):  
P. R. Desjardins ◽  
I. M. Mendelson ◽  
K. M. Anderson
Keyword(s):  
Mammary Gland ◽  
Protein Kinase ◽  
Cyclic Amp ◽  
Ammonium Sulfate ◽  
Protein Kinases ◽  
Volume Fraction ◽  
Minor Component ◽  
Void Volume ◽  
Protein Kinase Activity ◽  
Rat Mammary Gland

1. Extracts from rat mammary gland nuclei contain cyclic AMP - independent protein kinases which phosphorylate casein rather than histone.2. A major increase in nuclear protein kinase activity occurred during late pregnancy and was maintained with the onset of lactation.3. Two major peaks of activity were resolved by chromatography of nuclear extracts on DEAE-Sephadex; the first (NI) appeared in the void volume and the second (NII) was eluted by 0.05–0.12 M ammonium sulfate. Several other regions of lesser activity were also present.4. Protein kinases in the cytosol 105 000 × g supernatant, precipitated by 70% ammonium sulfate, dialyzed against buffer, and chromatographed on DEAE-Sephadex, yielded a major peak in the void volume and a minor component at about 0.20 M ammonium sulfate. Both components phosphorylated histone in preference to casein, and this was stimulated by cyclic AMP if histone was the substrate, but only the first (void volume) fraction was cyclic AMP -dependent when casein was used.5. Most of RNA polymerases Ib and II, derived from the nucleolus and nucleoplasm, respectively, appeared in column fractions distinct from those containing the major NI and NII protein kinases.6. Cyclic AMP altered the amount of RNA product synthesized by polymerases Ib and II, but the explanation for this is unknown. Due to their elution profiles and cyclic AMP - independence, protein kinases NI and NII are excluded from playing a catalytic role in these effects; participation of quantitatively minor protein kinases which co-elute with polymerase Ib and II is not yet excluded.

scholarly journals Recent Advances in Protein Kinase Activity Analysis Based on Nanomaterials

2019 ◽  
Vol 20 (6) ◽  
pp. 1440 ◽  
Author(s):  
Zhiyong Yan ◽  
Pingye Deng ◽  
Yang Liu
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Protein Kinase Activity ◽  
Signal Transducer ◽  
Post Translational Modifications ◽  
Over Expression ◽  
Surface Areas ◽  
Sensing Platforms ◽  
Proliferation And Apoptosis ◽  
Biochemical Research

Protein phosphorylation regulated by protein kinases, as well as their dephosphorylation, is one of the most common post-translational modifications, and plays important roles in physiological activities, such as intracellular signal communications, gene transcription, cell proliferation and apoptosis. Over-expression of protein kinases is closely associated with various diseases. Consequently, accurate detection of protein kinases activities and their relevant inhibitors screening is critically important, not only to the biochemical research, but also to the clinical diagnosis and therapy. Nanomaterials, taking advantage of large surface areas, as well as excellent electrical, catalytic, magnetic and optical properties, have been utilized as target concentrators, recognition components, signal transducer or amplification elements in protein kinase related assays. This review summarizes the recent representative works to highlight the applications of nanomaterials in different biosensor technologies for protein kinases activities detection and their inhibitors screening. First, different nanomaterials developed for phosphoprotein/phosphopeptide enrichment and phosphate recognition are introduced. Next, representative works are selected that mainly focus on the utilization of nanomaterials as signal transducer or amplification elements in various protein kinases sensing platforms, such as electrochemical, colorimetric, fluorescent, and mass spectroscopy-based approaches. Finally, the major challenges and perspectives of nanomaterials being applied in protein kinases related assays are discussed.

scholarly journals Mutational Activation of ErbB2 Reveals a New Protein Kinase Autoinhibition Mechanism

2007 ◽  
Vol 283 (3) ◽  
pp. 1588-1596 ◽  
Author(s):  
Ying-Xin Fan ◽  
Lily Wong ◽  
Jinhui Ding ◽  
Nikolay A. Spiridonov ◽  
Richard C. Johnson ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Kinase Activity ◽  
Human Cancer ◽  
Kinase Domain ◽  
Mitogen Activated Protein Kinase ◽  
Protein Kinase Activity ◽  
Mitogen Activated Protein ◽  
Cancer Mutations ◽  
Mutational Activation ◽  
New Protein

Autoinhibition plays a key role in the control of protein kinase activity. ErbB2 is a unique receptor-tyrosine kinase that does not bind ligand but possesses an extracellular domain poised to engage other ErbBs. Little is known about the molecular mechanism for ErbB2 catalytic regulation. Here we show that ErbB2 kinase is strongly autoinhibited, and a loop connecting the αC helix and β4 sheet within the kinase domain plays a major role in the control of kinase activity. Mutations of two Gly residues at positions 776 and 778 in this loop dramatically increase ErbB2 catalytic activity. Kinetic analysis demonstrates that mutational activation is due to ∼10- and ∼7-fold increases in ATP binding affinity and turnover number, respectively. Expression of the activated ErbB2 mutants in cells resulted in elevated ligand-independent ErbB2 autophosphorylation, ErbB3 phosphorylation, and stimulation of mitogen-activated protein kinase. Molecular modeling suggests that the ErbB2 kinase domain is stabilized in an inactive state via a hydrophobic interaction between the αC-β4 and activation loops. Importantly, many ErbB2 human cancer mutations have been identified in the αC-β4 loop, including the activating G776S mutation studied here. Our findings reveal a new kinase regulatory mechanism in which the αC-β4 loop functions as an intramolecular switch that controls ErbB2 activity and suggests that loss of αC-β4 loop-mediated autoinhibition is involved in oncogenic activation of ErbB2.

scholarly journals Toxoplasma gondiiAttachment to Host Cells Is Regulated by a Calmodulin-like Domain Protein Kinase

2001 ◽  
Vol 276 (15) ◽  
pp. 12369-12377 ◽  
Author(s):  
Heidi Kieschnick ◽  
Therese Wakefield ◽  
Carl Anthony Narducci ◽  
Con Beckers
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Host Cells ◽  
Protein Kinase Activity ◽  
Calcium Dependent ◽  
Dependent Protein ◽  
Calcium Dependent Protein Kinases ◽  
Domain Protein

The role of calcium-dependent protein kinases in the invasion ofToxoplasma gondiiinto its animal host cells was analyzed. KT5926, an inhibitor of calcium-dependent protein kinases in other systems, is known to block the motility ofToxoplasmatachyzoites and their attachment to host cells.In vivo, KT5926 blocks the phosphorylation of only three parasite proteins, and in parasite extracts only a single KT5926-sensitive protein kinase activity was detected. This activity was calcium-dependent but did not require calmodulin. In a search for calcium-dependent protein kinases inToxoplasma, two members of the class of calmodulin-like domain protein kinases (CDPKs) were detected. TgCDPK2 was only expressed at the mRNA level in tachyzoites, but no protein was detected. TgCDPK1 protein was expressed inToxoplasmatachyzoites and cofractionated precisely with the peak of KT5926-sensitive protein kinase activity. TgCDPK1 kinase activity was calcium-dependent but did not require calmodulin or phospholipids. TgCDPK1 was found to be inhibited effectively by KT5926 at concentrations that block parasite attachment to host cells.In vitro, TgCDPK1 phosphorylated three parasite proteins that migrated identical to the three KT5926-sensitive phosphoproteins detectedin vivo. Based on these observations, a central role is suggested for TgCDPK1 in regulatingToxoplasmamotility and host cell invasion.

Investigations on myelinogenesis in vitro: II. The occurrence and regulation of protein kinases by thyroid hormone in primary cultures of cells dissociated from embryonic mouse brain

1987 ◽  
Vol 7 (2) ◽  
pp. 159-165 ◽  
Author(s):  
G. Shanker ◽  
R. A. Pieringer
Keyword(s):  
Thyroid Hormone ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Mouse Brain ◽  
Primary Cultures ◽  
Calf Serum ◽  
Phosphatidyl Serine ◽  
Protein Kinase Activity ◽  
Embryonic Mouse

The occurrence and regulation by thyroid hormone of four protein kinases (cyclic AMP independent and dependent, calcium/calmodulin stimulated, and calcium/phosphatidyl serine stimulated protein kinases) was studied in primary cultures of cells dissociated from embryonic mouse brain. Serum from a thyroidectomized calf, which contained low levels of L-3,5,3′-triiodothyronine, T3 (<25 ng/100 ml), and thyroxine, T4 (<1 μg/100 ml) was used in the culture medium in place of normal calf-serum (T3, 130 ng/100 ml; T4 5.9 μg/100 ml) to render the cultures responsive to exogenously added T3. Cultures grown in hypothyroid calf-serum containing medium had less cAMP dependent and independent protein kinase activity than control cultures grown in normal calf-serum containing medium. However, this activity was restorable to a considerable degree if the cultures grown in hypothyroid calf serum containing medium were supplemented with L-3,5,3′-triiodothyronine (T3). The presence of calcium/calmodulin stimulated protein kinase was also distinctly observed. In comparison, the activity of calcium/phosphatidyl serine stimulated protein kinase was less than the other protein kinases.

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