In silico profiling and structural insights of missense mutations in RET protein kinase domain by molecular dynamics and docking approach

2014 ◽  
Vol 10 (3) ◽  
pp. 421-436 ◽  
Author(s):  
C. George Priya Doss ◽  
B. Rajith ◽  
Chiranjib Chakraboty ◽  
V. Balaji ◽  
R. Magesh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Kinase ◽  
In Silico ◽  
Kinase Domain ◽  
Missense Mutations ◽  
Protein Kinase Domain ◽  
Docking Approach ◽  
Structural Insights

scholarly journals Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability

2017 ◽  
Vol 55 (1) ◽  
pp. 28-38 ◽  
Author(s):  
Mark J Hamilton ◽  
Richard C Caswell ◽  
Natalie Canham ◽  
Trevor Cole ◽  
Helen V Firth ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
Intellectual Disability ◽  
Protein Kinase ◽  
Developmental Delay ◽  
Congenital Heart ◽  
Kinase Domain ◽  
Dominant Negative ◽  
Missense Mutations ◽  
Protein Kinase Domain

IntroductionRecent evidence has emerged linking mutations in CDK13 to syndromic congenital heart disease. We present here genetic and phenotypic data pertaining to 16 individuals with CDK13 mutations.MethodsPatients were investigated by exome sequencing, having presented with developmental delay and additional features suggestive of a syndromic cause.ResultsOur cohort comprised 16 individuals aged 4–16 years. All had developmental delay, including six with autism spectrum disorder. Common findings included feeding difficulties (15/16), structural cardiac anomalies (9/16), seizures (4/16) and abnormalities of the corpus callosum (4/11 patients who had undergone MRI). All had craniofacial dysmorphism, with common features including short, upslanting palpebral fissures, hypertelorism or telecanthus, medial epicanthic folds, low-set, posteriorly rotated ears and a small mouth with thin upper lip vermilion. Fifteen patients had predicted missense mutations, including five identical p.(Asn842Ser) substitutions and two p.(Gly717Arg) substitutions. One patient had a canonical splice acceptor site variant (c.2898–1G>A). All mutations were located within the protein kinase domain of CDK13. The affected amino acids are highly conserved, and in silico analyses including comparative protein modelling predict that they will interfere with protein function. The location of the missense mutations in a key catalytic domain suggests that they are likely to cause loss of catalytic activity but retention of cyclin K binding, resulting in a dominant negative mode of action. Although the splice-site mutation was predicted to produce a stable internally deleted protein, this was not supported by expression studies in lymphoblastoid cells. A loss of function contribution to the underlying pathological mechanism therefore cannot be excluded, and the clinical significance of this variant remains uncertain.ConclusionsThese patients demonstrate that heterozygous, likely dominant negative mutations affecting the protein kinase domain of the CDK13 gene result in a recognisable, syndromic form of intellectual disability, with or without congenital heart disease.

scholarly journals Highlighting the Role of Cdk6 Associated MicroRNAs in Cancer Treatment Using In Silico Approaches

2020 ◽  
pp. 1-14
Author(s):  
Sidra Batool ◽  
Muhammad Sibte Hasan Mahmood ◽  
Tiyyaba Furqan ◽  
Sidra Batool
Keyword(s):  
Breast Cancer ◽  
Protein Kinase ◽  
In Silico ◽  
Drug Target ◽  
In Silico Analysis ◽  
Kinase Domain ◽  
Protein Kinase Domain ◽  
Over Expression ◽  
Silico Analysis

MicroRNAs (miRNAs) are small non-coding RNA’s that controls the regulation of a gene. Due to the over expression or under expression of miRNAs it leads to cause tumor or any other type of cancers such as, melanoma, lymphoma, cardiovascular issue, breast cancer etc. So, miRNAs can be used as a drug target for cancer therapy. This study aimed to check binding cavities of microRNA's involved in regulation of CDK6 protein. There are 23 different families of miRNAs that are involved in regulation of CDK6. Each family has one or more miRNAs. All these miRNAs are involved in the up regulation or downregulation of a gene, which lead to different type of cancers. All miRNAs of each family docked with mRNA CDK6 protein. After performing in silico analysis of binding interactions of mRNA with miRNAs the results were further refined by their comparison with information regarding their energies, interaction of the mRNA and miRNAs. The results show that all miRNAs lie in Protein Kinase domain, but the residues that lie is different within the families and across the families.

In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach

2021 ◽  
Vol 27 (2) ◽  
Author(s):  
Marzieh Gharouni ◽  
Hamid Mosaddeghi ◽  
Jamshid Mehrzad ◽  
Ali Es-haghi ◽  
Alireza Motavalizadehkakhky
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Metal Ion ◽  
Methyl Transferase ◽  
Zinc Metal ◽  
Structural Insights

The Eukaryotic Protein Kinase Domain

2005 ◽  
pp. 181-209 ◽  
Author(s):  
Arvin C. Dar ◽  
Leanne E. Wybenga-Groot ◽  
Frank Sicheri
Keyword(s):  
Protein Kinase ◽  
Kinase Domain ◽  
Protein Kinase Domain ◽  
Eukaryotic Protein Kinase ◽  
Eukaryotic Protein

scholarly journals Structural pathway for allosteric activation of the autophagic PI 3-kinase complex I

2019 ◽  
Vol 116 (43) ◽  
pp. 21508-21513 ◽  
Author(s):  
Lindsey N. Young ◽  
Felix Goerdeler ◽  
James H. Hurley
Keyword(s):  
Protein Kinase ◽  
Complex I ◽  
Structural Changes ◽  
Kinase Domain ◽  
Activation Loop ◽  
Class Iii ◽  
Lipid Kinase ◽  
Protein Kinase Domain ◽  
Autophagy Induction ◽  
Enzymatic Activation

Autophagy induction by starvation and stress involves the enzymatic activation of the class III phosphatidylinositol (PI) 3-kinase complex I (PI3KC3-C1). The inactive basal state of PI3KC3-C1 is maintained by inhibitory contacts between the VPS15 protein kinase and VPS34 lipid kinase domains that restrict the conformation of the VPS34 activation loop. Here, the proautophagic MIT domain-containing protein NRBF2 was used to map the structural changes leading to activation. Cryoelectron microscopy was used to visualize a 2-step PI3KC3-C1 activation pathway driven by NRFB2 MIT domain binding. Binding of a single NRBF2 MIT domain bends the helical solenoid of the VPS15 scaffold, displaces the protein kinase domain of VPS15, and releases the VPS34 kinase domain from the inhibited conformation. Binding of a second MIT stabilizes the VPS34 lipid kinase domain in an active conformation that has an unrestricted activation loop and is poised for access to membranes.

scholarly journals FLR-4, a Novel Serine/Threonine Protein Kinase, Regulates Defecation Rhythm in Caenorhabditis elegans

2005 ◽  
Vol 16 (3) ◽  
pp. 1355-1365 ◽  
Author(s):  
Masaya Take-uchi ◽  
Yuri Kobayashi ◽  
Koutarou D. Kimura ◽  
Takeshi Ishihara ◽  
Isao Katsura
Keyword(s):  
Caenorhabditis Elegans ◽  
Protein Kinase ◽  
Temperature Shift ◽  
Kinase Domain ◽  
Temperature Sensitive ◽  
Missense Mutations ◽  
Wild Type ◽  
Hydrophobic Region ◽  
Pharyngeal Muscles ◽  
Unique Structural Feature

The defecation behavior of the nematode Caenorhabditis elegans is controlled by a 45-s ultradian rhythm. An essential component of the clock that regulates the rhythm is the inositol trisphosphate receptor in the intestine, but other components remain to be discovered. Here, we show that the flr-4 gene, whose mutants exhibit very short defecation cycle periods, encodes a novel serine/threonine protein kinase with a carboxyl terminal hydrophobic region. The expression of functional flr-4::GFP was detected in the intestine, part of pharyngeal muscles and a pair of neurons, but expression of flr-4 in the intestine was sufficient for the wild-type phenotype. Furthermore, laser killing of the flr-4–expressing neurons did not change the defecation phenotypes of wild-type and flr-4 mutant animals. Temperature-shift experiments with a temperature-sensitive flr-4 mutant suggested that FLR-4 acts in a cell-functional rather than developmental aspect in the regulation of defecation rhythms. The function of FLR-4 was impaired by missense mutations in the kinase domain and near the hydrophobic region, where the latter allele seemed to be a weak antimorph. Thus, a novel protein kinase with a unique structural feature acts in the intestine to increase the length of defecation cycle periods.

scholarly journals Sti1 and Cdc37 Can Stabilize Hsp90 in Chaperone Complexes with a Protein Kinase

2004 ◽  
Vol 15 (4) ◽  
pp. 1785-1792 ◽  
Author(s):  
Paul Lee ◽  
Arsalan Shabbir ◽  
Christopher Cardozo ◽  
Avrom J. Caplan
Keyword(s):  
Protein Kinase ◽  
Kinase Domain ◽  
Mitogen Activated Protein Kinase ◽  
Protein Kinase Domain ◽  
Relative Contribution ◽  
Expression Studies ◽  
Mitogen Activated Protein ◽  
Gene Expression Studies ◽  
Kinase Pathway

Hsp90 functions in association with several cochaperones for folding of protein kinases and transcription factors, although the relative contribution of each to the overall reaction is unknown. We assayed the role of nine different cochaperones in the activation of Ste11, a Saccharomyces cerevisiae mitogen-activated protein kinase kinase kinase. Studies on signaling via this protein kinase pathway was measured by α-factor-stimulated induction of FIG1 or lacZ, and repression of HHF1. Several cochaperone mutants tested had reduced FIG1 induction or HHF1 repression, although to differing extents. The greatest defects were in cpr7Δ, sse1Δ, and ydj1Δ mutants. Assays of Ste11 kinase activity revealed a pattern of defects in the cochaperone mutant strains that were similar to the gene expression studies. Overexpression of CDC37, a chaperone required for protein kinase folding, suppressed defects the sti1Δ mutant back to wild-type levels. CDC37 overexpression also restored stable Hsp90 binding to the Ste11 protein kinase domain in the sti1Δ mutant strain. These data suggest that Cdc37 and Sti1 have functional overlap in stabilizing Hsp90:client complexes. Finally, we show that Cns1 functions in MAP kinase signaling in association with Cpr7.

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