Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

Tong, Junsen; Yang, Hong-So; Eom, Soo Hyun; Chun, ChangJu; Im, Young Jun

doi:10.1016/j.bbrc.2014.08.073

Cited by 11 publications

(6 citation statements)

References 19 publications

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“…The mutation calls were then validated for confidence by Sanger sequencing using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, USA). Genotyping prioritization was based on whether the mutation was 1) located in a functional domain or motif of the protein, according to the Human Protein Reference Database (http://www.hprd.org), Pfam (http://pfam.xfam.org/), and existing literature2150515253545556575859, 2) functionally important, such as causing a frame shift, stop gain, or cysteine gain/loss, 3) novel, as in not documented in the NCBI dbSNP database (Build 137) (http://www.ncbi.nlm.nih.gov/SNP/), the 1000 Genomes Project (http://www.1000genomes.org/), the Exome Variant Server of NHLBI GO Exome Sequencing Project (ESP6500SI-V2) (http://evs.gs.washington.edu/EVS/), or the Human Genetic Variation Database of Japanese genetic variation consortium (http://www.genome.med.kyoto-u.ac.jp/SnpDB), and 4) predicted to be deleterious by in silico analytic methods. In addition to PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) and SIFT (http://sift.jcvi.org/) that were originally incorporated in the Ingenuity Variant Caller, we also employed PROVEAN (http://provean.jcvi.org/index.php), PMut (http://www.ngrl.org.uk/Manchester/page/pmut), Mutation Taster (http://www.mutationtaster.org/), and PANTHER (http://pantherdb.org/) for enhanced prediction of the consequences of protein alterations.…”

Section: Methodsmentioning

confidence: 99%

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Xing

Kimura

Wang

et al. 2016

Sci Rep

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PSD-95 associated PSD proteins play a critical role in regulating the density and activity of glutamate receptors. Numerous previous studies have shown an association between the genes that encode these proteins and schizophrenia (SZ) and autism spectrum disorders (ASD), which share a substantial portion of genetic risks. We sequenced the protein-encoding regions of DLG1, DLG2, DLG4, DLGAP1, DLGAP2, and SynGAP in 562 cases (370 SZ and 192 ASD patients) on the Ion PGM platform. We detected 26 rare (minor allele frequency <1%), non-synonymous mutations, and conducted silico functional analysis and pedigree analysis when possible. Three variants, G344R in DLG1, G241S in DLG4, and R604C in DLGAP2, were selected for association analysis in an independent sample set of 1315 SZ patients, 382 ASD patients, and 1793 healthy controls. Neither DLG4-G241S nor DLGAP2-R604C was detected in any samples in case or control sets, whereas one additional SZ patient was found that carried DLG1-G344R. Our results suggest that rare missense mutations in the candidate PSD genes may increase susceptibility to SZ and/or ASD. These findings may strengthen the theory that rare, non-synonymous variants confer substantial genetic risks for these disorders.

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Section: Methodsmentioning

confidence: 99%

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Xing

Kimura

Wang

et al. 2016

Sci Rep

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“…In some cases MBP fusion protein structures simply have been presented as faits accomplis , with no backstory whatsoever . In most instances, however, at least a brief description of the difficulties encountered with expression, solubility, stability, or crystallization of the target protein (or a combination of these factors) is provided as a rationale for crystallizing the MBP fusion protein . Remarkably, in only two cases is any mention made of attempts to crystallize proteins using multiple fusion partners.…”

Section: Mbp As a Crystallization Chaperonementioning

confidence: 99%

Crystal structures of MBP fusion proteins

Waugh

2016

Protein Science

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Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare.

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“…The family of discs large-associated protein (DLGAP) composed of five members (DLGAP1-5) were originally found in rats, which have three key domains, including a 14-amino-acid repeat domain (5), a dynein light chain domain (6) and a guanylate kinase-associated protein homology domain (7). DLGAP1-4 have been reported to participate in a variety of neurological disorders, such as cerebellar ataxia, obsessive compulsive disorder and autism spectrum disease (8)(9)(10).…”

Section: Introductionmentioning

confidence: 99%

Knockdown of DLGAP5 suppresses cell proliferation, induces G₂/M phase arrest and apoptosis in ovarian cancer

Zhang

Liu

Tang³

et al. 2021

Exp Ther Med

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Discs large-associated protein 5 (DLGAP5) is a microtubule-associated protein and is reported to exert oncogenic role in tumorigenesis, including lung cancer and hepatocellular carcinoma. However, the prognostic value and biological function of DLGAP5 in ovarian cancer (OC) still remain unclear. The present study investigated the expression pattern of DLGAP5 by searching the Oncomine microarray database. The correlation between DLGAP5 and survival prognosis of OC patients was analyzed by the online tool KM-plotter. Knockdown of DLGAP5 was achieved by transfection with small interfering RNA targeting DLGAP5 in two OC cell lines (SKOV3 and CAOV3). Cell proliferation was assessed by Cell Counting Kit-8 assay and colony-formation assay. Flow cytometry was utilized to determine the effects of DLGAP5 on cell cycle distribution and apoptosis. The present study data showed that DLGAP5 was significantly upregulated in OC and its higher expression was associated with poor survival prognosis. Knockdown of DLGAP5 significantly suppressed cell proliferation, induced cell cycle G 2 /M phase arrest and apoptosis. Western blot analysis further demonstrated that DLGAP5 knockdown downregulated the expression of CDK1, Cyclin B1 and Bcl-2, but upregulated Bax expression. Collectively, these data demonstrate that DLGAP5 might be a promising prognostic therapeutic target for OC treatment.

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Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

Cited by 11 publications

References 19 publications

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Crystal structures of MBP fusion proteins

Knockdown of DLGAP5 suppresses cell proliferation, induces G₂/M phase arrest and apoptosis in ovarian cancer

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Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

Cited by 11 publications

References 19 publications

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders

Crystal structures of MBP fusion proteins

Knockdown of DLGAP5 suppresses cell proliferation, induces G2/M phase arrest and apoptosis in ovarian cancer

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Knockdown of DLGAP5 suppresses cell proliferation, induces G₂/M phase arrest and apoptosis in ovarian cancer