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  1. Article: The cyclophilin-like domain of Ran-binding protein-2 modulates selectively the activity of the ubiquitin-proteasome system and protein biogenesis.

    Yi, Haiqing / Friedman, Julie L / Ferreira, Paulo A

    The Journal of biological chemistry

    2007  Volume 282, Issue 48, Page(s) 34770–34778

    Abstract: ... with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358 ...

    Abstract The ubiquitin-proteasome system (UPS) plays a critical role in protein degradation. The 19S regulatory particle (RP) of the 26S proteasome mediates the recognition, deubiquitylation, unfolding, and channeling of ubiquitylated substrates to the 20S proteasome. Several subunits of the 19S RP interact with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358) associates specifically with at least one subunit, S1, of the base subcomplex of the 19S RP, but the functional implications of this interaction on the UPS activity are elusive. This study shows the CLD of RanBP2 promotes selectively the accumulation of a subset of reporter substrates of the UPS, such as the ubiquitin (Ub)-fusion yellow fluorescent protein (YFP) degradation substrate, Ub(G76V)-YFP, and the N-end rule substrate, Ub-R-YFP. Conversely, the degradation of endoplasmic reticulum and misfolded proteins, and of those linked to UPS-independent degradation, is not affected by CLD. The selective effect of CLD on the UPS in vivo is independent of, and synergistic with, proteasome inhibitors, and CLD does not affect the intrinsic proteolytic activity of the 20S proteasome. The inhibitory activity of CLD on the UPS resides in a purported SUMO binding motif. We also found two RanBP2 substrates, RanGTPase-activating protein and retinitis pigmentosa GTPase regulator interacting protein-1alpha1, whose steady-state levels are selectively modulated by CLD. Hence, the CLD of RanBP2 acts as a novel auxiliary modulator of the UPS activity; it may contribute to the molecular and subcellular compartmentation of the turnover of properly folded proteins and modulation of the expressivity of several neurological diseases.
    MeSH term(s) Amino Acid Motifs ; Animals ; Bacterial Proteins/chemistry ; COS Cells ; Cattle ; Cell Line ; Chlorocebus aethiops ; Cyclophilins/chemistry ; Enzyme Inhibitors/pharmacology ; Luminescent Proteins/chemistry ; Models, Genetic ; Molecular Chaperones/chemistry ; Molecular Chaperones/physiology ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Pore Complex Proteins/physiology ; Proteasome Endopeptidase Complex/chemistry ; Proteasome Endopeptidase Complex/metabolism ; Proteasome Inhibitors ; Protein Structure, Tertiary ; Proteins/chemistry ; Recombinant Fusion Proteins/chemistry ; Ubiquitin/chemistry
    Chemical Substances Bacterial Proteins ; Enzyme Inhibitors ; Luminescent Proteins ; Molecular Chaperones ; Nuclear Pore Complex Proteins ; Proteasome Inhibitors ; Proteins ; Recombinant Fusion Proteins ; Ubiquitin ; ran-binding protein 2 ; yellow fluorescent protein, Bacteria ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Cyclophilins (EC 5.2.1.-)
    Language English
    Publishing date 2007-10-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M706903200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: The Cyclophilin-like Domain of Ran-binding Protein-2 Modulates Selectively the Activity of the Ubiquitin-Proteasome System and Protein Biogenesis

    Yi, Haiqing / Friedman, Julie L / Ferreira, Paulo A

    Journal of biological chemistry. 2007 Nov. 30, v. 282, no. 48

    2007  

    Abstract: ... with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358 ...

    Abstract The ubiquitin-proteasome system (UPS) plays a critical role in protein degradation. The 19S regulatory particle (RP) of the 26S proteasome mediates the recognition, deubiquitylation, unfolding, and channeling of ubiquitylated substrates to the 20S proteasome. Several subunits of the 19S RP interact with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358) associates specifically with at least one subunit, S1, of the base subcomplex of the 19S RP, but the functional implications of this interaction on the UPS activity are elusive. This study shows the CLD of RanBP2 promotes selectively the accumulation of a subset of reporter substrates of the UPS, such as the ubiquitin (Ub)-fusion yellow fluorescent protein (YFP) degradation substrate, UbG⁷⁶V-YFP, and the N-end rule substrate, Ub-R-YFP. Conversely, the degradation of endoplasmic reticulum and misfolded proteins, and of those linked to UPS-independent degradation, is not affected by CLD. The selective effect of CLD on the UPS in vivo is independent of, and synergistic with, proteasome inhibitors, and CLD does not affect the intrinsic proteolytic activity of the 20S proteasome. The inhibitory activity of CLD on the UPS resides in a purported SUMO binding motif. We also found two RanBP2 substrates, RanGTPase-activating protein and retinitis pigmentosa GTPase regulator interacting protein-1α1, whose steady-state levels are selectively modulated by CLD. Hence, the CLD of RanBP2 acts as a novel auxiliary modulator of the UPS activity; it may contribute to the molecular and subcellular compartmentation of the turnover of properly folded proteins and modulation of the expressivity of several neurological diseases.
    Language English
    Dates of publication 2007-1130
    Size p. 34770-34778.
    Publishing place American Society for Biochemistry and Molecular Biology
    Document type Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Estimating the Gibbs Hydration Energies of Actinium and Trans-Plutonium Actinides.

    Friedman, Ran

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2022  Volume 24, Issue 2, Page(s) e202200516

    Abstract: The use of actinides for medical, scientific and technological purposes has gained momentum in the recent years. This creates a need to understand their interactions with biomolecules, both at the interface and as they become complexed. Calculation of ... ...

    Abstract The use of actinides for medical, scientific and technological purposes has gained momentum in the recent years. This creates a need to understand their interactions with biomolecules, both at the interface and as they become complexed. Calculation of the Gibbs binding energies of the ions to biomolecules, i. e., the Gibbs energy change associated with a transfer of an ion from the water phase to its binding site, could help to understand the actinides' toxicities and to design agents that bind them with high affinities. To this end, there is a need to obtain accurate reference values for actinide hydration, that for most actinides are not available from experiment. In this study, a set of ionic radii is developed that enables future calculations of binding energies for Pu
    MeSH term(s) Actinium ; Plutonium ; Thermodynamics ; Actinoid Series Elements/chemistry ; Water/chemistry
    Chemical Substances Actinium (NIK1K0956U) ; Plutonium (53023GN24M) ; Actinoid Series Elements ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-11-04
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2025223-7
    ISSN 1439-7641 ; 1439-4235
    ISSN (online) 1439-7641
    ISSN 1439-4235
    DOI 10.1002/cphc.202200516
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Serine/threonine kinase Mirk/Dyrk1B is an inhibitor of epithelial cell migration and is negatively regulated by the Met adaptor Ran-binding protein M.

    Zou, Yonglong / Lim, Seunghwan / Lee, Kangmoon / Deng, Xiaobing / Friedman, Eileen

    The Journal of biological chemistry

    2003  Volume 278, Issue 49, Page(s) 49573–49581

    Abstract: ... the Met adaptor protein Ran-binding protein M (RanBPM) was identified as a Mirk-binding protein by yeast ...

    Abstract Minibrain-related kinase (Mirk)/Dyrk1B is an arginine-directed serine/threonine kinase that is active in skeletal muscle development but is also expressed in various carcinomas. In the current study, the Met adaptor protein Ran-binding protein M (RanBPM) was identified as a Mirk-binding protein by yeast two-hybrid analysis. The Mirk-RanBPM association was confirmed by glutathione S-transferase pull-down assays, co-immunoprecipitation studies, and in vivo cross-linking. Met plays an important role in tumor cell invasion and cell migration. RanBPM has been reported to bind to the tyrosine kinase domain of the hepatocyte growth factor (HGF) receptor Met, enhance Met downstream signaling, and enhance HGF-induced A704 kidney carcinoma cell invasion (Wang, D., Li, Z., Messing, E. M., and Wu, G. (2002) J. Biol. Chem. 277, 36216-36222). We made a stable Mirk-inducible subline from nontransformed Mv1Lu lung epithelial cells and now demonstrate that induction of Mirk inhibited the migration of these cells in wounding experiments and inhibited their invasion through polycarbonate Transwell filters. Furthermore the ability of Mirk to inhibit Mv1Lu cell migration was attenuated when cells were exposed to HGF or to elevated levels of transiently expressed RanBPM. RanBPM inhibited the kinase activity of Mirk/Dyrk1B and Dyrk1A. In addition, RanBPM and HGF inhibited the function of Mirk as a transcriptional coactivator. Our findings suggest that Mirk plays a role in modulating cell migration through opposing the action of the Met signaling cascade adaptor protein RanBPM.
    MeSH term(s) Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Animals ; Cell Line ; Cell Movement/physiology ; Cytoskeletal Proteins ; Epithelial Cells/cytology ; Humans ; Nuclear Proteins/physiology ; Protein Serine-Threonine Kinases/physiology ; Protein-Tyrosine Kinases/physiology ; Trans-Activators/physiology ; Transcription, Genetic/physiology ; Two-Hybrid System Techniques ; ran GTP-Binding Protein/physiology ; Dyrk Kinases
    Chemical Substances Adaptor Proteins, Signal Transducing ; Cytoskeletal Proteins ; Nuclear Proteins ; Ran binding protein 9 ; Trans-Activators ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; ran GTP-Binding Protein (EC 3.6.5.2)
    Language English
    Publishing date 2003-09-18
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M307556200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Preferential Binding of Lanthanides to Methanol Dehydrogenase Evaluated with Density Functional Theory.

    Friedman, Ran

    The journal of physical chemistry. B

    2021  Volume 125, Issue 9, Page(s) 2251–2257

    Abstract: Methanol dehydrogenase (MDH) is an enzyme used by certain bacteria for the oxidation of methanol to formaldehyde, which is a necessary metabolic reaction. The discovery of a lanthanide-dependent MDH reveals that lanthanide ions ( ... ...

    Abstract Methanol dehydrogenase (MDH) is an enzyme used by certain bacteria for the oxidation of methanol to formaldehyde, which is a necessary metabolic reaction. The discovery of a lanthanide-dependent MDH reveals that lanthanide ions (Ln
    MeSH term(s) Alcohol Oxidoreductases ; Density Functional Theory ; Lanthanoid Series Elements ; Methanol
    Chemical Substances Lanthanoid Series Elements ; Alcohol Oxidoreductases (EC 1.1.-) ; alcohol dehydrogenase (acceptor) (EC 1.1.2.8) ; Methanol (Y4S76JWI15)
    Language English
    Publishing date 2021-03-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c11077
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The molecular mechanisms behind activation of FLT3 in acute myeloid leukemia and resistance to therapy by selective inhibitors.

    Friedman, Ran

    Biochimica et biophysica acta. Reviews on cancer

    2021  Volume 1877, Issue 1, Page(s) 188666

    Abstract: Acute myeloid leukemia is an aggressive cancer, which, in spite of increasingly better understanding of its genetic background remains difficult to treat. Mutations in the FLT3 gene are observed in ≈30% of the patients. Most of these mutations are ... ...

    Abstract Acute myeloid leukemia is an aggressive cancer, which, in spite of increasingly better understanding of its genetic background remains difficult to treat. Mutations in the FLT3 gene are observed in ≈30% of the patients. Most of these mutations are internal tandem duplications (ITDs) of a sequence within the protein coding region, an activation mechanism that is almost non-existent with other genes and cancers. As patients each carry their own unique set of mutations, it is challenging to understand how ITDs activate the protein, and ascertain the risk for each individual patient. Available treatment options are limited due to development of drug resistance. Here, recent studies are reviewed that help to better understand the molecular mechanism behind activation of the FLT3 protein due to mutations. It is argued that difference in mutation sequences and especially location might be coupled to prognosis. When it comes to FLT3 inhibitors, key differences between them can be attributed to the mode of inhibition (type-1 and type-2 inhibitors), effective inhibitory coefficient in the blood plasma and off-target binding. Accounting for the position and length of insertions may in the future be used to predict prognosis and rationalise treatment. Development of new inhibitors must take into account the potential for resistance mutations. Inhibitors aimed at multiple specific targets are currently being developed. These, and as well as combination therapies will hopefully lead to longer periods during which targeted FLT3 therapy will remain effective.
    MeSH term(s) Humans ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/genetics ; Mutation ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; fms-Like Tyrosine Kinase 3/genetics
    Chemical Substances Protein Kinase Inhibitors ; FLT3 protein, human (EC 2.7.10.1) ; fms-Like Tyrosine Kinase 3 (EC 2.7.10.1)
    Language English
    Publishing date 2021-12-08
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2918802-7
    ISSN 1879-2561 ; 0304-419X
    ISSN (online) 1879-2561
    ISSN 0304-419X
    DOI 10.1016/j.bbcan.2021.188666
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: QM/MM-Based Energy Decomposition Analysis Method for Large Systems.

    Xiong, Xuewei / Friedman, Ran / Wu, Wei / Su, Peifeng

    The journal of physical chemistry. A

    2024  Volume 128, Issue 18, Page(s) 3529–3538

    Abstract: In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) ...

    Abstract In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) can be applied to describe the interactions of large-scale systems combined with various QM/MM platforms. By using the examples of a hydrated hydronium ion complex in water solution, the barnase-barstar complex, and MMP-13-pyrimidinetrione in a metalloprotein, the capability of GKS-EDA(QM/MM) for various interactions in large systems is validated.
    Language English
    Publishing date 2024-04-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.4c00183
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Combination strategies to overcome drug resistance in FLT

    Yang, Jingmei / Friedman, Ran

    Cancer cell international

    2023  Volume 23, Issue 1, Page(s) 161

    Abstract: Background: Acute myeloid leukaemia (AML) remains difficult to treat despite the development of novel formulations and targeted therapies. Activating mutations in the FLT3 gene are common among patients and make the tumour susceptible to FLT3 inhibitors, ...

    Abstract Background: Acute myeloid leukaemia (AML) remains difficult to treat despite the development of novel formulations and targeted therapies. Activating mutations in the FLT3 gene are common among patients and make the tumour susceptible to FLT3 inhibitors, but resistance to such inhibitors develops quickly.
    Methods: We examined combination therapies aimed at FLT3
    Results: We show that AML cells express CDK4 and that the CDK4/6 inhibitors palbociclib and abemaciclib inhibit cellular growth. PI3K inhibitors were also effective in inhibiting the growth of AML cell lines that express FLT3-ITD. Whereas resistance to quizartinib develops quickly, the combinations overcome such resistance.
    Conclusions: This study suggests that a multi-targeted intervention involving a CDK4/6 inhibitor with a FLT3 inhibitor or a pan-PI3K inhibitor might be a valuable therapeutic strategy for AML to overcome drug resistance. Moreover, many patients cannot tolerate high doses of the drugs that were studied (quizartinib, palbociclib and PI3K inhibitors) for longer periods, and it is therefore of high significance that the drugs act synergistically and lower doses can be used.
    Language English
    Publishing date 2023-08-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2091573-1
    ISSN 1475-2867
    ISSN 1475-2867
    DOI 10.1186/s12935-023-03000-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Synergy and antagonism between azacitidine and FLT3 inhibitors.

    Yang, Jingmei / Friedman, Ran

    Computers in biology and medicine

    2023  Volume 169, Page(s) 107889

    Abstract: Synergetic interactions between drugs can make a drug combination more effective. Alternatively, they may allow to use lower concentrations and thus avoid toxicities or side effects that not only cause discomfort but might also reduce the overall ... ...

    Abstract Synergetic interactions between drugs can make a drug combination more effective. Alternatively, they may allow to use lower concentrations and thus avoid toxicities or side effects that not only cause discomfort but might also reduce the overall survival. Here, we studied whether synergy exists between agents that are used for treatment of acute myeloid leukaemia (AML). Azacitidine is a demethylation agent that is used in the treatment of AML patients that are unfit for aggressive chemotherapy. An activating mutation in the FLT3 gene is common in AML patients and in the absence of specific treatment makes prognosis worse. FLT3 inhibitors may be used in such cases. We sought to determine whether combination of azacitidine with a FLT3 inhibitor (gilteritinib, quizartinib, LT-850-166, FN-1501 or FF-10101) displayed synergy or antagonism. To this end, we calculated dose-response matrices of these drug combinations from experiments in human AML cells and subsequently analysed the data using a novel consensus scoring algorithm. The results show that combinations that involved non-covalent FLT3 inhibitors, including the two clinically approved drugs gilteritinib and quizartinib were antagonistic. On the other hand combinations with the covalent inhibitor FF-10101 had some range of concentrations where synergy was observed.
    MeSH term(s) Humans ; Amides ; Aniline Compounds/pharmacology ; Aniline Compounds/therapeutic use ; Azacitidine/pharmacology ; Azacitidine/therapeutic use ; Benzothiazoles ; fms-Like Tyrosine Kinase 3/genetics ; fms-Like Tyrosine Kinase 3/therapeutic use ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/genetics ; Mutation ; Phenylurea Compounds ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Pyrazines ; Pyrimidines
    Chemical Substances Amides ; Aniline Compounds ; Azacitidine (M801H13NRU) ; Benzothiazoles ; FF-10101 ; FLT3 protein, human (EC 2.7.10.1) ; fms-Like Tyrosine Kinase 3 (EC 2.7.10.1) ; gilteritinib (66D92MGC8M) ; Phenylurea Compounds ; Protein Kinase Inhibitors ; Pyrazines ; Pyrimidines ; quizartinib (7LA4O6Q0D3)
    Language English
    Publishing date 2023-12-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107889
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Correction to: Exciton effect in new generation of carbon nanotubes: graphdiyne nanotubes.

    Houshmand, Fatemeh / Friedman, Ran / Jalili, Seifollah / Schofield, Jeremy

    Journal of molecular modeling

    2023  Volume 29, Issue 3, Page(s) 61

    Language English
    Publishing date 2023-02-03
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-023-05456-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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