메뉴 건너뛰기




Volumn 17, Issue 11, 2012, Pages 13376-13389

Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch

Author keywords

Analogues; Aptamer; C di GMP; DOSY; Endo S c di GMP; Fluorescence; G quadruplex; Polymorphism; Vc2 RNA

Indexed keywords

CYCLIC GMP; DRUG DERIVATIVE;

EID: 84870231825     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules171113376     Document Type: Article
Times cited : (18)

References (44)
  • 2
    • 22644438480 scopus 로고    scopus 로고
    • C-di-GMP: The dawning of a novel bacterial signalling system
    • Römling, U.; Gomelsky, M.; Galperin, M.Y. C-di-GMP: The dawning of a novel bacterial signalling system. Mol. Microbiol. 2005, 57, 629-639.
    • (2005) Mol. Microbiol. , vol.57 , pp. 629-639
    • Römling, U.1    Gomelsky, M.2    Galperin, M.Y.3
  • 4
    • 84860582172 scopus 로고    scopus 로고
    • When the PilZ don't work: Effectors for cyclic di-GMP action in bacteria
    • Ryan, R.P.; Tolker-Nielsen, T.; Dow, J.M. When the PilZ don't work: Effectors for cyclic di-GMP action in bacteria. Trends Microbiol. 2012, 20, 235-242.
    • (2012) Trends Microbiol. , vol.20 , pp. 235-242
    • Ryan, R.P.1    Tolker-Nielsen, T.2    Dow, J.M.3
  • 5
    • 84862527194 scopus 로고    scopus 로고
    • Sensing the messenger: The diverse ways that bacteria signal through c-di-GMP
    • Krasteva, P.V.; Giqlio, K.M.; Sondermann, H. Sensing the messenger: The diverse ways that bacteria signal through c-di-GMP. Protein Sci. 2012, 21, 929-948.
    • (2012) Protein Sci. , vol.21 , pp. 929-948
    • Krasteva, P.V.1    Giqlio, K.M.2    Sondermann, H.3
  • 6
    • 84864389119 scopus 로고    scopus 로고
    • Cyclic di-GMP, an established secondary messenger still speeding up
    • Römling, U. Cyclic di-GMP, an established secondary messenger still speeding up. Environ. Microbiol. 2012, 14, 1817-1829.
    • (2012) Environ. Microbiol. , vol.14 , pp. 1817-1829
    • Römling, U.1
  • 9
  • 11
    • 77950859347 scopus 로고    scopus 로고
    • Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by pilz domain proteins
    • Ko, J.; Ryu, K.S.; Kim, H.; Shin, J.S.; Lee, J.O.; Cheong, C.; Choi, B.S. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins. J. Mol. Biol. 2010, 398, 97-110.
    • (2010) J. Mol. Biol. , vol.398 , pp. 97-110
    • Ko, J.1    Ryu, K.S.2    Kim, H.3    Shin, J.S.4    Lee, J.O.5    Cheong, C.6    Choi, B.S.7
  • 13
    • 79954598477 scopus 로고    scopus 로고
    • Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout
    • Habazettl, J.; Allan, M.G.; Jenal, U.; Grzesiek, S. Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout. J. Biol. Chem. 2011, 286, 14304-14314.
    • (2011) J. Biol. Chem. , vol.286 , pp. 14304-14314
    • Habazettl, J.1    Allan, M.G.2    Jenal, U.3    Grzesiek, S.4
  • 14
    • 47249089614 scopus 로고    scopus 로고
    • Identification of FleQ from pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor
    • Hickman, J.W.; Harwood, C.S. Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol. Microbiol. 2008, 69, 376-389.
    • (2008) Mol. Microbiol. , vol.69 , pp. 376-389
    • Hickman, J.W.1    Harwood, C.S.2
  • 15
    • 84867302540 scopus 로고    scopus 로고
    • The FleQ protein from pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP
    • Baraquet, C.; Murakami, K.; Parsek, M.R.; Harwood, C.S. The FleQ protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP. Nucleic Acids Res. 2012, 40, 7207-7218.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 7207-7218
    • Baraquet, C.1    Murakami, K.2    Parsek, M.R.3    Harwood, C.S.4
  • 17
    • 79956338019 scopus 로고    scopus 로고
    • Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches
    • Smith, K.D.; Shanahan, C.A.; Moore, E.L.; Simon, A.C.; Strobel, S.A. Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches. Proc. Natl. Acad. Sci. USA 2011, 108, 7757-7762.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 7757-7762
    • Smith, K.D.1    Shanahan, C.A.2    Moore, E.L.3    Simon, A.C.4    Strobel, S.A.5
  • 19
    • 46149116544 scopus 로고    scopus 로고
    • Stereospecificity, substrate, and inhibitory properties of nucleoside diphosphate analogs for creatine and pyruvate kinases
    • Wennefors, C.K.; Dobrikov, M.I.; Xu, Z.; Li, P.; Shaw, B.R. Stereospecificity, substrate, and inhibitory properties of nucleoside diphosphate analogs for creatine and pyruvate kinases. Bioorg. Chem. 2008, 36, 169-177.
    • (2008) Bioorg. Chem. , vol.36 , pp. 169-177
    • Wennefors, C.K.1    Dobrikov, M.I.2    Xu, Z.3    Li, P.4    Shaw, B.R.5
  • 20
    • 7044222422 scopus 로고    scopus 로고
    • Oligonucleotide incorporation of 8-thio-2′-deoxyguanosine
    • Hamm, M.L.; Cholera, R.; Hoey, C.L.; Gill, T.J. Oligonucleotide incorporation of 8-thio-2′-deoxyguanosine. Org. Lett. 2004, 6, 3817-3820.
    • (2004) Org. Lett. , vol.6 , pp. 3817-3820
    • Hamm, M.L.1    Cholera, R.2    Hoey, C.L.3    Gill, T.J.4
  • 21
    • 34347264416 scopus 로고    scopus 로고
    • Substrate specificity of fpg (MutM) and hOGG1, two repair glycosylases
    • Hamm, M.L.; Gill, T.J.; Nicolson, S.C.; Summers, M.R. Substrate specificity of Fpg (MutM) and hOGG1, two repair glycosylases. J. Am. Chem. Soc. 2007, 129, 7724-7725.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 7724-7725
    • Hamm, M.L.1    Gill, T.J.2    Nicolson, S.C.3    Summers, M.R.4
  • 24
  • 25
    • 35548990179 scopus 로고    scopus 로고
    • Stable analogues of aminoacyl-tRNA for inhibition of an essential step of bacterial cell-wall synthesis
    • Chemama, M.; Fonvielle, M.; Villet, R.; Arthur, M.; Valéry, J.M.; Etheve-Quelquejeu, M. Stable analogues of aminoacyl-tRNA for inhibition of an essential step of bacterial cell-wall synthesis. J. Am. Chem. Soc. 2007, 129, 12642-12643.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 12642-12643
    • Chemama, M.1    Fonvielle, M.2    Villet, R.3    Arthur, M.4    Valéry, J.M.5    Etheve-Quelquejeu, M.6
  • 26
    • 77249096959 scopus 로고    scopus 로고
    • Exploring chemical modifications for siRNA therapeutics: A structural and functional outlook
    • Shukla, S.; Sumaria, C.S.; Pradeepkumar, P.I. Exploring chemical modifications for siRNA therapeutics: A structural and functional outlook. ChemMedChem 2010, 5, 328-349.
    • (2010) ChemMedChem , vol.5 , pp. 328-349
    • Shukla, S.1    Sumaria, C.S.2    Pradeepkumar, P.I.3
  • 27
    • 79959275876 scopus 로고    scopus 로고
    • Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins
    • Wang, J.; Zhou, J.; Donaldson, G.P.; Nakayama, S.; Yan, L.; Lam, Y.F.; Lee, V.T.; Sintim, H.O. Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins. J. Am. Chem. Soc. 2011, 133, 9320-9330.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 9320-9330
    • Wang, J.1    Zhou, J.2    Donaldson, G.P.3    Nakayama, S.4    Yan, L.5    Lam, Y.F.6    Lee, V.T.7    Sintim, H.O.8
  • 28
    • 80053311154 scopus 로고    scopus 로고
    • Differential analogue binding by two classes of c-di-GMP riboswitches
    • Shanahan, C.A.; Gaffney, B.L.; Jones, R.A.; Strobel, S.A. Differential analogue binding by two classes of c-di-GMP riboswitches. J. Am. Chem. Soc. 2011, 133, 15578-15592.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 15578-15592
    • Shanahan, C.A.1    Gaffney, B.L.2    Jones, R.A.3    Strobel, S.A.4
  • 29
    • 79953178284 scopus 로고    scopus 로고
    • Interactions of the c-di-GMP riboswitch with its second messenger ligand
    • Smith, K.D.; Strobel, S.A. Interactions of the c-di-GMP riboswitch with its second messenger ligand. Biochem. Soc. Trans. 2011, 39, 647-651.
    • (2011) Biochem. Soc. Trans. , vol.39 , pp. 647-651
    • Smith, K.D.1    Strobel, S.A.2
  • 31
    • 77956344104 scopus 로고    scopus 로고
    • Synthesis of cyclic di-nucleotidic acids as potential inhibitors targeting diguanylate cyclase
    • Ching, S.M.; Tan, W.J.; Chua, K.L.; Lam, Y. Synthesis of cyclic di-nucleotidic acids as potential inhibitors targeting diguanylate cyclase. Bioorg. Med. Chem. 2010, 18, 6657-6665.
    • (2010) Bioorg. Med. Chem. , vol.18 , pp. 6657-6665
    • Ching, S.M.1    Tan, W.J.2    Chua, K.L.3    Lam, Y.4
  • 32
    • 84863772351 scopus 로고    scopus 로고
    • Synthesis and characterization of a fluorescent analogue of cyclic di-GMP
    • Sharma, I.M.; Dhanaraman, T.; Mathew, R.; Chatterji, D. Synthesis and characterization of a fluorescent analogue of cyclic di-GMP. Biochemistry 2012, 51, 5443-5453.
    • (2012) Biochemistry , vol.51 , pp. 5443-5453
    • Sharma, I.M.1    Dhanaraman, T.2    Mathew, R.3    Chatterji, D.4
  • 33
    • 84863135772 scopus 로고    scopus 로고
    • Differential binding of 2′-biotinylated analogs of c-di-GMP with c-di-GMP riboswitches and binding proteins
    • Luo, Y.; Zhou, J.; Watt, S.K.; Lee, V.T.; Dayie, T.K.; Sintim, H.O. Differential binding of 2′-biotinylated analogs of c-di-GMP with c-di-GMP riboswitches and binding proteins. Mol. Biosyst. 2012, 8, 772-778.
    • (2012) Mol. Biosyst. , vol.8 , pp. 772-778
    • Luo, Y.1    Zhou, J.2    Watt, S.K.3    Lee, V.T.4    Dayie, T.K.5    Sintim, H.O.6
  • 34
    • 0037020351 scopus 로고    scopus 로고
    • Efficient and simple solid-phase synthesis of short cyclic oligodeoxynucleotides bearing a phosphorothioate linkage
    • Smietana, M.; Kool, E.T. Efficient and simple solid-phase synthesis of short cyclic oligodeoxynucleotides bearing a phosphorothioate linkage. Angew. Chem. Int. Ed. Engl. 2002, 41, 3704-3707.
    • (2002) Angew. Chem. Int. Ed. Engl. , vol.41 , pp. 3704-3707
    • Smietana, M.1    Kool, E.T.2
  • 35
    • 84866702967 scopus 로고    scopus 로고
    • Structural polymorphism of c-di-GMP bound to an EAL domain and in complex with a type II PilZ-domain protein
    • Chin, K.H.; Kuo, W.T.; Yu, Y.J.; Liao, Y.T.; Yang, M.T.; Chou, S.H. Structural polymorphism of c-di-GMP bound to an EAL domain and in complex with a type II PilZ-domain protein. Acta Crystallogr. D Biol. Crystallogr. 2012, 68, 1380-1392.
    • (2012) Acta Crystallogr. D Biol. Crystallogr. , vol.68 , pp. 1380-1392
    • Chin, K.H.1    Kuo, W.T.2    Yu, Y.J.3    Liao, Y.T.4    Yang, M.T.5    Chou, S.H.6
  • 36
    • 33744904451 scopus 로고    scopus 로고
    • Polymorphism of the signaling molecule c-di-GMP
    • Zhang, Z.; Kim, S.; Gaffney, B.L.; Jones, R.A. Polymorphism of the signaling molecule c-di-GMP. J. Am. Chem. Soc. 2006, 128, 7015-7024.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 7015-7024
    • Zhang, Z.1    Kim, S.2    Gaffney, B.L.3    Jones, R.A.4
  • 37
    • 11244341190 scopus 로고    scopus 로고
    • C-di-GMP displays a monovalent metal ion-dependent polymorphism
    • Zhang, Z.; Gaffney, B.L.; Jones, R.A. C-di-GMP displays a monovalent metal ion-dependent polymorphism. J. Am. Chem. Soc. 2004, 126, 16700-16701.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16700-16701
    • Zhang, Z.1    Gaffney, B.L.2    Jones, R.A.3
  • 38
    • 70450206724 scopus 로고    scopus 로고
    • Revision A02; Software for technical computation; Gaussian Inc.: Wallingford, CT, USA
    • Gaussian 09, Revision A02; Software for technical computation; Gaussian Inc.: Wallingford, CT, USA, 2009.
    • (2009) Gaussian 09
  • 39
    • 84855952253 scopus 로고    scopus 로고
    • Oligomer formation of the bacterial second messenger c-di-GMP: Reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations
    • Gentner, M.; Allan, M.G.; Zaehringer, F.; Schirmer, T.; Grzesiek, S. Oligomer formation of the bacterial second messenger c-di-GMP: Reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations. J. Am. Chem. Soc. 2012, 134, 1019-1029.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 1019-1029
    • Gentner, M.1    Allan, M.G.2    Zaehringer, F.3    Schirmer, T.4    Grzesiek, S.5
  • 40
    • 71449123530 scopus 로고    scopus 로고
    • Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
    • Kulshina, N.; Baird, N.J.; Ferré-D'Amaré, A.R. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat. Struct. Mol. Biol. 2009, 16, 1212-1217.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1212-1217
    • Kulshina, N.1    Baird, N.J.2    Ferré-D'Amaré, A.R.3
  • 42
    • 77956021842 scopus 로고    scopus 로고
    • Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch
    • Smith, K.D.; Lipchock, S.V.; Livingston, A.L.; Shanahan, C.A.; Strobel, S.A. Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch. Biochemistry 2010, 49, 7351-7359.
    • (2010) Biochemistry , vol.49 , pp. 7351-7359
    • Smith, K.D.1    Lipchock, S.V.2    Livingston, A.L.3    Shanahan, C.A.4    Strobel, S.A.5
  • 43
    • 84865016402 scopus 로고    scopus 로고
    • Nanomolar fluorescent detection of c-di-GMP using a modular aptamer strategy
    • Nakayama, S.; Luo, Y.; Zhou, J.; Dayie, T.K.; Sintim, H.O. Nanomolar fluorescent detection of c-di-GMP using a modular aptamer strategy. Chem. Commun. (Camb.) 2012, 48, 9059-9061.
    • (2012) Chem. Commun. (Camb.) , vol.48 , pp. 9059-9061
    • Nakayama, S.1    Luo, Y.2    Zhou, J.3    Dayie, T.K.4    Sintim, H.O.5
  • 44
    • 35348914895 scopus 로고    scopus 로고
    • Photomodulation of PS-modified oligonucleotides containing azobenzene substituent at pre-selected positions in phosphate backbone
    • Patnaik, S.; Kumar, P.; Garg, B.S.; Gandhi, R.P.; Gupta, K.C. Photomodulation of PS-modified oligonucleotides containing azobenzene substituent at pre-selected positions in phosphate backbone. Bioorg. Med. Chem. 2007, 15, 7840-7849.
    • (2007) Bioorg. Med. Chem. , vol.15 , pp. 7840-7849
    • Patnaik, S.1    Kumar, P.2    Garg, B.S.3    Gandhi, R.P.4    Gupta, K.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.