메뉴 건너뛰기




Volumn 29, Issue 7, 2011, Pages 915-919

Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs

Author keywords

Bioremediation; Docking; Molecular dynamics; PAH; PhnI

Indexed keywords

AROMATIC RINGS; COMPUTATIONAL RESOURCES; COMPUTATIONAL STUDIES; DIOXYGENASES; DOCKING CALCULATIONS; EXTERIOR SURFACES; INNER CORE; MOLECULAR DYNAMICS CALCULATION; OPTIMAL POSITION; PAH; PHNI; RAPID DETERMINATION; SMALL IONS; SPHINGOMONAS;

EID: 79955846512     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.03.001     Document Type: Article
Times cited : (8)

References (26)
  • 1
    • 0034733121 scopus 로고    scopus 로고
    • New synthetic approaches to polycyclic aromatic hydrocarbons and their carcinogenic oxidized metabolites: Derivatives of benzo[s]picene, benzo[rst]pentaphene, and dibenzo[b,def]chrysene
    • DOI 10.1021/jo9918044
    • F.J. Zhang, C. Cortez, R.G. Harvey, New synthetic approaches to polycyclic aromatic hydrocarbons and their carcinogenic oxidized metabolites: derivatives of benzo[s]picene, benzo[rst]pentaphene, and dibenzo[b,def]chrysene, J. Org. Chem. 65 (2000) 3952-3960. (Pubitemid 32063396)
    • (2000) Journal of Organic Chemistry , vol.65 , Issue.13 , pp. 3952-3960
    • Zhang, F.-J.1    Cortez, C.2    Harvey, R.G.3
  • 2
    • 0037701540 scopus 로고    scopus 로고
    • Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: Evidence for two ring-hydroxylating dioxygenases
    • DOI 10.1128/JB.185.13.3828-3841.2003
    • S. Krivobok, S. Kuony, C. Meyer, M. Louwagie, J.C. Willison, Y. Jouanneau, Identification of pyrene-induced proteins in Mycobacterium sp strain 6PY1: evidence for two ring-hydroxylating dioxygenases, J. Bacteriol. 185 (2003) 3828-3841. (Pubitemid 36735934)
    • (2003) Journal of Bacteriology , vol.185 , Issue.13 , pp. 3828-3841
    • Krivobok, S.1    Kuony, S.2    Meyer, C.3    Louwagie, M.4    Willison, J.C.5    Jouanneau, Y.6
  • 5
    • 67649770254 scopus 로고    scopus 로고
    • Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review
    • A.K. Haritash, C.P. Kaushik, Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review, J. Hazard. Mater. 169 (2009) 1-15.
    • (2009) J. Hazard. Mater. , vol.169 , pp. 1-15
    • Haritash, A.K.1    Kaushik, C.P.2
  • 6
    • 0034102192 scopus 로고    scopus 로고
    • Purification, partial characterization, and reactivity with aromatic compounds of two laccases from Marasmius quercophilus strain 17
    • A.M. Farnet, S. Criquet, S. Tagger, G. Gil, J. Le Petit, Purification, partial characterization, and reactivity with aromatic compounds of two laccases from Marasmius quercophilus strain 17, Can. J. Microbiol. 46 (2000) 189-194. (Pubitemid 30173599)
    • (2000) Canadian Journal of Microbiology , vol.46 , Issue.3 , pp. 189-194
    • Farnet, A.M.1    Criquet, S.2    Tagger, S.3    Gil, G.4    Le, P.J.5
  • 7
    • 0036141384 scopus 로고    scopus 로고
    • Interactions between a polycyclic aromatic hydrocarbon mixture and the microbial communities in a natural freshwater sediment
    • DOI 10.1016/S0045-6535(01)00064-9, PII S0045653501000649
    • G.J. Verrhiest, B. Clement, B. Volat, B. Montuelle, Y. Perrodin, Interactions between a polycyclic aromatic hydrocarbon mixture and the microbial communities in a natural freshwater sediment, Chemosphere 46 (2002) 187-196. (Pubitemid 34081103)
    • (2002) Chemosphere , vol.46 , Issue.2 , pp. 187-196
    • Verrhiest, G.J.1    Clement, B.2    Volat, B.3    Montuelle, B.4    Perrodin, Y.5
  • 8
    • 26444576427 scopus 로고    scopus 로고
    • Computer evaluation of protein segments removal effects from naphthalene 1,2-dioxygenase enzyme on polycyclic aromatic hydrocarbons interaction
    • DOI 10.1016/j.bej.2005.08.011, PII S1369703X05002354
    • V. Librando, S. Forte, Computer evaluation of protein segments removal effects from naphthalene 1,2-dioxygenase enzyme on polycyclic aromatic hydrocarbons interaction, Biochem. Eng. J. 27 (2005) 161-166. (Pubitemid 41428313)
    • (2005) Biochemical Engineering Journal , vol.27 , Issue.2 , pp. 161-166
    • Librando, V.1    Forte, S.2
  • 9
    • 42549124282 scopus 로고    scopus 로고
    • Assessment of organic pollutants in coastal sediments, UAE
    • DOI 10.1007/s00254-007-0880-x, Advances and challenges of GIS and DBMS applications in karst
    • E.A.A. Gawad, M. Al Azab, M.M. Lotfy, Assessment of organic pollutants in coastal sediments, UAE, Environ. Geol. 54 (2008) 1091-1102. (Pubitemid 351575146)
    • (2008) Environmental Geology , vol.54 , Issue.5 , pp. 1091-1102
    • Abdel, G.E.A.1    Al, A.M.2    Lotfy, M.M.3
  • 10
    • 10044275318 scopus 로고    scopus 로고
    • Oil spill in the Río de la Plata estuary, Argentina: 2-Hydrocarbon disappearance rates in sediments and soils
    • DOI 10.1016/j.envpol.2004.07.028, PII S0269749104003410
    • J.C. Colombo, A. Barreda, C. Bilos, N. Cappelletti, M.C. Migoya, C. Skorupka, Oil spill in the Rio de la Plata estuary, Argentina: 2-hydrocarbon disappearance rates in sediments and soils, Environ. Pollut. 134 (2005) 267-276. (Pubitemid 39612462)
    • (2005) Environmental Pollution , vol.134 , Issue.2 , pp. 267-276
    • Colombo, J.C.1    Barreda, A.2    Bilos, C.3    Cappelletti, N.4    Migoya, M.C.5    Skorupka, C.6
  • 11
    • 0042827500 scopus 로고    scopus 로고
    • Distribution and source recognition of polycyclic aromatic hydrocarbons in the sediments of Hsin-ta Harbour and adjacent coastal areas, Taiwan
    • M.D. Fang, C.L. Lee, C.S. Yu, Distribution and source recognition of polycyclic aromatic hydrocarbons in the sediments of Hsin-ta Harbour and adjacent coastal areas, Taiwan, Mar. Pollut. Bull. 46 (2003) 941-953.
    • (2003) Mar. Pollut. Bull. , vol.46 , pp. 941-953
    • Fang, M.D.1    Lee, C.L.2    Yu, C.S.3
  • 12
    • 67650122851 scopus 로고    scopus 로고
    • Distribution and characteristics of polycyclic aromatic hydrocarbons (PAHs) in sediments of Hadhramout coastal area, Gulf of Aden, Yemen
    • A.R. Mostafa, T.L. Wade, S.T. Sweet, A.K.A. Al-Alimi, A.O. Barakat, Distribution and characteristics of polycyclic aromatic hydrocarbons (PAHs) in sediments of Hadhramout coastal area, Gulf of Aden, Yemen, J. Mar. Syst. 78 (2009) 1-8.
    • (2009) J. Mar. Syst. , vol.78 , pp. 1-8
    • Mostafa, A.R.1    Wade, T.L.2    Sweet, S.T.3    Al-Alimi, A.K.A.4    Barakat, A.O.5
  • 14
    • 34248166634 scopus 로고    scopus 로고
    • Trophic dilution of polycyclic aromatic hydrocarbons (PAHs) in a marine food web from Bohai Bay, North China
    • Y. Wan, X.H. Jin, J.Y. Hu, F. Jin, Trophic dilution of polycyclic aromatic hydrocarbons (PAHs) in a marine food web from Bohai Bay, North China, Environ. Sci. Technol. 41 (2007) 3109-3114.
    • (2007) Environ. Sci. Technol. , vol.41 , pp. 3109-3114
    • Wan, Y.1    Jin, X.H.2    Hu, J.Y.3    Jin, F.4
  • 15
    • 52949098735 scopus 로고    scopus 로고
    • Development of a programmed temperature vaporization-gas chromatography-tandem mass spectrometry method for polycyclic aromatic hydrocarbons analysis in biota samples at ultratrace levels
    • V. Fernandez-Gonzalez, S. Muniategui-Lorenzo, P. Lopez-Mahia, D. Prada-Rodriguez, Development of a programmed temperature vaporization-gas chromatography-tandem mass spectrometry method for polycyclic aromatic hydrocarbons analysis in biota samples at ultratrace levels, J. Chromatogr. A 1207 (2008) 136-145.
    • (2008) J. Chromatogr. A , vol.1207 , pp. 136-145
    • Fernandez-Gonzalez, V.1    Muniategui-Lorenzo, S.2    Lopez-Mahia, P.3    Prada-Rodriguez, D.4
  • 16
    • 34247578182 scopus 로고    scopus 로고
    • The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1
    • DOI 10.1111/j.1742-4658.2007.05783.x
    • J. Jakoncic, Y. Jouanneau, C. Meyer, V. Stojanoff, The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1, FEBS J. 274 (2007) 2470-2481. (Pubitemid 46669334)
    • (2007) FEBS Journal , vol.274 , Issue.10 , pp. 2470-2481
    • Jakoncic, J.1    Jouanneau, Y.2    Meyer, C.3    Stojanoff, V.4
  • 17
    • 33845483902 scopus 로고    scopus 로고
    • The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1
    • DOI 10.1016/j.bbrc.2006.11.117, PII S0006291X06025630
    • J. Jakoncic, Y. Jouanneau, C. Meyer, V. Stojanoff, The catalytic pocket of the ringhydroxylating dioxygenase from Sphingomonas CHY-1, Biochem. Biophys. Res. Commun. 352 (2007) 861-866. (Pubitemid 44913990)
    • (2007) Biochemical and Biophysical Research Communications , vol.352 , Issue.4 , pp. 861-866
    • Jakoncic, J.1    Jouanneau, Y.2    Meyer, C.3    Stojanoff, V.4
  • 18
    • 36749025740 scopus 로고    scopus 로고
    • An Insilco approach to bioremediation: Laccase as a case study
    • DOI 10.1016/j.jmgm.2007.05.005, PII S1093326307000915
    • P.S. Suresh, A. Kumar, R. Kumar, V.P. Singh, An in silco approach to bioremediation: laccase as a case study, J. Mol. Graph. Model. 26 (2008) 845-849. (Pubitemid 350213442)
    • (2008) Journal of Molecular Graphics and Modelling , vol.26 , Issue.5 , pp. 845-849
    • Suresh, P.S.1    Kumar, A.2    Kumar, R.3    Singh, V.P.4
  • 20
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983) 926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 22
    • 69349096918 scopus 로고    scopus 로고
    • Molecular docking study of A(3) adenosine receptor antagonists and pharmacophore-based drug design
    • J. Wei, H. Li, W.L. Qu, Q.Z. Gao, Molecular docking study of A(3) adenosine receptor antagonists and pharmacophore-based drug design, Neurochem. Int. 55 (2009) 637-642.
    • (2009) Neurochem. Int. , vol.55 , pp. 637-642
    • Wei, J.1    Li, H.2    Qu, W.L.3    Gao, Q.Z.4
  • 23
    • 76149120388 scopus 로고    scopus 로고
    • Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • O. Trott, A.J. Olson, Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem. 31 (2010) 455-461.
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 24
    • 84861407812 scopus 로고    scopus 로고
    • Computation of tunnels in protein molecules using Delaunay triangulation
    • P. Medek, P. Benes, J. Sochor, Computation of tunnels in protein molecules using Delaunay triangulation, J. WSCG 15 (2007) 107-114.
    • (2007) J. WSCG , vol.15 , pp. 107-114
    • Medek, P.1    Benes, P.2    Sochor, J.3
  • 25
    • 62649132420 scopus 로고    scopus 로고
    • Biodegradation of chrysene, an aromatic hydrocarbon by Polyporus sp S133 in liquid medium
    • T. Hadibarata, S. Tachibana, K. Itoh, Biodegradation of chrysene, an aromatic hydrocarbon by Polyporus sp S133 in liquid medium, J. Hazard. Mater. 164 (2009) 911-917.
    • (2009) J. Hazard. Mater. , vol.164 , pp. 911-917
    • Hadibarata, T.1    Tachibana, S.2    Itoh, K.3
  • 26
    • 34548267542 scopus 로고    scopus 로고
    • Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species
    • M. Pappalardo, D. Milardi, D. Grasso, C. La Rosa, Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species, New J. Chem. 31 (2007) 901-905.
    • (2007) New J. Chem. , vol.31 , pp. 901-905
    • Pappalardo, M.1    Milardi, D.2    Grasso, D.3    La Rosa, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.