Analysis of rare codon and mRNA structure about ustilago maydis CYP51 and molecular docking with fungicide tebuconazole

Progress in Biochemistry and Biophysics

Volumn 38, Issue 8, 2011, Pages 751-758

  Li, Shu Xiang ^a   Han, Rui ^a,b   Yuan, Li Ling ^a   Xiong, Li ^a   Yuan, Yong Ze ^a   Yang, Jiang Ke ^c   Yan, Yun Jun ^c   Liu, De Li ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

^b QINGHAI UNIVERSITY   (China)

^c HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Homology modeling; Molecular docking; Rare codon; Translation initiation region (TIR); UmCYP51

Indexed keywords

ESCHERICHIA COLI; USTILAGO MAYDIS;

EID: 81355160904     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2010.00617     Document Type: Article

References (24)

1. Lepesheva G, Hargrove T, Kleshchenko Y, et al. CYP51: A major drug target in the cytochrome P450 superfamily. Lipids, 2008, 43(12): 1117-1125
2. Lamb D C, Kelly D E, Venkateswarlu K, et al. Generation of a complete, soluble, and catalytically active sterol 14 alphademethylase- reductase complex. Biochemistry, 1999, 38 (27): 8733-8738
3. Sheng C, Miao Z, Ji H, et al. Three-dimensional model of lanosterol 14 alpha-demethylase from cryptococcus neoformans: active-site characterization and insights into azole binding. Antimicrob Agents Chemother, 2009, 53(8): 3487-3495
4. Zhao L, Liu D L, Zhang Q Y, et al. Expression and homology modeling of sterol 14 alpha-demethylase from Penicillium digitatum. FEMS Microbiol Lett, 2007, 277(1): 37-43 (Pubitemid 350045655)
5. Lepesheva GI, Park H W, Hargrove T Y, et al. Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections. J Biol Chem, 2010, 285(3): 1773-1780
6. Strushkevich N, Usanov S A, Park H W. Structural basis of human CYP51 inhibition by antifungal azoles. J Mol Biol, 2010, 397(4): 1067-1078
7. Han R, Deng L F, Li C, et al. Chin J Biotech, 2008, 24 (10): 1747-1753
8. Zhang J, Shi X F, Liu C Q, et al. Prog Biochem Biophys, 2001, 28(4): 523-527
9. Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, 22(22): 4673-4680 (Pubitemid 24354800)
10. Eswar N, Webb B, Marti-renom M A, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci, 2007, 2(12): 15-32
11. Lindahl E, Hess B, Vander S D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model, 2001, 7(8): 306-317 (Pubitemid 36153547)
12. van Gunsteren WF, Billeter S R, Eising A A, et al. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Groningen: vdf Hochschulverlag AG an der ETH Z?rich and BIOMOS b.v., 1996: 21-25
13. YORK D, YANG W. The fast fourier poisson method for calculating ewald sums. J ChemPhys, 1994, 101(4): 3298-3300
14. Laskowski R A, Macarthur MW, Moss D S, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystall, 1993, 26(2): 283-291
15. Morris G M, Goodsell D S, HallidayR S, et al. Automated docking using a Lamarckian genetic algorithmand an empirical binding free energy function. J Comput Chem, 1998, 19(14): 1639-1662 (Pubitemid 128590223)
16. Zhu HM, Chen WZ, WangC X, et al. Acta ChimSin, 2004, 62(8): 745-749
17. Li B, Liu M, Hu WX. Acta Phys-ChimSin, 2010, 26(01): 206-214
18. Cong X J, Tan J J, Wang C X, et al. Prog Biochem Biophys, 2010, 37(8):904-915
19. Wallace A C, Laskowski R A, Thornton J M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng, 1995, 8(2): 127-134
20. Azizian H, Bahrami H, Pasalar P, et al. Molecular modeling of Helicobacter pylori arginase and the inhibitor coordination interactions. J Mol Graphi Mod, 2010, 28(7): 626-635
21. Ma X H, Chen W Z, Wang C X, et al. Bull Acad Mili Med Sci, 2005, 29(4): 255-358
22. Ganoza M C, Kofoid E C, Marliere P, et al. Potential secondary structure at translation-initiation sites. Nucleic Acids Research, 1987, 15(1): 345-360 (Pubitemid 17222740)
23. Rex G, Surin B, Besse G, et al. The mechanism of translational coupling in Escherichia coli. Higher order structure in the atpHA mRNA acts as a conformational switch regulating the access of de novo initiating ribosomes. J Biol Chem, 1994, 269 (27): 18118-18127
24. De S M, Vanduin J. Control of translation by mRNA secondary structure in Escherichia coli: a quantitative analysis of literature data. J Mol Biol, 1994, 244(2): 144-150