The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif

Journal of Physical Chemistry B

Volumn 114, Issue 43, 2010, Pages 13839-13846

  Zhang, Yubo ^a   Baaden, Marc ^b   Yan, Junjie ^a   Shao, Jinzhen ^a   Qiu, Su ^c   Wu, Yingliang ^c   Ding, Yi ^a  

^a BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^b France   (France)

^c WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPLEXATION; COMPUTER SIMULATION; DYNAMICS; FREE ENERGY; HYDROPHOBICITY; MITOCHONDRIA; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; OXYGEN;

BINDING FREE ENERGY; BINDING MECHANISMS; BINDING MODES; CLUSTERING ANALYSIS; CYTOSOLS; ENERGY MINIMIZATION; EXPERIMENTAL DATA; EXPERT KNOWLEDGE; EXPLICIT SOLVENTS; GENERALIZED BORN; HYDROPHOBIC INTERACTIONS; INTERMOLECULAR DISTANCE; MD SIMULATION; MITOCHONDRIAL PROTEIN; MITOCHONDRIAL SUPEROXIDE; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR RECOGNITION MECHANISM; ORYZA SATIVA; OUTER MEMBRANE; RELATIVE FREE ENERGY; SCANNING TECHNIQUES; SEQUENCE ALIGNMENTS; SOLVATION MODELS; STRUCTURAL BASIS; SUPER OXIDE DISMUTASE; TRANSLOCASES;

BINDING ENERGY;

EID: 78549279787     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp103547s     Document Type: Article

References (39)

1. Saitoh, T.; Igura, M.; Obita, T.; Ose, T.; Kojima, R.; Maenaka, K.; Endo, T.; Kohda, D. EMBO J. 2007, 26, 4777.
2. Abe, Y.; Shodai, T.; Muto, T.; Mihara, K.; Torii, H.; Nishikawa, S.; Endo, T.; Kohda, D. Cell (Cambridge, MA, U. S.) 2000, 100, 551.
3. Rapaport, D. J. Cell Biol. 2005, 171, 419.
4. Iwahashi, J.; Yamazaki, S.; Komiya, T.; Nomura, N.; Nishikawa, S.; Endo, T.; Mihara, K. J. Biol. Chem. 1997, 272, 18467.
5. Likic, V. A.; Perry, A.; Hulett, J.; Derby, M.; Traven, A.; Waller, R. F.; Keeling, P. J.; Koehler, C. M.; Curran, S. P.; Gooley, P. R.; Lithgow, T. J. Mol. Biol. 2005, 347, 81.
6. Bohnert, M.; Pfanner, N.; van der Laan, M. FEBS Lett. 2007, 581, 2802.
7. Komiya, T.; Rospert, S.; Koehler, C.; Looser, R.; Schatz, G.; Mihara, K. EMBO J. 1998, 17, 3886.
8. Schleiff, E.; Shore, G. C.; Goping, I. S. J. Biol. Chem. 1997, 272, 17784.
9. Heins, L.; Schmitz, U. K. Plant J. 1996, 9, 829.
10. Perry, A. J.; Rimmer, K. A.; Mertens, H. D.; Waller, R. F.; Mulhern, T. D.; Lithgow, T.; Gooley, P. R. Plant Physiol. Biochem. 2008, 46, 265.
11. Werhahn, W.; Niemeyer, A.; Jansch, L.; Kruft, V.; Schmitz, U. K.; Braun, H. Plant Physiol. 2001, 125, 943.
12. Perry, A. J.; Hulett, J. M.; Likic, V. A.; Lithgow, T.; Gooley, P. R. Curr. Biol. 2006, 16, 221.
13. Ramage, L.; Junne, T.; Hahne, K.; Lithgow, T.; Schatz, G. EMBO J. 1993, 12, 4115.
14. Endo, T.; Kohda, D. Biochim. Biophys. Acta 2002, 1592, 3.
15. Durrieu, M. P.; Lavery, R.; Baaden, M. Biophys. J. 2008, 94, 3436.
16. Yi, H.; Qiu, S.; Cao, Z.; Wu, Y.; Li, W. Proteins 2008, 70, 844.
17. Qiu, S.; Yi, H.; Liu, H.; Cao, Z.; Wu, Y.; Li, W. J. Chem. Inf. Model. 2009, 49, 1831.
18. Law, R. J.; Capener, C.; Baaden, M.; Bond, P. J.; Campbell, J.; Patargias, G.; Arinaminpathy, Y.; Sansom, M. S. J. Mol. Graphics Modell. 2005, 24, 157.
19. Chen, R.; Li, L.; Weng, Z. Proteins 2003, 52, 80.
20. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235.
21. Guex, N.; Peitsch, M. C. Electrophoresis 1997, 18, 2714.
22. von Heijne, G. EMBO J. 1986, 5, 1335.
23. Roise, D.; Theiler, F.; Horvath, S. J.; Tomich, J. M.; Richards, J. H.; Allison, D. S.; Schatz, G. EMBO J. 1988, 7, 649.
24. Moberg, P.; Nilsson, S.; Stahl, A.; Eriksson, A. C.; Glaser, E.; Maler, L. J. Mol. Biol. 2004, 336, 1129.
25. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668.
26. Han, S.; Yi, H.; Yin, S. J.; Chen, Z. Y.; Liu, H.; Cao, Z. J.; Wu, Y. L.; Li, W. X. J. Biol. Chem. 2008, 283, 19058.
27. Wu, Y.; Cao, Z.; Yi, H.; Jiang, D.; Mao, X.; Liu, H.; Li, W. Biophys. J. 2004, 87, 105.
28. Yi, H.; Cao, Z.; Yin, S.; Dai, C.; Wu, Y.; Li, W. J. Proteome Res. 2007, 6, 611.
29. Qiu, D.; Shenkin, P.; Hollinger, F.; Still, C. J. Phys. Chem. A 1997, 101, 3005.
30. Tsui, V.; Case, D. A. J. Am. Chem. Soc. 2000, 122, 2489.
31. Wang, J.; Cieplak, P.; Kollman, P. J. Comput. Chem. 2000, 21, 1049.
32. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. J. Comput. Chem. 2005, 26, 1701.
33. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
34. Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577.
35. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
36. Thompson, J. D.; Higgins, D. G.; Gibson, T. J. Nucleic Acids Res. 1994, 22, 4673.
37. R Development Core Team. R: A language and enVironment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria, 2009.
38. Muto, T.; Obita, T.; Abe, Y.; Shodai, T.; Endo, T.; Kohda, D. J. Mol. Biol. 2001, 306, 137.
39. Cordes, F. S.; Bright, J. N.; Sansom, M. S. J. Mol. Biol. 2002, 323, 951.