Crystallographic snapshots of Tom20-mitochondrial presequence interactions with disulfide-stabilized peptides

Biochemistry

Volumn 50, Issue 24, 2011, Pages 5487-5496

  Saitoh, Takashi ^a   Igura, Mayumi ^a   Miyazaki, Yusuke ^a   Ose, Toyoyuki ^a,c   Maita, Nobuo ^b   Kohda, Daisuke ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKUSHIMA   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE METHODS; BOUND STATE; CO-CRYSTALS; COVALENT ATTACHMENT; CYTOSOLS; DISULFIDE BONDS; INTERACTION MODES; INTERMOLECULAR DISULFIDE BOND; MITOCHONDRIAL PROTEIN; N-TERMINALS; PRECURSOR PROTEINS; PROTEIN-PEPTIDE INTERACTIONS; UNBOUND STATE;

BIOSYNTHESIS; COVALENT BONDS; OPTIMIZATION; PEPTIDES;

MITOCHONDRIA;

DISULFIDE; REDUCING AGENT; TRANSLOCASE OF OUTER MITOCHONDRIAL MEMBRANE 20;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; COVALENT BOND; CRYSTAL STRUCTURE; CRYSTALLIZATION; CYTOSOL; DISULFIDE BOND; MITOCHONDRION; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN SYNTHESIS; X RAY CRYSTALLOGRAPHY;

ALDEHYDE DEHYDROGENASE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; CRYSTALLOGRAPHY, X-RAY; DISULFIDES; MITOCHONDRIAL PROTEINS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; RATS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECOMBINANT PROTEINS;

EID: 79959195166     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200470x     Document Type: Article

References (37)

1. Bruce, B. D. (2001) The paradox of plastid transit peptides: conservation of function despite divergence in primary structure Biochim. Biophys. Acta 1541, 2-21 (Pubitemid 34024825)
2. Pandey, K. N. (2010) Small peptide recognition sequence for intracellular sorting Curr. Opin. Biotechnol. 21, 611-620
3. Christophe, D., Christophe-Hobertus, C., and Pichon, B. (2000) Nuclear targeting of proteins: how many different signals? Cell Signal 12, 337-341 (Pubitemid 30261549)
4. Schatz, G. and Dobberstein, B. (1996) Common principles of protein translocation across membranes Science 271, 1519-1526 (Pubitemid 26097210)
5. Pfanner, N. (2000) Protein sorting: recognizing mitochondrial presequences Curr. Biol. 10, R412-415
6. Erijman, A., Aizner, Y., and Shifman, J. M. (2011) Multispecific recognition: mechanism, evolution, and design Biochemistry 50, 602-611
7. Schreiber, G. and Keating, A. E. (2011) Protein binding specificity versus promiscuity Curr. Opin. Struct. Biol. 21, 50-61
8. Vaynberg, J., Fukuda, T., Chen, K., Vinogradova, O., Velyvis, A., Tu, Y., Ng, L., Wu, C., and Qin, J. (2005) Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility Mol. Cell 17, 513-523 (Pubitemid 40269116)
9. Meenan, N. A., Sharma, A., Fleishman, S. J., Macdonald, C. J., Morel, B., Boetzel, R., Moore, G. R., Baker, D., and Kleanthous, C. (2010) The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction Proc. Natl. Acad. Sci. U.S.A. 107, 10080-10085
10. Huang, H., Harrison, S. C., and Verdine, G. L. (2000) Trapping of a catalytic HIV reverse transcriptase template:primer complex through a disulfide bond Chem. Biol. 7, 355-364 (Pubitemid 30319704)
11. Fremont, D. H., Hendrickson, W. A., Marrack, P., and Kappler, J. (1996) Structures of an MHC class II molecule with covalently bound single peptides Science 272, 1001-1004 (Pubitemid 26259315)
12. Hennecke, J., Carfi, A., and Wiley, D. C. (2000) Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1 EMBO J. 19, 5611-5624
13. Pellegrini, L., Yu, D. S., Lo, T., Anand, S., Lee, M., Blundell, T. L., and Venkitaraman, A. R. (2002) Insights into DNA recombination from the structure of a RAD51-BRCA2 complex Nature 420, 287-293 (Pubitemid 35398178)
14. Freund, C., Kuhne, R., Park, S., Thiemke, K., Reinherz, E. L., and Wagner, G. (2003) Structural investigations of a GYF domain covalently linked to a proline-rich peptide J. Biomol. NMR 27, 143-149 (Pubitemid 37045645)
15. Janda, C. Y., Li, J., Oubridge, C., Hernandez, H., Robinson, C. V., and Nagai, K. (2010) Recognition of a signal peptide by the signal recognition particle Nature 465, 507-510
16. Jiang, J., Maes, E. G., Taylor, A. B., Wang, L., Hinck, A. P., Lafer, E. M., and Sousa, R. (2007) Structural basis of J cochaperone binding and regulation of Hsp70 Mol. Cell 28, 422-433 (Pubitemid 350030560)
17. Guo, M., Bhaskar, B., Li, H., Barrows, T. P., and Poulos, T. L. (2004) Crystal structure and characterization of a cytochrome c peroxidase-cytochrome c site-specific cross-link Proc. Natl. Acad. Sci. U.S.A. 101, 5940-5945 (Pubitemid 38520507)
18. Corn, J. E. and Berger, J. M. (2007) FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies Structure 15, 773-780 (Pubitemid 47042428)
19. Chacinska, A., Koehler, C. M., Milenkovic, D., Lithgow, T., and Pfanner, N. (2009) Importing mitochondrial proteins: machineries and mechanisms Cell 138, 628-644
20. Dolezal, P., Likic, V., Tachezy, J., and Lithgow, T. (2006) Evolution of the molecular machines for protein import into mitochondria Science 313, 314-318 (Pubitemid 44480948)
21. von Heijne, G. (1986) Mitochondrial targeting sequences may form amphiphilic helices EMBO J. 5, 1335-1342
22. Obita, T., Muto, T., Endo, T., and Kohda, D. (2003) Peptide library approach with a disulfide tether to refine the Tom20 recognition motif in mitochondrial presequences J. Mol. Biol. 328, 495-504 (Pubitemid 36407589)
23. Muto, T., Obita, T., Abe, Y., Shodai, T., Endo, T., and Kohda, D. (2001) NMR identification of the Tom20 binding segment in mitochondrial presequences J. Mol. Biol. 306, 137-143 (Pubitemid 33032869)
24. Yamamoto, H., Itoh, N., Kawano, S., Yatsukawa, Y., Momose, T., Makio, T., Matsunaga, M., Yokota, M., Esaki, M., Shodai, T., Kohda, D., Hobbs, A. E., Jensen, R. E., and Endo, T. (2011) Dual role of the receptor Tom20 in specificity and efficiency of protein import into mitochondria Proc. Natl. Acad. Sci. U.S.A. 108, 91-96
25. Abe, Y., Shodai, T., Muto, T., Mihara, K., Torii, H., Nishikawa, S., Endo, T., and Kohda, D. (2000) Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20 Cell 100, 551-560
26. Igura, M., Ose, T., Obita, T., Sato, C., Maenaka, K., Endo, and Kohda, D. (2005) Crystallization and preliminary X-ray analysis of mitochondrial presequence receptor Tom20 in complex with a presequence from aldehyde dehydrogenase Acta Crystallogr. F61, 514-517 (Pubitemid 44210876)
27. Saitoh, T., Igura, M., Obita, T., Ose, T., Kojima, R., Maenaka, K., Endo, T., and Kohda, D. (2007) Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states EMBO J. 26, 4777-4787 (Pubitemid 350126793)
28. Perry, A. J., Rimmer, K. A., Mertens, H. D., Waller, R. F., Mulhern, T. D., Lithgow, T., and Gooley, P. R. (2008) Structure, topology and function of the translocase of the outer membrane of mitochondria Plant Physiol. Biochem. 46, 265-274
29. Perry, A. J., Hulett, J. M., Likic, V. A., Lithgow, T., and Gooley, P. R. (2006) Convergent evolution of receptors for protein import into mitochondria Curr. Biol. 16, 221-229 (Pubitemid 43190221)
30. Rimmer, K. A., Foo, J. H., Ng, A., Petrie, E. J., Shilling, P. J., Perry, A. J., Mertens, H. D., Lithgow, T., Mulhern, T. D., and Gooley, P. R. (2011) Recognition of mitochondrial targeting sequences by the import receptors Tom20 and Tom22 J. Mol. Biol. 405, 804-818
31. Zhang, Y., Baaden, M., Yan, J., Shao, J., Qiu, S., Wu, Y., and Ding, Y. (2010) The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif J. Phys. Chem. B 114, 13839-13846
32. Leduc, A. M., Trent, J. O., Wittliff, J. L., Bramlett, K. S., Briggs, S. L., Chirgadze, N. Y., Wang, Y., Burris, T. P., and Spatola, A. F. (2003) Helix-stabilized cyclic peptides as selective inhibitors of steroid receptor-coactivator interactions Proc. Natl. Acad. Sci. U.S.A. 100, 11273-11278 (Pubitemid 37205925)
33. Shiau, A. K., Barstad, D., Loria, P. M., Cheng, L., Kushner, P. J., Agard, D. A., and Greene, G. L. (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen Cell 95, 927-937 (Pubitemid 29019045)
34. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276, 307-326 (Pubitemid 27085611)
35. Collaborative Computational Project 4 (1994) The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 50, 760-763
36. Chang, C. E., McLaughlin, W. A., Baron, R., Wang, W., and McCammon, J. A. (2008) Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association Proc. Natl. Acad. Sci. U.S.A. 105, 7456-7461 (Pubitemid 351830039)
37. Erlanson, D. A., Braisted, A. C., Raphael, D. R., Randal, M., Stroud, R. M., Gordon, E. M., and Wells, J. A. (2000) Site-directed ligand discovery Proc. Natl. Acad. Sci. U.S.A. 97, 9367-9372 (Pubitemid 30650781)