Oligomerization states of Bowman-Birk inhibitor by atomic force microscopy and computational approaches
Corresponding Author
Luciano P. Silva
Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Luciano P. Silva, Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, 70910-900, Brazil===
Sonia M. Freitas, Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil===
Search for more papers by this authorRicardo B. Azevedo
Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorPaulo C. Morais
Institute of Physics, Applied Physics Division, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorManuel M. Ventura
Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorCorresponding Author
Sonia M. Freitas
Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Luciano P. Silva, Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, 70910-900, Brazil===
Sonia M. Freitas, Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil===
Search for more papers by this authorCorresponding Author
Luciano P. Silva
Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Luciano P. Silva, Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, 70910-900, Brazil===
Sonia M. Freitas, Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil===
Search for more papers by this authorRicardo B. Azevedo
Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorPaulo C. Morais
Institute of Physics, Applied Physics Division, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorManuel M. Ventura
Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Search for more papers by this authorCorresponding Author
Sonia M. Freitas
Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil
Luciano P. Silva, Laboratory of Morphology and Morphogenesis, Department of Genetics and Morphology, Institute of Biology, University of Brasilia, Brasilia, DF, 70910-900, Brazil===
Sonia M. Freitas, Laboratory of Biophysics, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, DF, Brazil===
Search for more papers by this authorAbstract
Several methods have been applied to study protein–protein interaction from structural and thermodynamic point of view. The present study reveals that atomic force microscopy (AFM), molecular modeling, and docking approaches represent alternative methods offering new strategy to investigate structural aspects in oligomerization process of proteinase inhibitors. The topography of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) was recorded by AFM and compared with computational rigid-bodies docking approaches. Multimeric states of BTCI identified from AFM analysis showed globular–ellipsoidal shapes. Monomers, dimers, trimers, and hexamers were the most prominent molecular arrays observed in AFM images as evaluated by molecular volume calculations and corroborated by in silico docking and theoretical approaches. We therefore propose that BTCI adopts stable and well-packed self-assembled states in monomer–dimer–trimer–hexamer equilibrium. Although there are no correlation between specificity and packing efficiency among proteinases and proteinase inhibitors, the AFM and docked BTCI analyses suggest that these assemblies may exist in situ to play their potential function in oligomerization process. Proteins 2005. © 2005 Wiley-Liss, Inc.
REFERENCES
- 1 Wodak SJ, Janin J. Structural basis of macromolecular recognition. Adv Protein Chem 2003; 61: 9–73.
- 2 Engel J, Kammerer RA. What are oligomerization domains good for? Matrix Biol 2000; 19: 283–288.
- 3 Jaenicke R, Böhm G. The stability of proteins in extreme environments. Curr Opin Struct Biol 1998; 8: 738–748.
- 4 Zhao X, Ghaffari S, Lodish H, Malashkevich VN, Kim PS. Structure of the Bcr-Abl oncoprotein oligomerization domain. Nat Struct Biol 2002; 9: 117–120.
- 5 Engel A, Muller DJ. Observing single biomolecules at work with the atomic force microscope. Nat Struct Biol 2000; 7: 715–718.
- 6 Leite JRSA, Silva LP, Taveira CC, Teles RCL, Freitas SM, Azevedo RB. Topographical analysis of Schizolobium parahyba chymotrypsin inhibitor (SPCI) by atomic force microscopy. Protein Peptide Lett 2002; 9: 179–184.
- 7 Silva LP. Atomic force microscopy and proteins. Protein Peptide Lett 2002; 9: 117–125.
- 8 Müller DJ, Heymann JB, Oesterhelt F, Moller C, Gaub H, Buldt G, Engel A. Atomic force microscopy of native purple membrane. Biochim Biophys Acta 2000; 1460: 27–38.
- 9 Chamberlain AK, MacPhee CE, Zurdo J, Morozova-Roche LA, Hill HAO, Dobson CM, Davis JJ. Ultrastructural organization of amyloid fibrils by atomic force microscopy. Biophys J 2000; 79: 3282–3293.
- 10 Stoddard BL, Koshland DE. Prediction of the structure of a receptor protein complex using a binary docking method. Nature 1992; 358: 774–776.
- 11 Tovchigrechko A, Wells CA, Vakser IA. Docking of protein models. Protein Sci 2002; 11: 1888–1896.
- 12 Myshkin E, Leontis NB, Bullerjahn GS. Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to photosystem I: Modeling the electron transfer complex. Biophys J 2002; 82: 3305–3313.
- 13 Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein–protein complexes. Proc Natl Acad Sci USA 1999; 96: 8477–8482.
- 14 Laskowski M, Kato I. Protein inhibitors of proteinases. Annu Rev Biochem 1980; 49: 593–626.
- 15 Radisky ES, Koshland, D. E. A clogged gutter mechanism for protease inhibitors. Proc Natl Acad Sci USA 2002; 99: 10316–10321.
- 16 Park HS, Lin Q, Hamilton AD. Modulation of protein–protein interactions by synthetic receptors: Design of molecules that disrupt serine protease–proteinaceous inhibitor interaction. Proc Natl Acad Sci USA 2002; 99: 5105–5109.
- 17 Franco OL, Freitas SM, Santos RC, Batista JAN, Mendes ACM, Araújo MAM, Monnerat RG, Sá MFG. Effects of black-eyed pea trypsin/chymotrypsin inhibitor on proteolytic activity and on development of Anthonomus grandis. Phytochemistry 2003; 63: 343–349.
- 18 Morhy L, Ventura MM The complete amino-acid sequence of the Vigna-unguiculata (L) Walp seed trypsin and chymotrypsin inhibitor. An Acad Bras Cienc 1987; 59: 71–81.
- 19 Silva LP, Leite JRSA, Bloch C Jr, Freitas SM. Stability of a black eyed pea trypsin/chymotrypsin inhibitor (BTCI). Protein Peptide Lett 2000; 7: 397–401.
- 20 deFreitas SM, Mello LV, Silva MCM, Vriend G, Neshich G, Ventura MM. Analysis of the black-eyed pea trypsin and chymotrypsin inhibitor alpha-chymotrypsin complex. FEBS Lett 1997; 409: 121–128.
- 21 Ventura MM, Mizuta K Ikemoto H. Solvent perturbation and surface accessibility of the tryptophyl and tyrosyl groups in black-eyed pea trypsin and chymotrypsin inhibitor. An Acad Bras Cienc 1984; 56: 217–220.
- 22 Ventura MM, OliveiraMartim CD, Morhy L. Trypsin and chymotrypsin inhibitor from black-eyed pea (Vigna-sinensis L).6. Isolation and properties of complexes with trypsin and chymotrypsin. An Acad Bras Cienc 1975; 47: 335–346.
- 23 Ventura MM, Mizuta K, Ikemoto H. Self-association of the black-eyed pea trypsin and chymotrypsin inhibitor in solution—a study by light-scattering. An Acad Bras Cienc 1981; 53: 195–201.
- 24 Gottschalk M, Venu K, Halle B. Protein self-association in solution: The bovine pancreatic trypsin inhibitor decamer. Biophys J 2003; 84: 3941–3958.
- 25 Ventura MM, Xavier-Filho J. A trypsin and chymotrypsin inhibitor from black-eyed pea (Vigna sinensis).I. Purification and partial characterization. An Acad Bras Cienc 1966; 38: 553–566.
- 26 Bittencourt SET, Silva LP, Azevedo RB, Cunha RB, Lima CMR, Ricart CAO, Sousa MV. The plant cytolytic protein enterolobin assumes a dimeric structure in solution. FEBS Lett 2003; 549: 47–51.
- 27 Brand GD, Leite JRSA, Silva LP, Albuquerque S, Prates MV, Azevedo RB, Carregaro V, Silva JS, Sá VCL, Brandãeo RA, Bloch C Jr. Dermaseptins from Phyllomedusa oreades and Phyllomedusa distincta—Anti-trypanosoma cruzi activity without cytotoxicity to mammalian cells. J Biol Chem 2002; 277: 49332–49340.
- 28 Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997; 18: 2714–2723.
- 29 Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996; 14: 51–55.
- 30 Miller S, Janin J, Lesk AM, Cyrus C. Interior and surface of monomeric proteins. J Mol Biol 1987; 196: 641–656.
- 31 Janin J, Miller S, Chotia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 1988; 204: 155–164.
- 32 Stawiski EW, Baucom AE, Lohr SC, Gregoret LM. Predicting protein function from structure: Unique structural features of proteases. Proc Natl Acad Sci USA 2000; 97: 3954–3958.
- 33 Scheuring S, Ringler P, Borgnia M, Stahlberg H, Müller DJ, Agre P, Engel A. High resolution AFM topographs of the Escherichia coli water channel aquaporin Z. EMBO J 1999; 18: 4981–4987.
- 34 Wishart DS, Willard L, Richards FM, Sykes BD. VADAR: a comprehensive program for protein structure evaluation. Alberta, Canada: University of Alberta; 1994; version 1.2.
- 35 Lee BK, Richards FM. Interpretation of protein structures—estimation of static accessibility. J Mol Biol 1971; 55: 379–400.
- 36 Schneider SW, Larmer J, Henderson RM, Oberleithner H. Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy. Pflug Arch Eur J Phys 1998; 43: 362–367.
- 37 Yang Y, Wang H, Eriea DA. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. Methods 2003; 29: 175–187.
- 38 Harpaz Y, Gerstein M, Chothia C. Volume changes on protein-folding. Structure 1994; 2: 641–649.
- 39 Xue Y, Ratcli GC, Wang H, Davis-Searles PR, Gray MD, Erie DA, Redinbo MR. A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3′-5′ exonuclease and 5′-protruding strand endonuclease activities. Biochemistry 2002; 41: 2901–2912.
Citing Literature
