Repeat protein architectures predicted by a continuum representation of fold space

Protein Science

Volumn 15, Issue 4, 2006, Pages 753-760

  Hausrath, Andrew C ^a   Goriely, Alain ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Arizona   (United States)

Author keywords

Fold evolution; Polyhelix; Protein fold space; Repeat proteins

Indexed keywords

ANKYRIN; HELIX LOOP HELIX PROTEIN; TETRATRICOPEPTIDE REPEAT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

ALGORITHMS; COMPUTER GRAPHICS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 33645503251     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051971106     Document Type: Article

References (35)

1. Andrade, M.A., Petosa, C., O'Donoghue, S.I., Muller, C.W., and Bork, P. 2001. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 309: 1-18.
2. Banavar, J.R., Maritan, A., Micheletti, C., and Trovato, A. 2002. Geometry and physics of proteins. Proteins 47: 315-322.
3. Binz, H.K., Stumpp, M.T., Forrer, P., Amstutz, P., and Pluckthun, A. 2003. Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332: 489-503.
4. Chothia, C. 1992. Proteins - 1000 families for the molecular biologist. Nature 357: 543-544.
5. Cingolani, G., Petosa, C., Weis, K., and Muller, C.W. 1999. Structure of importin-β-bound to the IBB domain of importin-αa. Nature 399: 221-229.
6. Cui, Y., Wong, W.H., Bornberg-Bauer, E., and Chan, H.S. 2002. Recombinatoric exploration of novel folded structures: A heteropolymerbased model of protein evolutionary landscapes. Proc. Natl. Acad. Sci. 99: 809-814.
7. Dahiyat, B.I. and Mayo, S.L. 1997. De novo protein design: Fully automated sequence selection. Science 278: 82-87.
8. Dwyer, M.A. and Hellinga, H.W. 2004. Periplasmic binding proteins: A versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 14: 495-504.
9. Goriely, A. and Tabor, M. 1997. Nonlinear dynamics of filaments. 1. Dynamical instabilities. Physica D. 105: 20-44.
10. Groves, M.R. and Barford, D. 1999. Topological characteristics of helical repeat proteins. Curr. Opin. Struct. Biol. 9: 383-389.
11. Groves, M.R., Hanlon, N., Turowski, P., Hemmings, B.A., and Barford, D. 1999. The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs. Cell 96: 99-110.
12. Harrison, A., Pearl, F., Mott, R., Thornton, J., and Orengo, C. 2002. Quantifying the similarities within fold space. J. Mol. Biol. 323: 909-926.
13. Hou, J.T., Sims, G.E., Zhang, C., and Kim, S.H. 2003. A global representation of the protein fold space. Proc. Natl. Acad. Sci. 100: 2386-2390.
14. Klapper, I. and Qian, H. 1998. Remarks on discrete and continuous largescale models of DNA dynamics. Biophys. J. 74: 2504-2514.
15. Kohl, A., Binz, H.K., Forrer, P., Stumpp, M.T., Pluckthun, A., and Grutter, M.G. 2003. Designed to be stable: Crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. 100: 1700-1705.
16. Koradi, R., Billeter, M., and Wuthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
17. Kraulis, P.J. 1991. MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946-950.
18. Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., and Baker, D. 2003. Design of a novel globular protein fold with atomiclevel accuracy. Science 302: 1364-1368.
19. Li, H., Helling, R., Tang, C., and Wingreen, N. 1996. Emergence of preferred structures in a simple model of protein folding. Science 273: 666-669.
20. Macken, C.A. and Perelson, A.S. 1989. Protein evolution on rugged landscapes. Proc. Natl. Acad. Sci. 86: 6191-6195.
21. Main, E.R.G., Xiong, Y., Cocco, M.J., D'Andrea, L., and Regan, L. 2003. Design of stable a-helical arrays from an idealized TPR motif. Structure 11: 497-508.
22. Manning, R.S., Maddocks, J.H., and Kahn, J.D. 1996. A continuum rod model of sequence-dependent DNA structure. J. Chem. Phys. 105: 5626-5646.
23. Maritan, A., Micheletti, C., Trovato, A., and Banavar, J.R. 2000. Optimal shapes of compact strings. Nature 406: 287-290.
24. Marko, J.F. and Siggia, E.D. 1994. Bending and twisting elasticity of DNA. Macromolecules 27: 981-988.
25. Merritt, E.A. and Bacon, D.J. 1997. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277: 505-524.
26. Mosavi, L.K., Minor, D.L., and Peng, Z.Y. 2002. Consensus-derived structural determinants of the ankyrin repeat motif. Proc. Natl. Acad. Sci. 99: 16029-16034.
27. Plaxco, K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
28. Rice, L.M. and Brunger, A.T. 1999. Crystal structure of the vesicular transport protein Sec17: Implications for SNAP function in SNARE complex disassembly. Mol. Cell 4: 85-95.
29. Shindyalov, I.N. and Bourne, P.E. 2000. An alternative view of protein fold space. Proteins 38: 247-260.
30. Smith, J.M. 1970. Natural selection and concept of a protein space. Nature 225: 563-564.
31. Steegborn, C., Danot, O., Huber, R., and Clausen, T. 2001. Crystal structure of transcription factor MaIT domain III: A novel helix repeat fold implicated in regulated oligomerization. Structure 9: 1051-1060.
32. Stumpp, M.T., Forrer, P., Binz, H.K., and Pluckthun, A. 2003. Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J. Mol. Biol. 332: 471-487.
33. Trovato, A., Hoang, T.X., Banavar, J.R., Maritan, A., and Seno, F. 2005. What determines the structures of native folds of proteins? J. Phys. Condens. Matter 17: S1515-S1522.
34. Zhang, C.O. and DeLisi, C. 1998. Estimating the number of protein folds. J. Mol. Biol. 284: 1301-1305.
35. Zhang, X.J. and Matthews, B.W. 1995. EDPDB - A multifunctional tool for protein-structure analysis. J. Appl. Crystallogr. 28: 624-630.