Circular Permutation of Proteins

Protein Engineering Handbook, Volume 1 & Volume 2

Volumn 2, Issue , 2011, Pages 453-471

  Meister, Glenna E ^a   Kanwar, Manu ^a   Ostermeier, Marc ^a  

^a Johns Hopkins University   (United States)

Author keywords

Circular permutation; Directed evolution; Genetic rearrangement; Protein engineering; Protein evolution; Random circular permutation

Indexed keywords

EID: 84884643359     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527634026.ch18     Document Type: Chapter

References (61)

1. Guddat, L.W., Bardwell, J.C., and Martin, J.L. (1998) Crystal structures of reduced, and oxidized DsbA: investigation of domain motion, and thiolate stabilization . Structure,6,757-67 .
2. Manjasetty, B.A., Hennecke, J., Glockshuber, R., and Heinemann, U. (2004) Structure of circularly permuted DsbA(Q100T99): preserved global fold, and local structural adjustments . Acta Crystallographica. Section D, Biological Crystallography,60,304-9 .
3. Krishna, M.M., and Englander, S.W. (2005) The N-terminal to C-terminal motif in protein folding, and function . Proceedings of the National Academy of Sciences of the United States of America,102,1053-8 .
4. Graf, R., and Schachman, H.K. (1996) Random circular permutation of genes, and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase . Proceedings of the National Academy of Sciences of the United States of America,93,11591-6 .
5. Hennecke, J., Sebbel, P., and Glockshuber, R. (1999) Random circular permutation of DsbA reveals segments that are essential for protein folding, and stability . Journal of Molecular Biology,286,1197-215 .
6. Iwakura, M., Nakamura, T., Yamane, C., and Maki, K. (2000) Systematic circular permutation of an entire protein reveals essential folding elements . Nature Structural Biology,7,580-5 .
7. Qian, Z., and Lutz, S. (2005) Improving the catalytic activity of Candida antarctica lipase B by circular permutation . Journal of the American Chemical Society,127,13466-7 .
8. Topell, S., and Glockshuber, R. (2002) Circular permutation of the green fl uorescent protein . Methods in Molecular Biology (Clifton, N.J.),183,31-48 .
9. Lindqvist, Y., and Schneider, G. (1997) Circular permutations of natural protein sequences: structural evidence . Current Opinion in Structural Biology,7,422-7 .
10. Weiner, J. III, and Bornberg-Bauer, E. (2006) Evolution of circular permutations in multidomain proteins . Molecular Biology, and Evolution,23,734-43 .
11. Cunningham, B.A., Hemperly, J.J., Hopp, T.P., and Edelman, G.M. (1979) Favin versus concanavalin A: circularly permuted amino acid sequences . Proceedings of the National Academy of Sciences of the United States of America,76,3218-22 .
12. Carrington, D.M., Auffret, A., and Hanke, D.E. (1985) Polypeptide ligation occurs during post-translational modifi cation of concanavalin A . Nature,313,64-7 .
13. Mulvenna, J.P., Wang, C., and Craik, D.J. (2006) CyBase: a database of cyclic protein sequence, and structure . Nucleic Acids Research,34, D192-4 .
14. Guruprasad, K., Tormakangas, K., Kervinen, J., and Blundell, T.L. (1994) Comparative modeling of barley-grain aspartic proteinase: a structural rationale for observed hydrolytic specifi city . FEBS Letters,352,131-6 .
15. Ponting, C.P., and Russell, R.B. (1995) Swaposins: circular permutations within genes encoding saposin homologues . Trends in Biochemical Sciences,20,179-80 .
16. Malone, T., Blumenthal, R.M., and Cheng, X. (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases,, and suggests a catalytic mechanism for these enzymes . Journal of Molecular Biology,253,618-32 .
17. Vogel, C., and Morea, V. (2006) Duplication, divergence, and formation of novel protein topologies . BioEssays,28,973-8 .
18. Bujnicki, J.M. (2002) Sequence permutations in the molecular evolution of DNA methyltransferases . BMC Evolutionary Biology,2, doi: 10.1186/1471-2148-2-3.
19. Peisajovich, S.G., Rockah, L., and Tawfik, D.S. (2006) Evolution of new protein topologies through multistep gene rearrangements . Nature Genetics,38,168-74 .
20. Uliel, S., Fliess, A., and Unger, R. (2001) Naturally occurring circular permutations in proteins . Protein Engineering,14,533-42 .
21. Uliel, S., Fliess, A., Amir, A., and Unger, R. (1999) A simple algorithm for detecting circular permutations in proteins . Bioinformatics (Oxford, England),15,930-6 .
22. Weiner, J. III, Thomas, G., and Bornberg-Bauer, E. (2005) Rapid motif-based prediction of circular permutations in multi-domain proteins . Bioinformatics (Oxford, England),21,932-7 .
23. Jung, J., and Lee, B. (2001) Circularly permuted proteins in the protein structure database . Protein Science,10,1881-6 .
24. Chen, L., Wu, L.Y., Wang, Y., Zhang, S., and Zhang, X.S. (2006) Revealing divergent evolution, identifying circular permutations, and detecting active-sites by protein structure comparison . BMC Structural Biology,6,18 .
25. Jeltsch, A. (1999) Circular permutations in the molecular evolution of DNA methyltransferases . Journal of Molecular Evolution,49,161-4 .
26. Goldenberg, D.P., and Creighton, T.E. (1983) Circular, and circularly permuted forms of bovine pancreatic trypsin inhibitor . Journal of Molecular Biology,165,407-13 .
27. Luger, K., Hommel, U., Herold, M., Hofsteenge, J., and Kirschner, K. (1989) Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo . Science (New York, N.Y.),243,206-10 .
28. Buchwalder, A., Szadkowski, H., and Kirschner, K. (1992) A fully active variant of dihydrofolate reductase with a circularly permuted sequence . Biochemistry,31,1621-30 .
29. Heinemann, U., and Hahn, M. (1995) Circular permutation of polypeptide chains: implications for protein folding, and stability . Progress in Biophysics, and Molecular Biology,64,121-43 .
30. Ostermeier, M., and Benkovic, S.J. (2001) Construction of hybrid gene libraries involving the circular permutation of DNA . Biotechnology Letters,23,303-10 .
31. Yang, Y.R., and Schachman, H.K. (1993) Aspartate transcarbamoylase containing circularly permuted catalytic polypeptide chains . Proceedings of the National Academy of Sciences of the United States of America,90,11980-4 .
32. Cheltsov, A.V., Barber, M.J., and Ferreira, G.C. (2001) Circular permutation of 5-aminolevulinate synthase. Mapping the polypeptide chain to its function . The Journal of Biological Chemistry,276,19141-9 .
33. Guntas, G. (2005) Creation of molecular switches by combinatorial protein engineering, PhD Thesis, Johns Hopkins University, Baltimore.
34. Bulaj, G., Koehn, R.E., and Goldenberg, D.P. (2004) Alteration of the disulfi de-coupled folding pathway of BPTI by circular permutation . Protein Science,13,1182-96 .
35. Lindberg, M., Tangrot, J., and Oliveberg, M. (2002) Complete change of the protein folding transition state upon circular permutation . Nature Structural Biology,9,818-22 .
36. Gebhard, L.G., Risso, V.A., Santos, J., Ferreyra, R.G., Noguera, M.E., and Ermacora, M.R. (2006) Mapping the distribution of conformational information throughout a protein sequence . Journal of Molecular Biology,358,280-8 .
37. Kreitman, R.J., Puri, R.K., and Pastan, I. (1994) A circularly permuted recombinant interleukin 4 toxin with increased activity . Proceedings of the National Academy of Sciences of the United States of America,91,6889-93 .
38. Kreitman, R.J., Puri, R.K., and Pastan, I. (1995) Increased antitumor activity of a circularly permuted interleukin 4-toxin in mice with interleukin 4 receptor-bearing human carcinoma . Cancer Research,55,3357-63 .
39. Kawakami, M., Kawakami, K., and Puri, R.K. (2003) Interleukin-4-Pseudomonas exotoxin chimeric fusion protein for malignant glioma therapy . Journal of Neuro-Oncology,65,15-25 .
40. Kawakami, M., Kawakami, K., Kioi, M., Leland, P., and Puri, R.K. (2005) Hodgkin lymphoma therapy with interleukin-4 receptor-directed cytotoxin in an infi ltrating animal model . Blood,105,3707-13 .
41. Kioi, M., Takahashi, S., Kawakami, M., Kawakami, K., Kreitman, R.J., and Puri, R.K. (2005) Expression, and targeting of interleukin-4 receptor for primary, and advanced ovarian cancer therapy . Cancer Research,65,8388-96 .
42. McWherter, C.A., Feng, Y., Zurfluh, L.L., Klein, B.K., Baganoff, M.P., Polazzi, J.O., Hood, W.F., Paik, K., Abegg, A.L., Grabbe, E.S., Shieh, J.J., Donnelly, A.M., and McKearn, J.P. (1999) Circular permutation of the granulocyte colony-stimulating factor receptor agonist domain of myelopoietin . Biochemistry,38,4564-71 .
43. Bessette, P.H., Rice, J.J., and Daugherty, P.S. (2004) Rapid isolation of high-affi nity protein binding peptides using bacterial display . Protein Engineering, Design, and Selection,17,731-9 .
44. Vogt, J., and Schulz, G.E. (1999) The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence . Structure,7,1301-9 .
45. Rice, J.J., Schohn, A., Bessette, P.H., Boulware, K.T., and Daugherty, P.S. (2006) Bacterial display using circularly permuted outer membrane protein OmpX yields high affi nity peptide ligands . Protein Science,15,825-36 .
46. Chalton, D.A., Musson, J.A., Flick-Smith, H., Walker, N., McGregor, A., Lamb, H.K., Williamson, E.D., Miller, J., Robinson, J.H., and Lakey, J.H. (2006) Immunogenicity of a Yersinia pestis vaccine antigen monomerized by circular permutation . Infection, and Immunity,74,6624-31 .
47. Sanders, K.E., Lo, J., and Sligar, S.G. (2002) Intersubunit circular permutation of human hemoglobin . Blood,100,299-305 .
48. Nordlund, H.R., Laitinen, O.H., Hytonen, V.P., Uotila, S.T., Porkka, E., and Kulomaa, M.S. (2004) Construction of a dual chain pseudotetrameric chicken avidin by combining two circularly permuted avidins . Journal of Biological Chemistry,279,36715-19 .
49. Wieligmann, K., Norledge, B., Jaenicke, R., and Mayr, E.M. (1998) Eye lens betaB2-crystallin: circular permutation does not influence the oligomerization state but enhances the conformational stability . Journal of Molecular Biology,280,721-9 .
50. Liang, J., Kim, J.R., Boock, J.T., Mansell, T.J., and Ostermeier, M. (2007) Ligand binding, and allostery can emerge simultaneously . Protein Science,16,929-37 .
51. Osuna, J., Perez-Blancas, A., and Soberon, X. (2002) Improving a circularly permuted TEM-1 beta-lactamase by directed evolution . Protein Engineering,15,463-70 .
52. Kojima, M., Ayabe, K., and Ueda, H. (2005) Importance of terminal residues on circularly permutated Escherichia coli alkaline phosphatase with high specifi c activity . Journal of Bioscience, and Bioengineering,100,197-202 .
53. Qian, Z., Fields, C.J., and Lutz, S. (2007) Investigating the structural, and functional consequences of circular permutation on lipase B from Candida antarctica . ChemBioChem,8,1989-96 .
54. Guntas, G., Mansell, T.J., Kim, J.R., and Ostermeier, M. (2005) Directed evolution of protein switches, and their application to the creation of ligand-binding proteins . Proceedings of the National Academy of Sciences of the United States of America,102,11224-9 .
55. Baird, G.S., Zacharias, D.A., and Tsien, R.Y. (1999) Circular permutation, and receptor insertion within green fluorescent proteins . Proceedings of the National Academy of Sciences of the United States of America,96,11241-6 .
56. Guntas, G., Mitchell, S.F., and Ostermeier, M. (2004) A molecular switch created by in vitro recombination of nonhomologous genes . Chemistry, and Biology,11,1483-7 .
57. Schwartz, T.U., Walczak, R., and Blobel, G. (2004) Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit . Protein Science,13,2814-18 .
58. Bittker, J.A., Le, B.V., Liu, J.M., and Liu, D.R. (2004) Directed evolution of protein enzymes using nonhomologous random recombination . Proceedings of the National Academy of Sciences of the United States of America,101,7011-16 .
59. MacBeath, G., Kast, P., and Hilvert, D. (1998) Redesigning enzyme topology by directed evolution . Science,279,1958-61 .
60. Tabtiang, R.K., Cezairliyan, B.O., Grant, R.A., Cochrane, J.C., and Sauer, R.T. (2005) Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure . Proceedings of the National Academy of Sciences of the United States of America,102,2305-9 .
61. Paavola, C.D., Chan, S.L., Mazzarella, K.M., McMillan, R.A., and Trent, J.D. (2006) A versatile platform for nanotechnology based on circular permutation of a chaperonin protein . Nanotechnology,17,1171-6 .