From synthetic coiled coils to functional proteins: Automated design of a receptor for the calmodulin-binding domain of calcineurin

Journal of Molecular Biology

Volumn 281, Issue 2, 1998, Pages 379-391

  Ghirlanda, Giovanna ^a   Lear, James D ^a   Lombardi, Angela ^b   Degrado, William F ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b Ctro Interuniversitario Ric Sui P   (Italy)

Author keywords

Calmodulin mimetic; De novo design; Molecular recognition; Peptide binding; Three helix bundle

Indexed keywords

CALCINEURIN; CALMODULIN; CALMODULIN BINDING PROTEIN;

ALGORITHM; ARTICLE; AUTOMATION; CIRCULAR DICHROISM; GEOMETRY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; ULTRACENTRIFUGATION;

EID: 0032516785     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1912     Document Type: Article

References (61)

1. Afshar M., Caves L.S.D., Guimard L., Hubbard R.E., Calas B., Grassy G., Haiech J. Investigating the high affinity and low sequence specificity of calmodulin binding to its targets. J. Mol. Biol. 244:1994;554-571
2. Alber T., Woolfson D.N. Predictiong oligomerization states of coiled coils. Protein Sci. 4:1995;1596-1607
3. Bayley P.M., Findlay W.A., Martin S.R. Target recognition by calmodulin dissecting the kinetics and affinity of interaction using short peptide sequences. Protein Sci. 5:1996;1215-1228
4. Betz S.F., DeGrado W.F. Controlling topology and native-like behavior of de novo designed peptides design and characterization of antiparallel four stranded coiled coils. Biochemistry. 35:1996;6955
5. Betz S.F., Fairman R., O'Neill K.T., Lear J.D., DeGrado W.F. Two- and three stranded peptide design. Phil. Trans. Roy. Soc. ser. B. 348:1995;81-88
6. Betz S.F., Liebman P.A., DeGrado W.F. De novo design of native proteins characterization of proteins intended to fold into antiparallel, ROP-like, four-helix bundles. Biochemistry. 36:1997;2450-2458
7. Boice J.A., Dieckmann G.R., DeGrado W.F., Fairman R. Thermodynamic analysis of a designed trhee-stranded coiled coil. Biochemistry. 35:1996;14480-14485
8. Broo K., Brive L., Lundh A.C., Ahlberg P., Baltzer L. The mechanism of self-catalyzed site-selective functionalization of a designed helix-loop-helix motif. J. Am. Chem. Soc. 118:1996;8172-8173
9. Broo K.S., Brive L., Ahlberg P., Baltzer L. Catalysis of hydrolysis and transesterification reactions of p-nitophenyl esters by a designed helix-loop-helix dimer. J. Am. Chem. Soc. 119:1997;11362-11372
10. Brooks I.S., Soneson K.K., Hensley P. Development and use of a Mac based data-analysis package for equilibrium sedimentation data from the analytical ultracentrifuge. Biophys. J. 64:1993;244
11. Bryson J.W., Betz S.F., Lu H.S., Suich D.J., Zhou H.X., O'Neil K.T., DeGrado W.F. Protein design, a hyerarchic approach. Science. 270:1995;935-941
12. Choma C.T., Lear J.D., Nelson M.J., Dutton P.L., Robertson D.E., DeGrado W.F. Design of a heme-binding four-helix bundle. J. Am. Chem. Soc. 116:1994;856-865
13. Clipston N.A., Crabtree G.R. Identification of calcineurin as a key signalling enzyme in T-lymphocyte activation. Nature. 357:1992;695-697
14. Cohn E.J., Edsall J.T. Proteins, Amino Acids and Peptides as Ions and Dipolar Ions. 1943;Reinhold Publishing Corp, New York
15. Coldren C.D., Hellinga H.W., Caradonna J.P. The rational design and construction of a cuboidal iron-sulfur protein. Proc. Natl Acad. Sci. USA. 94:1997;6635-6640
16. Crivici A., Ikura M. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24:1995;85-116
17. Dahiyat .B.I., Mayo S.L. Protein design automation. Protein Sci. 5:1996;895-903
18. Dahiyat B.I., Mayo S.L. Probing the role of packing specificity in protein design. Proc. Natl Acad. Sci. USA. 94:1997;10172-10177
19. Dahiyat B.I., Gordon D.B., Mayo S.L. Automated design of the surface positions of protein helices. Protein Sci. 6:1997;1333-1337
20. Desjarlais J., Handel T.M. De novo design of the hydrophobic cores of proteins. Protein Sci. 4:1995;2006-2018
21. Dunbrack R.L., Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein side-chains. Struct. Biol. 1:1994;334-355
22. Erickson-Viitanen S., DeGrado W.F. Recognition and characterization of calmodulin-binding sequences in peptides and proteins. Means A.R., Conn P.M. Methods in Enzymology. 139:1987;455-478 Academic Press, New York
23. Farid R.S., Moser C.C., Dutton P.L. Electron transfer in proteins. Curr. Opin. Struct. Biol. 3:1993;225-233
24. Gibney B.R., Mullholland S.E., Rabanal F., Dutton P.L. Ferredoxin and ferredoxin-heme maquettes. Proc. Natl. Acad. Sci. USA. 93:(26):1996;15041-15046
25. Griffith J.P., Kim J.L., Kim E.E., Sintchak M.D., Thomson J.A., Fitzgibbon M.A., Fleming M.A., Caron P.R., Hsiao K., Navia M.A. X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Cell. 82:1995;507-522
26. Harbury P.B., Zhang T., Kim P.S., Alber T. A switch between two-, three-, and four-stranded coiled coils. Science. 262:1993;1401-1407
27. Harding S.E., Rowe A.J., Horton J.C. Analytical Ultracentrifugation in Biochemistry and Polymer Science. 1992;The Royal Society of Chemistry, Cambridge, UK
28. Hecht M.H., Richardson J.S., Richardson D.C., Ogden R.C. De novo design, expression and characterization of felix a four-helix bundle protein of native-like sequence. Science. 249:1990;884-891
29. Ikura M., Clore M., Gronenborn A.M., Zhu G., Klee C.B., Bax A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 256:1992;632-638
30. Kinkaid R.L., Giri P.R., Higuchi S., Tamura J., Dixon S.C., Marietta C.A., Amorese D.A., Martini B.M. Cloning and characterization of molecular isoforms of the catalytic subunit of calcineurin using non-isotopic methods. J. Biol. Chem. 265:1990;11312-11319
31. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
32. Lau S.Y.M., Taneja A.K., Hodges R.S. Synthesis of a model protein of defined secondary and quaternary structure. J. Biol. Chem. 259:(21):1984;13253-13261
33. Lazar G.A., Desjarlais J.R., Handel T.M. De novo design of the hydrophobic core of ubiquitin. Protein Sci. 6:1997;1167-1178
34. Lombardi A., Bryson J.D., DeGrado W.F. De novo design of heterotrimeric coiled coil. Biopolymers. 40:1997;495-504
35. Lombardi A., Bryson J.W., Ghirlanda G., DeGrado W.F. Design of a synthetic receptor for thecalmodulin-binding domain of calcineurin. J. Am. Chem. Soc. 119:1997;12378-12379
36. Lovejoy B., Åkerfeldt K.S., DeGrado W.F., Eisenberg D. Crystallization of proton channel peptides. Protein Sci. 1:1992;1073-1077
37. Lukas T.J., Burgess W.H., Prendergast F.G., Lau W., Watterson D.M. Calmodulin binding domains characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase. Biochemistry. 25:1986;1458-1464
38. Lumb K.J., Kim P.S. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry. 34:1995;8642-8648
39. Mann C.J., Matthews C.R. Structure and stability of an early folding intermediate of Escherichia coli trp aporepressor measured by far-UV stopped-flow CD and ANS binding. Biochemistry. 32:1993;5282-5290
40. McGregor M.J., Islam S.A., Sternberg M.J.E. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198:1987;295-310
41. Meador W.E., Means A.R., Quiocho F.A. Target enzyme recognition by calmodulin 2.4 Å structure of a calmodulin-peptide complex. Science. 257:1992;1251-1255
42. Meador W.E., Means A.R., Quiocho F.A. Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures. Science. 262:1993;1718-1721
43. Monera O.D., Zhou N.E., Kay C.M., Hodges R.S. Comparison of antiparallel and parallel two-stranded a-helical coiled-coils. J. Biol. Chem. 268:1993;19218-19227
44. Myszka D.G., Chaiken I.M. Design and characterization of an intramolecular antiparallel coiled coil peptide. Biochemistry. 33:1994;2363-2372
45. Nastri F., Lombardi A., Morelli G., Maglio O., D'Auria G., Pedone C., Pavone V. Hemoprotein models based on a covalent helix-heme-helix sandwich 1. Design, synthesis, and characterization. Eur. J. Chem. 3:1997;340-349
46. Naurival S., Woolfson D.N., King D.S., Alber T. A designed heterotrimeric coiled coil. Biochemistry. 34:1995;11645-11651
47. d implications for engeneering crystals and supramolecular assemblies. Protein Sci. 6:1997;80-88
48. O'Keefe S.J., Tamura J., Kinkaid R.L., Tocci M.J., O'Neill E.A. FK-506- and CsA-sensitive activation of the interleukin-2 promoter by calcineurin. Nature. 357:1992;692-694
49. O'Neil K.T., DeGrado W.F. How calmodulin binds its targets sequence independent recognition of amphiphilic α-helices. Trends Biochem. Sci. 15:1990;59-64
50. O'Neil K.T., DeGrado W.F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science. 250:1990;646-651
51. O'Neil K.T., Hoess R.H., DeGrado W.F. Design of DNA-binding peptides based on the leucine zipper motif. Science. 249:1990;774-778
52. O'Shea E.K., Lumb K.H., Kim P.S. Peptide 'Velcro' design of a heterodimeric coiled coil. Curr. Biol. 3:1993;658-667
53. Pinto A.L., Hellinga H.W., Caradonna J.P. Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc. Natl. Acad. Sci. USA. 94:1997;5562-5567
54. Rabanal F., DeGrado W.F., Dutton P.L. Use of 2,2′-dithiobis(5-nitropyridine) for the heterodimerization of cysteine containing peptides. Introduction of the 5-nitro-2-pyridylsulfenyl group. Tetrahedron Letters. 37:1995;1347-1350
55. Robertson D.E., Farid R.S., Moser C.C., Urbauer J.L., Mulholland S.E., Pidikiti R., Lear J.D., Wand A.J., DeGrado W.F., Dutton P.L. Design and synthesis of multi-haem proteins. Nature. 368:1994;425-432
56. Rohl C.A., Chakrabartty A., Baldwin R.L. Helix propagation and N-cap propensities of the amino acids measured in alanine based peptides in 40 volume percent trifluoroethanol. Protein Sci. 5:1996;. 2623-2337
57. Santoro M.M., Bolen D.W. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl a-chymotrypsin using different denaturants. Biochemistry. 27:1988;8063-8068
58. Schafmeister C.E., Miercke L.J.W., Stroud R.M. Structure at 2.5 Å of a designed peptide that maintains solubility of membrane proteins. Science. 262:1993;734-738
59. Scott M.P., Biggins J. Introduction of a [4Fe-4S (S-cys)4]+1,+2 iron-sulfur center into a four-alpha helix protein using design parameters from the domain of the Fx cluster in the Photosystem I reaction center. Protein Sci. 6:1997;340-346
60. Su A., Mayo S.L. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6:1997;1701-1707
61. Zitzewitz J.A., Bilsel O., Luo J., Jones B.F., Matthews C.R. Probing the folding mechanism of a leucine zipper peptide by stopped-flow circular dichroism spectroscopy. Biochemistry. 34:1995;12812-12819