Automated design of the surface positions of protein helices

Protein Science

Volumn 6, Issue 6, 1997, Pages 1333-1337

  Dahiyat, Bassil I ^a   Benjamin Gordon, D ^a   Mayo, Stephen L ^b  

^a California Institute of Technology   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Coiled coils; Helix propensities; Protein design; Surface residues

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; GEL PERMEATION CHROMATOGRAPHY; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STABILITY;

EID: 0343742614     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060622     Document Type: Article

References (33)

1. Bernstein FC, Koetzle TF, Williams GJB, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
2. Betz SF, Degrado WF. 1996. Controlling topology and native-like behavior of de novo-designed peptides - Design and characterization of antiparallel 4-stranded coiled coils. Biochemistry 35:6955-6962.
3. Blaber M, Zhang XJ, Matthews BW. 1993. Structural basis of amino acid α helix propensity. Science 260:1637-1640.
4. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT. 1990. Deciphering the message in protein sequences: Tolerance to amino acid substitutions. Science 247:1306-1310.
5. Cantor CR, Schimmel PR. 1980. Biophysical chemistry. New York: W. H. Freeman and Company.
6. Chakrabartty A, Kortemme T, Baldwin RL. 1994. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 3:843-852.
7. Cohen C, Parry DAD. 1990. α-Helical coiled coils and bundles: How to design an α-helical protein. Proteins Struct Funct Genet 7:1-15.
8. Dahiyat BI, Mayo SL. 1996. Protein design automation. Protein Sci 5:895-903.
9. Dahiyat BI, Mayo SL. Probing the role of packing specificity in protein design. Proc Natl Acad Sci, in press.
10. Desjarlais JR, Handel TM. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci 4:2006-2018.
11. Desmet J, De Maeyer M, Hazes B, Lasters I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-542.
12. Desmet J, De Maeyer M, Lasters I. 1994. The dead-end elimination theorem: A new approach to the side-chain packing problem. In: Merz Jr K, Le Grand S, eds. The protein folding problem and tertiary structure prediction. Boston: Birkhauser. pp 307-337.
13. Dunbrack RL, Karplus M. 1993. Backbone-dependent rotamer library for proteins - An application to side-chain prediction. J Mol Biol 230:543-574.
14. Eisenberg D, McLachlan AD. 1986. Solvation energy in protein folding and binding. Nature 319:199-203.
15. Goldstein RF. 1994. Efficient rotamer elimination applied to protein side-chains and related spin-glasses. Biophys J 66:1335-1340.
16. Harbury PB, Tidor B, Kim PS. 1995. Repacking protein cores with backbone freedom: Structure prediction for coiled coils. Proc Natl Acad Sci USA 92:8408-8412.
17. Harbury PB, Zhang T, Kim PS, Alber T. 1993. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262:1401-1407.
18. Hellinga HW, Caradonna JP, Richards FM. 1991. Construction of new ligand-binding sites in proteins of known structure 2. Grafting of buried transition-metal binding site into Escherichia coli thioredoxin. J Mol Biol 222:787-803.
19. Hurley JH, Baase WA, Matthews BW. 1992. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J Mol Biol 224:1143-1154.
20. Huyghues-Despointes BMP, Klingler TM, Baldwin RL. 1995. Measuring the strength of side-chain hydrogen bonds in peptide helices: The gln·asp (i,i + 4) interaction. Biochemistry 34:13267-13271.
21. Klemba M, Gardner KH, Marino S, Clarke ND, Regan L. 1995. Novel metal-binding proteins by design. Nature Struct Biol 2:368-373.
22. Mayo SL, Olafson BD, Goddard III WA. 1990. Dreiding: A generic forcefield for molecular simulations. J Phys Chem 94:8897-8909.
23. Minor DL, Kim PS. 1994. Measurement of the β-sheet-forming propensities of amino acids. Nature 367:660-663.
24. Nautiyal S, Woolfson DN, King DS, Alber T. 1995. A designed heterotrimeric coiled coil. Biochemistry 34:11645-11651.
25. O'Neil KT, DeGrado WF. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646-651.
26. O'Shea EK, Klemm JD, Kim PS, Alber T. 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254:539-544.
27. O'Shea EK, Lumb KJ, Kim PS. 1993. Peptide velcro - Design of a heterodimeric coiled coil. Current Biology 3:658-667.
28. Ponder JW, Richards FM. 1987. Tertiary templates for proteins - Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775-791.
29. Reidhaar-Olson JF, Sauer RT. 1988. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241:53-57.
30. Smith CK, Withka JM, Regan L. 1994. A thermodynamic scale for the β-sheet-forming tendencies of amino acids. Biochemistry 33:5510-5517.
31. Stickle DF, Presta LG, Dill KA, Rose GD. 1992. Hydrogen-bonding in globular proteins. J Mol Biol 226:1143-1159.
32. Villegas V, Viguera AR, Aviles FX, Serrano L. 1996. Stabilization of proteins by rational design of a-helix stability using helix/coil transition theory. Folding and Design 1:29-34.
33. Zhang XJ, Baase WA, Matthews BW. 1991. Toward a simplification of the protein folding problem: A stabilizing polyalanine α helix engineered in T4 lysozyme. Biochemistry 30:2012-2017.