Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design

Protein Science

Volumn 9, Issue 7, 2000, Pages 1391-1394

  Strop, Pavel ^a   Marinescu, Andrei M ^a   Mayo, Stephen L ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Helix dipole interaction; Helix propensity; Protein design; Protein G

Indexed keywords

PROTEIN G;

ARTICLE; CIRCULAR DICHROISM; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; TEMPERATURE;

EID: 0033867241     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.7.1391     Document Type: Article

References (34)

1. Alexander P, Fahnestock S, Lee T, Orban J, Bryan P. 1992. Thermodynamic analysis of the folding of the streptococcal protein G 1gG-binding domains β1 and β2 - Why small proteins tend to have high denaturation temperatures. Biochemistry 31:3597-3603.
2. Bailey S. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D50:760-763.
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. Brünger AT. 1992. X-PLOR, version 3.1: A system for X-ray crystallography and NMR. New Haven, Connecticut: Yale University Press.
6. Chakrabartty A, Doig AJ, Baldwin RL. 1993. Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci USA 90:11332-11336.
7. Chakrabartty A, Kortemme T, Baldwin RL. 1994. Helix propensities of the amino-acids measured in alanine-based peplides without helix-stabilizing side-chain interactions. Protein Sci 3:843-852.
8. Creamer TP, Rose GD. 1994. Alpha-helix-forming propensities in peptides and proteins. Proteins 19:85-97.
9. Dahiyat BI, Gordon DB, Mayo SL. 1997a. Automated design of the surface positions of protein helices. Protein Sci 6:1333-1337.
10. Dahiyat BI, Mayo SL. 1996. Protein design automation. Protein Sci 5:895-903.
11. Dahiyat BI, Mayo SL. 1997a. De novo protein design: Fully automated sequence selection. Science 278:82-87.
12. Dahiyat BI, Mayo SL. 1997b. Probing the role of packing specificity in protein design. Proc Natl Acad Sci USA 94:10172-10177.
13. Dahiyat BI, Sarisky CA, Mayo SL. 1997b. De novo protein design: Towards fully automated sequence selection. J Mol Biol 273:789-796.
14. Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL. 1994. Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N-and C-capping. Biochemistry 33:3396-3403.
15. Esnouf RM. 1997. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph 15:133-138.
16. Gallagher T, Alexander P, Bryan P, Gilliland GL. 1994. 2 crystal-structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 33:4721-4729.
17. Hemsley A. Arnheim N, Toney MD, Cortopassi G, Galas DJ. 1989. A simple method for site-directed mutagenesis using the polymerase chain reaction. Nucleic Acid Res 17:6545-6551.
18. Huyghues-Despointes BMP, Scholtz JM, Baldwin R. 1993. Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide. Protein Sci 2:16604-16611.
19. Johnson BH, Hecht MH. 1994. Recombinant proteins can be isolated from E. coli cells by repeated cycles of freezing and thawing. Biotechnology 12:1357-1360.
20. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. 1991. Improved methods for building protein models in electron: Density maps and the location of errors in these models. Acta Crystallogr A47:110-119.
21. Laskowski RA, Macarthur MW, Moss DS, Thornton JM. 1993. Procheck: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283.
22. Lockhart DJ, Kim PS. 1992. Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science 257:947-951.
23. Lockhart DJ, Kim PS. 1993. Electrostatic screening of charge and dipole interactions with the helix backbone. Science 260:198-202.
24. Merritt EA, Bacon DJ. 1997. Raster3D photorealistic molecular graphics. Methods Enzymol 277:505-524.
25. Minor DL, Kim PS. 1994. Measurement of the β-sheet-forming propensities of amino acids. Nature 367:660-663.
26. Nicholson H, Anderson DE, Dao-pin S, Matthews BW. 1991. Analysis of the interaction between charged side chains and the alpha-helix dipole using designed thermostable mutants of phage T4 lysozyme. Biochemistry 30: 9816-9828.
27. Nicholson H, Becktel WJ, Matthews BW. 1988. Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles. Nature 336:651-656.
28. O'Neil KT, DeGrado WF. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646-651.
29. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
30. Reidhaar-Olson JF, Sauer RT. 1988. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241: 53-57.
31. Smith CK, Withka JM, Regan L. 1994. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33:5510-5517.
32. Walter S. Hubner B, Hahn U, Schmid FX. 1995. Destabilisation of a protein helix by electrostatic interactions. J Mol Biol 252:133-143.
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.
34. Zhao H, Arnold FH. 1999. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng 12:47-53.