Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2

Protein Science

Volumn 11, Issue 12, 2002, Pages 2924-2931

  Nauli, Sehat ^a,b   Kuhlman, Brian ^a   Trong, Isolde Le ^b   Stenkamp, Ronald E ^a,b   Teller, David ^a,b   Baker, David ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

hairpin design; Computational protein design; Crystal structure of protein G; Protein folding; Protein G

Indexed keywords

PROTEIN G; PROTEIN NUG1; PROTEIN NUG2; UNCLASSIFIED DRUG; G SUBSTRATE; G-SUBSTRATE; NERVE PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HYDROGEN BOND; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN VARIANT; SOLVATION; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; KINETICS; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN DENATURATION; PROTEIN ENGINEERING; PROTEIN SECONDARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NERVE TISSUE PROTEINS; PROTEIN DENATURATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 0036892410     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0216902     Document Type: Article

References (26)

1. Bonneau, R. and Baker, D. 2001. Ab initio protein structure prediction: Progress and prospects. Annu. Rev. Biophys. Biomol. Struct. 30: 173-189.
2. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
3. Bryson, J.W., Betz, S.F., Lu, H.S., Suich, D.J., Zhou, H.X., O'Neil, K.T., and DeGrado, W.F. 1995. Protein design: A hierarchic approach. Science 270: 935-941.
4. Cordes, M.H., Davidson, A.R., and Sauer, R.T. 1996. Sequence space, folding and protein design. Curr. Opin. Struct. Biol. 6: 3-10.
5. Dahiyat, B.I. and Mayo, S.L. 1996. Protein design automation. Protein Sci. 5: 895-903.
6. -. 1997. De novo protein design: Fully automated sequence selection. Science 278: 82-87.
7. Desjarlais, J.R. and Handel, T.M. 1995. New strategies in protein design. Curr. Opin. Biotechnol. 6: 460-466.
8. Dunbrack, Jr., R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
9. Gallagher, T., Alexander, P., Bryan, P., and Gilliland, G.L. 1994. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 33: 4721-4729.
10. Gordon, D.B., Marshall, S.A., and Mayo, S.L. 1999. Energy functions for protein design. Curr. Opin. Struct. Biol. 9: 509-513.
11. Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T., and Kim, P.S. 1998. Highresolution protein design with backbone freedom. Science 282: 1462-1467.
12. Kissinger, C.R., Gehlhaar, D.K., and Fogel, D.B. 1999. Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr. 55: 484-491.
13. Kuhlman, B. and Baker, D. 2000. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. 97: 10383-10388.
14. Kuhlman, B., O'Neill, J.W., Kim, D.E., Zhang, K.Y., and Baker, D. 2002. Accurate computer-based design of a new backbone conformation in the second turn of protein L. J. Mol. Biol. 315: 471-477.
15. Lazaridis, T. and Karplus, M. 1999. Effective energy function for proteins in solution. Proteins. 35: 133-152.
16. Malakauskas, S.M. and Mayo, S.L. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5: 470-475.
17. McCallister, E.L., Alm, E., and Baker, D. 2000. Critical role of β-hairpin formation in protein G folding. Nat. Struct. Biol. 7: 669-673.
18. McRee, D.E. 1999. XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125: 156-165.
19. Minor, Jr., D.L and Kim, P.S. 1994. Measurement of the β-sheet-forming propensities of amino acids. Nature 367: 660-663.
20. Nauli, S., Kuhlman, B., and Baker, D. 2001. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8: 602-605.
21. Navaza, J. 2001. Implementation of molecular replacement in AMoRe. Acta Crystallogr. D Biol. Crystallogr. 57: 1367-1372.
22. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276A: 307-326.
23. Sibanda, B.L. and Thornton, J.M. 1985. β-hairpin families in globular proteins. Nature 316: 170-174.
24. Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C., and Baker, D. 1999. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34: 82-95.
25. Smith, C.K. and Regan, L. 1995. Guidelines for protein design: The energetics of β sheet side chain interactions. Science 270: 980-982.
26. Smith, C.K., Withka, J.M., and Regan, L. 1994. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33: 5510-5517.