Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 40, 2008, Pages 15334-15339

  Islam, Mohammad Monirul ^a   Sohya, Shihori ^a   Noguchi, Keiichi ^a   Yohda, Masafumi ^a   Kuroda, Yutaka ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

Native structure; Protein design; Protein folding; Protein structure; Sequence simplification

Indexed keywords

ALANINE; BOVINE PANCREATIC TRYPSIN INHIBITOR; TRYPSIN INHIBITOR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DISULFIDE BOND; PLASTICITY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEIN VARIANT;

ALANINE; AMINO ACID SUBSTITUTION; ANIMALS; APROTININ; CATTLE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN FOLDING;

BOVINAE;

EID: 55749087870     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0802699105     Document Type: Article

References (37)

1. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230.
2. 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.
3. Rose GD (2000) Lysozyme among the Lilliputians. Proc Natl Acad Sci USA 97:526-528.
4. Plaxco KW, Riddle DS, Grantcharova V, Baker D (1998) Simplified proteins: Minimalist solutions to the "protein folding problem." Curr Opin Struct Biol 8:80-85.
5. Kallenbach N (2001) Breaking open a protein barrel. Proc Natl Acad Sci USA 98:2958-2960.
6. Kuroda Y, Kim PS (2000) Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine. J Mol Biol 298:493-501.
7. Schafmeister CE, LaPorte SL, Miercke LJ, Stroud RM (1997) A designed four helix bundle protein with native-like structure. Nat Struct Biol 4:1039-1046.
8. Riddle DS, et al. (1997) Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol 4:805-809.
9. Walter KU, Vamvaca K, Hilvert D (2005) An active enzyme constructed from a 9-amino acid alphabet. J Biol Chem 280:37742-37746.
10. Akanuma S, Kigawa T, Yokoyama S (2002) Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc Natl Acad Sci USA 99:13549-13553.
11. Cunningham BC, Wells JA (1989) High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244:1081-1085.
12. Heinz DW, Baase WA, Matthews BW (1992) Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. Proc Natl Acad Sci USA 89:3751-3755.
13. Brown BM, Sauer RT (1999) Tolerance of Arc repressor to multiple-alanine substitutions. Proc Natl Acad Sci USA 96:1983-1988.
14. Kato A, Yamada M, Nakamura S, Kidokoro S, Kuroda Y (2007) Thermodynamic properties of BPTI variants with highly simplified amino acid sequences. J Mol Biol 372:737-746.
15. Gassner NC, Baase WA, Matthews BW (1996) A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci USA 93:12155-12158.
16. Chen J, Lu Z, Sakon J, Stites WE (2004) Proteins with simplified hydrophobic cores compared to other packing mutants. Biophys Chem 110:239-248.
17. Yu MH, Weissman JS, Kim PS (1995) Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis. J Mol Biol 249:388-397.
18. Hagihara Y, et al. (2002) Screening for stable mutants with amino acid pairs substituted for the disulfide bond between residues 14 and 38 of bovine pancreatic trypsin inhibitor (BPTI). J Biol Chem 277:51043-51048.
19. Staley JP, Kim PS (1992) Complete folding of bovine pancreatic trypsin inhibitor with only a single disulfide bond. Proc Natl Acad Sci USA 89:1519-1523.
20. Ohgushi M, Wada A (1983) "Molten-globule state": A compact form of globular proteins with mobile side-chains. FEBS Lett 164:21-24.
21. Kuwajima K (1989) The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins 6:87-103.
22. Harrison SC, Durbin R (1985) Is there a single pathway for the folding of a polypeptide chain? Proc Natl Acad Sci USA 82:4028-4030.
23. 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.
24. Alexander PA, He Y, Chen Y, Orban J, Bryan PN (2007) The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci USA 104:11963-11968.
25. Fischer D, Rice D, Bowie JU, Eisenberg D (1996) Assigning amino acid sequences to 3-dimensional protein folds. FASEB J 10:126-136.
26. Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358:86-89.
27. Jin W, Kambara O, Sasakawa H, Tamura A, Takada S (2003) De novo design of foldable proteins with smooth folding funnel: Automated negative design and experimental verification. Structure 11:581-590.
28. Alvizo O, Allen BD, Mayo SL (2007) Computational protein design promises to revolutionize protein engineering. BioTechniques 42:31, 33, 35 passim.
29. Kuhlman B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368.
30. Otwinowski Z, Minor W (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276(Part A):307-326.
31. Wlodawer A, Walter J, Huber R, Sjolin L (1984) Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and x-ray refinement of crystal form II. J Mol Biol 180:301-329.
32. Collaborative Computational Project, Number 4. (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
33. Sheldrick GM (1997) SHELXL-97: Program for the Refinement of Crystal Structures.
34. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
35. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: A unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D 55:191-205.
36. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
37. Davis IW, et al. (2007) MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W83.