SpringerProtocols: Abstract: Protein Engineering

Protein Engineering

By: Sonia Longhi^{2 3}, François Ferron^{2 3}, Marie-Pierre Egloff^{2 3}

Abstract

Full Text

Download PDF (808K)

This chapter focuses on protein engineering strategies that aim to increase the chances of obtaining crystals suitable for X-ray diffraction. The chapter is divided into three main parts: one dealing with protein engineering through a bioinformatics approach, the second focusing on DNA modifications via random mutagenesis, and the third describing a nonexhaustive number of in vitro modifications based on site-directed mutagenesis.

Affiliation(s): (2) Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Marseille, France
(3) Architecture et Fonction des Macromolécules Biologiques, Universités Aix-Marseille I et II, Marseille, France

Book Title: Macromolecular Crystallography Protocols: Volume 1, Preparation and Crystallization of Macromolecules

Series: Methods in Molecular Biology | Volume: 363 | Pub. Date: Feb-05-2007 | Page Range: 59-90 | DOI: 10.1007/978-1-59745-209-0_4

Subject: Protein Science

Key Words: Crystallization - mutagenesis - limited proteolysis - error-proned PCR - DNA shuffling - bioinformatics

References

Download References

1.	Gerstein, M. (1998) Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33, 518–534. <Occurrence Type="DOI"><Handle>10.1002/(SICI)1097-0134(19981201)33:4<518::AID-PROT5>3.0.CO;2-J</Handle></Occurrence>

2.	Gerstein, M. (1998) How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des. 3, 497–512. <Occurrence Type="DOI"><Handle>10.1016/S1359-0278(98)00066-2</Handle></Occurrence>

3.	Sulzenbacher, G., Gruez, A., Roig-Zamboni, V., et al. (2002) A medium-throughput crystallization approach. Acta Crystallogr. D Biol. Crystallogr. 58, 2109–2115.

4.	Ding, H. T., Ren, H., Chen, Q., et al. (2002) Parallel cloning, expression, purification and crystallization of human proteins for structural genomics. Acta Crystallogr. D Biol. Crystallogr. 58, 2102–2108.

5.	Skinner, M. M. and Terwilliger, T. C. (1996) Potential use of additivity of mutational effects in simplifying protein engineering. Proc. Natl. Acad. Sci. USA 93, 10,753–10,757.

6.	Heinz, D. W., Baase, W. A., and Matthews, B. W. (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.

7.	Dale, G. E., Kostrewa, D., Gsell, B., Stieger, M., and D’Arcy, A. (1999) Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus. Acta Crystallogr. D Biol. Crystallogr. 55, 1626–1629.

8.	Longhi, S., Nicolas, A., Creveld, L., et al. (1996) Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants. Proteins 26, 442–458. <Occurrence Type="DOI"><Handle>10.1002/(SICI)1097-0134(199612)26:4<442::AID-PROT5>3.0.CO;2-D</Handle></Occurrence>

9.	Martin, G., Keller, W., and Doublié, S. (2000) Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 19, 4193–4203.

10.	Egloff, M. P., Benarroch, D., Selisko, B., Romette, J. L., and Canard, B. (2002) An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 21, 2757–2768.

11.	Kawasaki, M. and Inagaki, F. (2001) Random PCR-based screening for soluble domains using green fluorescent protein. Biochem. Biophys. Res. Commun. 280, 842–844.

12.	Boone, M. and Upton, C. (2000) BLAST Search Updater: a notification system for new database matches. Bioinformatics 16, 1054–1055.

13.	Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235–242.

14.	Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.

15.	Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217.

16.	Rost, B. (1996) PHD: predicting one-dimensional protein structure by profile-based neural networks. Meth. Enzymol. 266, 525–539.

17.	Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308.

18.	Linding, R., Russell, R. B., Neduva, V., and Gibson, T. J. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701–3708.

19.	Lemesle-Varloot, L., Henrissat, B., Gaboriaud, C., Bissery, V., Morgat, A., and Mornon, J. P. (1990) Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72, 555–574. <Occurrence Type="DOI"><Handle>10.1016/0300-9084(90)90120-6</Handle></Occurrence>

20.	Johansson, K., Bourhis, J. M., Campanacci, V., Cambillau, C., Canard, B., and Longhi, S. (2003) Crystal structure of the measles virus phosphoprotein domain responsible for the induced folding of the C-terminal domain of the nucleoprotein. J. Biol. Chem. 278, 44,567–44,573.

21.	Waldo, G. S. (2003) Genetic screens and directed evolution for protein solubility. Curr. Opin. Chem. Biol. 7, 33–38. <Occurrence Type="DOI"><Handle>10.1016/S1367-5931(02)00017-0</Handle></Occurrence>

22.	Henikoff, S. (1984) Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28, 351–359. <Occurrence Type="DOI"><Handle>10.1016/0378-1119(84)90153-7</Handle></Occurrence>

23.	Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, Cold Spring Harbor, NY.

24.	Fromant, M., Blanquet, S., and Plateau, P. (1995) Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal. Biochem. 224, 347–353.

25.	Melnikov, A. and Youngman, P. J. (1999) Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus. Nucleic Acids Res. 27, 1056–1062.

26.	Cherry, J. R., Lamsa, M. H., Schneider, P., et al. (1999) Directed evolution of a fungal peroxidase. Nat. Biotechnol. 17, 379–384.

27.	Shafikhani, S., Siegel, R. A., Ferrari, E., and Schellenberger, V. (1997) Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. BioTechniques 23, 304–310.

28.	You, L. and Arnold, F. H. (1996) Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. Protein Eng. 9, 77–83.

29.	Grothues, D., Cantor, C. R., and Smith, C. L. (1993) PCR amplification of megabase DNA with tagged random primers (T-PCR). Nucleic Acids Res. 21, 1321–1322.

30.	Waldo, G. S., Standish, B. M., Berendzen, J., and Terwilliger, T. C. (1999) Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol. 17, 691–695.

31.	Stemmer, W. P. (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389–391.

32.	Crameri, A., Raillard, S. A., Bermudez, E., and Stemmer, W. P. (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288–291.

33.	Crameri, A., Whitehorn, E. A., Tate, E., and Stemmer, W. P. (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14, 315–319.

34.	Salamone, P. R., Kavakli, I. H., Slattery, C. J., and Okita, T. W. (2002) Directed molecular evolution of ADP-glucose pyrophosphorylase. Proc. Natl. Acad. Sci. USA 99, 1070–1075.

35.	Lorimer, I. A. and Pastan, I. (1995) Random recombination of antibody single chain Fv sequences after fragmentation with DNaseI in the presence of Mn²⁺. Nucleic Acids Res. 23, 3067–3068.

36.	Stemmer, W. P. (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10,747–10,751.

37.	Eakin, A. E., McGrath, M. E., McKerrow, J. H., Fletterick, R. J., and Craik, C. S. (1993) Production of crystallizable cruzain, the major cysteine protease from Trypanosoma cruzi. J. Biol. Chem. 268, 6115–6118.

38.	Kirchhofer, D., Guha, A., Nemerson, Y., et al. (1995) Activation of blood coagulation factor VIIa with cleaved tissue factor extracellular domain and crystallization of the active complex. Proteins 22, 419–425.

39.	Leppanen, V. M., Parast, C. V., Wong, K. K., Kozarich, J. W., and Goldman, A. (1999) Purification and crystallization of a proteolytic fragment of Escherichia coli pyruvate formate-lyase. Acta Crystallogr. D Biol. Crystallogr. 55, 531–533.

40.	Lemieux, M. J., Song, J., Kim, M. J., et al. (2003) Three-dimensional crystallizationof the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Protein Sci. 12, 2748–2756.

41.	Gaudier, M., Gaudin, Y., and Knossow, M. (2001) Cleavage of vesicular stomatitis virus matrix protein prevents self-association and leads to crystallization. Virology 288, 308–314.

42.	Vallee, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., and Howell, P. L. (2000) Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control. EMBO J. 19, 581–588.

43.	Nachon, F., Nicolet, Y., Viguie, N., Masson, P., Fontecilla-Camps, J. C., and Lockridge, O. (2002) Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase: expression, purification, characterization and crystallization. Eur. J. Biochem. 269, 630–637.

44.	Josephson, K., McPherson, D. T., and Walter, M. R. (2001) Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1. Acta Crystallogr. D Biol. Crystallogr. 57, 1908–1911.

45.	Zhang, F., Basinski, M. B., Beals, J. M., et al. (1997) Crystal structure of the obese protein leptin-E100. Nature 387, 206–209.

46.	Longenecker, K. L., Garrard, S. M., Sheffield, P. J., and Derewenda, Z. S. (2001) Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta Crystallogr. D Biol. Crystallogr. 57, 679–688.

47.	Baud, F. and Karlin, S. (1999) Measures of residue density in protein structures. Proc. Natl. Acad. Sci. USA 96, 12,494–12,499.

48.	Dasgupta, S., Iyer, G. H., Bryant, S. H., Lawrence, C. E., and Bell, J. A. (1997) Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 28, 494–514. <Occurrence Type="DOI"><Handle>10.1002/(SICI)1097-0134(199708)28:4<494::AID-PROT4>3.0.CO;2-A</Handle></Occurrence>

49.	Mateja, A., Devedjiev, Y., Krowarsch, D., et al. (2002) The impact of Glu—>Ala and Glu—>Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 A resolution. Acta Crystallogr. D Biol. Crystallogr. 58, 1983–1991.

50.	Jenkins, T. M., Hickman, A. B., Dyda, F., Ghirlando, R., Davies, D. R., and Craigie, R. (1995) Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues. Proc. Natl. Acad. Sci. USA 92, 6057–6061.

51.	Liu, Y., Manna, A., Li, R., et al. (2001) Crystal structure of the SarR protein from Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 98, 6877–6882.

52.	Center, R. J., Kobe, B., Wilson, K. A., et al. (1998) Crystallization of a trimeric human T cell leukemia virus type 1 gp21 ectodomain fragment as a chimera with maltose-binding protein. Protein Sci. 7, 1612–1619.

Comments (Loading...)

Post comment/View all comments