Effective improvement of D-phenylglycine aminotransferase solubility by protein crystal contact engineering

Journal of Molecular Microbiology and Biotechnology

Volumn 22, Issue 3, 2012, Pages 147-155

  Chantarasiri, Aiya ^a   Meevootisom, Vithaya ^a   Isarangkul, Duangnate ^a   Wiyakrutta, Suthep ^a  

^a Faculty of Science Mahidol University ^*  (Thailand)

Author keywords

D Phenylglycine aminotransferase; In vitro protein solubility; Protein crystal contact; Structure guided mutagenesis

Indexed keywords

ASPARTIC ACID; BACTERIAL ENZYME; DEXTRO PHENYLGLYCINE AMINOTRANSFERASE; GLUTAMIC ACID; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; COMPUTER MODEL; CRYSTAL STRUCTURE; ENZYME CONFORMATION; ENZYME MODIFICATION; ENZYME SPECIFICITY; ENZYME STABILITY; ISOELECTRIC POINT; MELTING POINT; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ENGINEERING; PROTEIN STRUCTURE; SOLUBILITY; STATIC ELECTRICITY;

ASPARTIC ACID; CIRCULAR DICHROISM; GLUTAMIC ACID; HYDROGEN-ION CONCENTRATION; ISOELECTRIC POINT; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SOLUBILITY; TEMPERATURE; TRANSAMINASES;

EID: 84864080802     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000339833     Document Type: Article

References (25)

1. Ahmad S, Gromiha M, Fawareh H, Sarai A: ASAView: database and tool for solvent accessibility representation in proteins. BMC Bioinf 2004; 5: 51.
2. Arnold K, Bordoli L, Kopp J, Schwede T: The Swiss-Model workspace: a web-based environment for protein structure homology modeling. Bioinformatics 2006; 22: 195-201. (Pubitemid 43205406)
3. Christendat D, Yee A, Dharamsi A, Kluger Y, Savchenko A, Cort JR, et al: Structural proteomics of an archaeon. Nat Struct Biol 2000; 7: 903-909.
4. Dasgupta S, Iyer GH, Bryant SH, Lawrence CE, Bell JA: Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 1997; 28: 494-514. (Pubitemid 27328566)
5. Evans P, Wyatt K, Wistow GJ, Bateman OA, Wallace BA, Slingsby C: The P23T cataract mutation causes loss of solubility of foldedD-crystallin. J Mol Biol 2004; 343: 435-444. (Pubitemid 39296876)
6. Fraczkiewicz R, Braun W: Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comput Chem 1998; 19: 319-333. (Pubitemid 128592649)
7. Golovanov AP, Hautbergue GM, Wilson SA, Lian LY: A simple method for improving protein solubility and long-term stability. J Am Chem Soc 2004; 126: 8933-8939. (Pubitemid 38971066)
8. Heukeshoven J, Dernick R: Characterization of a solvent system for separation of water-insoluble poliovirus proteins by reversedphase high-performance liquid chromatography. J Chromatog 1985; 326: 91-101. (Pubitemid 15069356)
9. Kato A, Maki K, Ebina T, Kuwajima K, Soda K, Kuroda Y: Mutational analysis of protein solubility enhancement using short peptide tags. Biopolymers 2007; 85: 12-18. (Pubitemid 46154815)
10. Kaur H, Raghava GP: Prediction of-turns in proteins from multiple alignment using neural network. Protein Sci 2003; 12: 627-634. (Pubitemid 36241119)
11. Khampha W, Meevootisom V, Wiyakrutta S: Spectrophotometric enzymatic cycling method using L-glutamate dehydrogenase and D-phenylglycine aminotransferase for determination of L-glutamate in foods. Anal Chim Acta 2004; 520: 133-139. (Pubitemid 39092895)
12. Kongsaeree P, Samanchart C, Laowanapiban P, Wiyakrutta S, Meevootisom V: Crystallization and preliminary X-ray crystallographic analysis of D-phenylglycine aminotransferase from Pseudomonas stutzeri ST201. Acta Crystallogr Sect D Biol Crystallogr 2003; 59: 953-954. (Pubitemid 36599384)
13. Lesser GJ, Rose GD: Hydrophobicity of amino acid subgroups in proteins. Proteins 1990; 8: 6-13. (Pubitemid 20235327)
14. Pace CN, Grimsley GR, Scholtz JM: Protein ionizable groups: pK values and their contribution to protein stability and solubility. J Biol Chem 2009; 284: 13285-13289.
15. Potterton E, Briggs P, Turkenburg M, Dodson E: A graphical user interface to the CCP4 program suite. Acta Crystallogr Sect D Biol Crystallogr 2003; 59: 1131-1137. (Pubitemid 36872348)
16. Rojanarata T, Ngawhirunpat T, Saehuan C, Wiyakrutta S, Meevootisom V: A simple, sensitive and green bi-enzymatic UV-spectrophotometric assay of amoxicillin formulations. Enzyme Microb Tech 2010; 46: 292-296.
17. Rost B: Twilight zone of protein sequence alignments. Protein Eng 1999; 12: 85-94. (Pubitemid 29103686)
18. Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, et al: SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res 2005; 33: 39-43.
19. Sorrequieta A, Ferraro G, Boggio SB, Valle EM: Free amino acid production during tomato fruit ripening: a focus on L-glutamate. Amino Acids 2010; 38: 1523-1532.
20. Trevino SR, Scholtz JM, Pace CN: Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa. J Mol Biol 2007; 366: 449-460. (Pubitemid 46136196)
21. Trevino SR, Scholtz JM, Pace CN: Measuring and increasing protein solubility. J Pharm Sci 2008; 97: 4155-4166.
22. Weichenberger CX, Sippl MJ: Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures. Structure 2006; 14: 967-972. (Pubitemid 43831657)
23. Wiyakrutta S, Meevootisom V: A stereo-inverting D-phenylglycine aminotransferase from Pseudomonas stutzeri ST-201: purification, characterization and application for D-phenylglycine synthesis. J Biotechnol 1997; 55: 193-203. (Pubitemid 27339264)
24. Yee A, Chang X, Pineda-Lucena A, Wu B, Semesi A, Le B, et al: An NMR approach to structural proteomics. Proc Natl Acad Sci USA 2002; 99: 1825-1830. (Pubitemid 34168974)
25. Yee A, Pardee K, Christendat D, Savchenko A, Edwards AM, Arrowsmith CH: Structural proteomics: toward high-throughput structural biology as a tool in functional genomics. Acc Chem Res 2003; 36: 183-189.