A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange

Bioinformatics

Volumn 29, Issue 11, 2013, Pages 1375-1381

  Lobanov, Mikhail Yu ^a   Suvorina, Masha Yu ^a   Dovidchenko, Nikita V ^a   Sokolovskiy, Igor V ^a   Surin, Alexey K ^a,b   Galzitskaya, Oxana V ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^b STATE RESEARCH CENTER FOR APPLIED MICROBIOLOGY AND BIOTECHNOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN; PROTON;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; DEUTERIUM HYDROGEN EXCHANGE; INTERNET; MASS SPECTROMETRY; SEQUENCE ANALYSIS;

AMINO ACIDS; DEUTERIUM EXCHANGE MEASUREMENT; INTERNET; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTONS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84878281109     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt168     Document Type: Article

References (48)

1. Bai, Y. et al. (1997) Absence of a stable intermediate on the folding pathway of protein A. Protein Sci., 6, 1449-1457.
2. Bycroft, M. et al. (1990) Detection and characterization of a folding intermediate in Barnase by NMR. Nature, 346, 488-490.
3. Chamberlain, A.K. et al. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat. Struct. Biol., 3, 782-787.
4. Craig, P.O. et al. (2011) Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. J. Am. Chem. Soc., 133, 17463-17472.
5. Dovidchenko, N.V. and Galzitskaya, O.V. (2008) Prediction of status residue to be protected or not protected from hydrogen exchange using amino acid sequence only. Open Biochem. J., 2, 77-80.
6. Dovidchenko, N.V. et al. (2009) Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain. Biochemistry, 74, 1091-1102
7. Englander, S.W. (2006) Hydrogen exchange and mass spectrometry: a historical perspective. J. Am. Soc. Spectrom., 17, 1481-1489.
8. Feeney, J. et al. (2011) NMR structures of Apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. Biochemistry, 50, 3609-3620.
9. Freund, C. et al. (1997) Comparison of the amide proton exchange behavior of the rapidly formed folding intermediate and the native state of an antibody scFv fragment. FEBS Lett., 407, 42-46.
10. Franzoni, L. et al. (2010) New insights on the protein-ligand interaction differences between the two primary cellular retinol carriers. J. Lipid Res., 51, 1332-1343.
11. Fontana, A. (1988) Structure and stability of thermophilic enzymes. Studies on thermolysin. Biophys. Chem., 29, 181-193.
12. Galzitskaya, O.V. et al. (2006) FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics, 22, 2948-2949.
13. Garbuzynskiy, S.O. et al. (2010) FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics, 26, 326-332.
14. Itzhaki, S.L. et al. (1997) Hydrogen exchange in chymotrypsin inhibitor 2 probed by denaturants and temperature. J. Mol. Biol., 270, 89-98.
15. Jacobs, D.J. et al. (2001) Protein flexibility predictions using graph theory. Proteins, 44, 150-165.
16. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
17. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
18. Kim, K.S. et al. (1993) Hydrogen exchange identifies native-state motional domains important in protein folding. Biochemistry, 32, 9600-9608.
19. Lacroix, E. et al. (1997) Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli. J. Mol. Biol., 271, 472-487.
20. Loh, S.N. et al. (1993) Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry, 32, 11022-11028.
21. Malmstroem, L. et al. (2009) On the use of hydrogen/deuterium exchange mass spectrometry data to improve de novo protein structure prediction. Rapid Commun. Mass Spectrom., 23, 459-461.
22. Milne, J.S. et al. (1998) Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Sci., 7, 739-745.
23. Morin, S. et al. (2009) NMR dynamics of PSE-4 beta-lactamase: an interplay of psns order and mus-ms motions in the active site. Biophys. J., 96, 4681-4691.
24. Morozova, L.A. et al. (1995) Structural basis of the stability of a lysozyme molten globule. Nat. Struct. Biol., 2, 871-875.
25. Mullins, L.S. et al. (1997) Conformational stability of ribonuclease T1 determined by hydrogen-deuterium exchange. Protein Sci., 6, 1387-1395.
26. Murzin, A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
27. Orban, J. et al. (1995) Assessment of stability differences in the protein G Bl and B2 domains from hydrogen-deuterium exchange: comparison with calorimetric data. Biochemistry, 34, 15291-15300.
28. Pan, Y. and Briggs, M.S. (1992) Hydrogen exchange in native and alcohol forms of ubiquitin. Biochemistry, 31, 11405-11412.
29. Perez, J.M. et al. (2001) Thermal unfolding of a llama antibody fragment: a twostate reversible process. Biochemistry, 40, 74-83.
30. Qiwen, W. et al. (1987) Amide proton exchange in the a-Amylase polypeptide inhibitor tendamistat studied by two-dimensional 1H nuclear magnetic resonance. Biochemistry, 26, 6488-6493.
31. Ranjan, N. et al. (2011) Solution structure and activation mechanism of ubiquitinlike small archaeal modifier proteins. J. Mol. Biol., 405, 1040-1055.
32. Rogov, V.V. et al. (2004) Solution Structure of the Escherichia coli YojN Histidinephosphotransferase domain and its interaction with cognate phosphoryl receiver domains. J. Mol. Biol., 343, 1035-1048.
33. Rose, G.D. et al. (1985) Turns in peptides and proteins. Adv. Protein Chem., 37, 1-109.
34. Russell, B.S. et al. (2003) Backbone dynamics and hydrogen exchange of Pseudomonas aeruginosa ferricytochrome c(551). J. Biol. Inorg. Chem., 8, 156-166.
35. Sadqi, M. et al. (1999) The native state conformational ensemble of the SH3 domain from alpha-spectrin. Biochemistry, 38, 8899-8906.
36. Salinas, R. et al. (2009) Solution structure of the C-terminal domain of multiprotein bridging factor 1 (MBF1) of Trichoderma reesei. Proteins, 75, 518-523.
37. Savitski, M.M. et al. (2007) Backbone carbonyl group basicities are related to gasphase fragmentation of peptides and protein folding. Angew. Chem. Int. Ed. Engl., 46, 1481-1484.
38. Sivaraman, T. et al. (2000) Comparison of the structural stability of two homologous toxins isolated from the Taiwan cobra (Naja naja atra) venom. Biochemistry, 39, 8705-8710.
39. Skinner, J.J. et al. (2012) Protein hydrogen exchange: testing current models. Protein Sci., 7, 987-995.
40. Suvorina, M.Y. et al. (2012) Comparison of experimental and theoretical data on hydrogen-deuterium exchange for ten globular proteins. Biochemistry, 77, 758-766.
41. Swint-Kruse, L. and Robertson, A.D. (1996) Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry, 35, 171-180.
42. Tartaglia, G.G. et al. (2007) Prediction of local structural stabilities of proteins from their amino acid sequences. Structure, 15, 139-143.
43. Varley, P. et al. (1993) Kinetics of folding of the all-beta sheet protein interleukin-1 beta. Science, 260, 1110-113.
44. Volkman, B.F. et al. (1998) Solution structure and backbone dynamics of component IV glycera dibranchiata monomeric hemoglobin-CO. Biochemistry, 37, 10906-10919.
45. Walma, T. et al. (2004) A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL. Structure, 12, 11-20.
46. Westhof, E. et al. (1984) Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature, 311, 123-126.
47. Wijesinha-Bettoni, R. et al. (2001) Comparison of the structural and dynamical properties of holo and apo bovine alpha-lactalbumin by NMR spectroscopy. J. Mol. Biol., 307, 885-898.
48. Yi, Q. and Baker, D. (1996) Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein Sci., 5, 1060-1066.