Large scale motions in a biosensor protein glucose oxidase: A combined approach by QENS, normal mode analysis, and molecular dynamics studies

Biopolymers

Volumn 89, Issue 7, 2008, Pages 582-594

  Tatke, Sujit S ^a   Loong, Chun K ^b   D'Souza, Nicolas ^b   Schoephoerster, Richard T ^a   Prabhakaran, M ^a  

^a Florida International University   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Glucose oxidase; Molecular dynamics; Normal mode analysis; Quasi neutron elastic scattering

Indexed keywords

AMINO ACIDS; CARBON NANOTUBES; COMPUTER SIMULATION; DYNAMICS; GLUCOSE; GLUCOSE SENSORS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; STABILITY;

BIO SENSOR; COVARIANT ANALYSIS; GLUCOSE OXIDASES; LYSINE RESIDUES; MOLECULAR DYNAMIC SIMULATION; NORMAL MODE ANALYSIS; QUASI NEUTRON ELASTIC SCATTERING; QUASI-ELASTIC NEUTRON SCATTERING; RADIUS OF GYRATION; ROOT MEAN SQUARE; SOLVENT ACCESSIBILITY; STRUCTURAL STABILITIES; STRUCTURE AND DYNAMICS; VIBRATIONAL FREQUENCIES;

GLUCOSE OXIDASE;

CARBON NANOTUBE; GLUCOSE OXIDASE;

ARTICLE; ASPERGILLUS NIGER; BIOSENSOR; CHEMICAL STRUCTURE; CONTROLLED STUDY; CRYSTALLOGRAPHY; ENERGY TRANSFER; IMAGE ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR SIZE; NERVE STIMULATION; NONHUMAN; PREDICTION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; GENETIC PROCEDURES; MOTION; NEUTRON; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; RADIATION SCATTERING;

BIOSENSING TECHNIQUES; COMPUTER SIMULATION; GLUCOSE OXIDASE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; NEUTRONS; PROTEIN STRUCTURE, TERTIARY; SCATTERING, RADIATION;

EID: 49149113053     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20956     Document Type: Article

References (35)

1. Delvaux, M.; Champagne-Demoustier, S. Biosens Bioelectron 2003, 18, 943-951.
2. Tatke, S. S.; Renugopalakrishnan, V.; Prabhakaran, M. Nano-technology 2004, 15, S685-S690.
3. Caronna, C.; Natali, F.; Cupane, C. Biophys Chem 2005, 116, 219-225.
4. Hayward, J. A.; Smith, J. C. Biophys J 2002, 82, 1216-1225.
5. Lechner, R. E. Physica, B. 301:83-93, 2001.
6. Karplus, M.; McCammon, J. A. Nat Struct Biol 2002, 9, 646-652.
7. Reat, V.; Patzelt, H.; Ferrand, M.; Pfister, C.; Oesterhelt, D.; Zaccai, G. Proc Natl Acad Sci USA 1998, 95, 4970-4975.
8. Fitter, J.; Lechner, R. E.; Buldt, G.; Dechner, N. A. Proc Natl Acad Sci USA 1996, 93, 7600-7605.
9. Prabhakaran, M.; Gursahani, S H.; Verma, C. S.; Guarduno-Juarez, R.; Renugopalakrishnan, V. J Phys Chem Solids 2004, 65, 1615-1622.
10. Bee, M. Quasielastic Neutron Scattering: Principles and Applications in Solid-State Chemistry, Biology and Materials Science; Hilger: Bristol, 1988.
11. Trouw, F. R.; Price, D. L. Annu Rev Phys Chem 1999, 50, 571-601.
12. Byron, O.; Gilbert, R. J. C. Curt Opin Biotechnol 2000, 11, 72-80.
13. Filabozz, I. A.; Di Bari, M.; Deriu, A.; Di Venere, A.; Andreani, C.; Rosato, N. J Phys Condens Matter 2005, 17, S3101-S3109.
14. Tehei, M. Æ.; Daniel, R Æ.; Zaccai, G. Eur Biophys J 2006, 35, 551-558.
15. Smith, J.; Cusack, S.; Tidor, B.; Karplus, M. J Chem Phys 1990, 93, 2974-2991.
16. Tarek, M.; Neumann, D. A.; Tobias, D. J. Chem Phys 2003, 292, 435-443.
17. Smith, J. Q Rev Biophys 1991, 24, 227-291.
18. Tnama, F.; Sanejouand, Y. H. Protein Eng 2001, 14, 1-6.
19. Hinsen, K. Proteins 1998, 33,417-429.
20. Wohlfahrt, G.; Witt, S.; Hendle, J.; Schomburg, D.; Kalisz, H. M.; Hecht, H. J. Acta Crystallogr 1999, D55, 969-977.
21. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol Mod 2001, 7, 306-317.
22. van Aalten, D. M. F.; Bywater, R.; Findlay, J. B. C.; Hendlich, M.; Hooft, R. W. W.; Vriend, G. J Comput Aid Mol Design 1996, 10, 255-262.
23. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684-3690.
24. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327-341.
25. Ichiye, T.; Karplus, M. Proteins 1991, 11, 205-217.
26. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Proteins 1993, 17, 412-425.
27. Tama, F.; Gadea, X.; Marques, O.; Sanejouand, Y. Proteins 2000, 41, 1-7.
28. Li, G.; Qiang Cui, Q. Biophys J 2002, 83, 2457-2474.
29. Bahar, I.; Atilgan, A. R.; Demirel, M. C.; Erman, B. Phys Rev Lett 1998, 80, 2733-2736.
30. Zhong, D.; Zewail A. H. Proc Natl Acad Sci USA 2001, 98, 11867-11872.
31. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Adv Chem Phys 1988, 71, 1-259.
32. Meyerd, M.; Wohlfahrtb, G.; Knäbleinc, J.; Schomburg, J. D. J Comput Aid Mol Design 1988, 12, 425-440.
33. Cusack, S.; Smith, J.; Finney, J.; Tidor, B.; Karplus, M. J Mol Biol 1988, 202, 903-908.
34. Jennifer, A. H.; Smith, J. C. Biophys J 2002, 82, 1216-1225.
35. Balog, E.; Smith, J. C.; Perahia, D. Phys Chem Chem Phys 2006, 8, 5543-5548.