Extension of the tryptophan x 2,1 dihedral angle-W3 band frequency relationship to a full rotation: Correlations and caveats

Biochemistry

Volumn 48, Issue 12, 2009, Pages 2777-2787

  Juszczak, Laura J ^a,c   Desamero, Ruel Z B ^b,c  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAND FREQUENCIES; CONTRIBUTING FACTORS; DIHEDRAL ANGLES; FULL WIDTH HALF MAXIMUMS; HYDROGEN BONDINGS; NONPOLAR INTERACTIONS; PRIMARY SCREENS; PROTEIN DATA BANKS; STERIC HINDRANCES; WEAK INTERACTIONS;

AMINES; BIOPOLYMERS; CHEMICAL REACTIONS; ELECTROSTATICS; HYDROGEN; HYDROGEN BONDS; POLYMERS; RADAR ANTENNAS; ROTATION;

AMINO ACIDS;

ANION; CATION; CRYSTALLIN; INDOLEAMINE; PROTEIN; TRYPTOPHAN; TRYPTOPHAN DERIVATIVE;

AMPLIFIER; ANIMAL EXPERIMENT; ARTICLE; CHEMICAL ENVIRONMENT; CHEMICAL INTERACTION; CHROMOSOME HIGH RESOLUTION BANDING ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; ELECTRICITY; EVALUATION; EXTENSION GENE; FREQUENCY ANALYZER; FREQUENCY MODULATION; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; MOLECULAR PHYLOGENY; NONHUMAN; PERIODICITY; PRIORITY JOURNAL; PROTEIN DATA BANK; RAMAN SPECTROMETRY; ROTATION; SACCHAROMYCES CEREVISIAE; STEREOSPECIFICITY; ULTRAVIOLET RADIATION; W3 BAND FREQUENCY; WILD TYPE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN DATABASE;

DATABASES, PROTEIN; HYDROPHOBICITY; MODELS, MOLECULAR; SPECTRUM ANALYSIS, RAMAN; TRYPTOPHAN;

EID: 65249108127     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801293v     Document Type: Article

References (58)

1. Maruyama, T., and Takeuchi, H. (1995) Effects of hydrogen bonding and side-chain conformation on the Raman bands of tryptophan-2,4,5,6,7-d5. J. Raman Spectrosc. 26, 319-324.
2. Miura, T., Takeuchi, H., and Harada, I. (1989) Tryptophan Raman bands sensitive to hydrogen bonding and side-chain conformation. J. Raman Spectrosc. 20, 667-671.
3. Takeuchi, H. (2003) Raman structural markers of tryptophan and histidine side chains in proteins. Biopolymers 72, 305-317.
4. -1 in the Raman spectra of tryptophan and related compounds. Spectrochim. Acta, Part A 42, 307-312.
5. Miura, T., Takeuchi, H., and Harada, I. (1988) Characterization of individual tryptophan side chains in proteins using Raman spectroscopy and hydrogen-deuterium exchange kinetics. Biochemistry 27, 88-94.
6. Takeuchi, H., and Harada, I. (1986) Normal coordinate analysis of the indole ring. Spectrochim. Acta, Part A 42, 1069-1078.
7. Maruyama, T., and Takeuchi, H. (1997) Water accessibility to the tryptophan indole N-H sites of gramicidin A transmembrane channel: detection of positional shifts of tryptophans 11 and 13 along the channel axis upon cation binding. Biochemistry 36, 10993-11001.
8. Miura, T., Takeuchi, H., and Harada, I. (1991) Raman spectroscopic characterization of tryptophan side chains in lysozyme bound to inhibitors: role of the hydrophobic box in the enzymatic function. Biochemistry 30, 6074-6080.
9. Spiro, T. G., and Grygon, C. A. (1988) Applications of ultraviolet resonance Raman spectroscopy to proteins. J. Mol. Struct. 173, 79-90.
10. Juszczak, L. J. (2004) Comparative vibrational spectroscopy of intracellular tau and extracellular collagen I reveals parallels of gelation and fibrillar structure. J. Biol. Chem. 279, 7395-7404.
11. Rozovsky, S., and McDermott, A. E. (2001) The time scale of the catalytic loop motion in triosephosphate isomerase. J. Mol. Biol. 310, 259-270.
12. Sampson, N. S., and Knowles, J. R. (1992) Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry 31, 8482-8487.
13. Putman, S. J., Coulson, A. F., Farley, I. R., Riddleston, B., and Knowles, J. R. (1972) Specificity and kinetics of triose phosphate isomerase from chicken muscle. Biochem. J. 129, 301-310.
14. Ellerby, L. M., Nishida, C. R., Nishida, F., Yamanaka, S. A., Dunn, B., Valentine, J. S., and Zink, J. I. (1992) Encapsulation of proteins in transparent porous silicate glasses prepared by the sol-gel method. Science (New York) 255, 1113-1115.
15. Juszczak, L. J., Hirsch, R. H., Nagel, R. L., and Friedman, J. M. (1998) Conformational differences in CO derivatives of HbA, HbC(βE6K) and HbS(βE6V) in the presence and absence of inositol hexaphosphate detected using ultraviolet resonance Raman spectroscopy. J. Raman Spectrosc. 29, 963-968.
16. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.
17. Frisch, M. J. T. G. W., Schlegel, H. B., Scuseria, G E., Robb, M. A., Cheeseman, J. R., Montgomery, J. J. A., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2004) Gaussian 03, Gaussian Inc., Wallingford, CT.
18. Becke, A. D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652.
19. Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a function of the electron density. Phys. ReV. B 37, 785-789.
20. Rauhut, G., and Pulay, P. (1995) Transferable scaling factors for density functional derived vibrational force fields. J. Phys. Chem. 99, 3093-3100.
21. Stephens, P. J., Devlin, F. J., Chabalowski, C. F., and Frisch, M. J. (1994) Ab initio calculations of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98, 11623-11627.
22. Pulay, P., Fogarasi, G., Pongor, G., Boggs, J. E., and Vargha, A. (1983) Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene. J. Am. Chem. Soc. 105, 7037-7047.
23. Dennington, R. K. T., II, Millam, J., Eppinnett, K., Hovell, W. L., and Gilliland, R. (2003) GaussView, Shawnee Mission, KS.
24. Sampson, N. S., and Knowles, J. R. (1992) Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosphosphate isomerase. Biochemistry 31, 8488-8494.
25. Lolis, E., and Petsko, G A. (1990) Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: implications for catalysis. Biochemistry 29, 6619-6625.
26. Rozovsky, S., Jogl, G., Tong, L., and McDermott, A. E. (2001) Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics. J. Mol. Biol. 310, 271-280.
27. Desamero, R., Rozovsky, S., Zhadin, N., McDermott, A., and Callender, R. (2003) Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation. Biochemistry 42, 2941-2951.
28. Lolis, E., Alber, T., Davenport, R. C., Rose, D., Hartman, F. C., and Petsko, G. A. (1990) Structure of yeast triosephosphate isomerase at 1.9-Å resolution. Biochemistry 29, 6609-6618.
29. McGregor, M. J., Islam, S. A., and Sternberg, M. J. (1987) Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198, 295-310.
30. Burely, S. K., and Petsko, G. A. (1988) Weakly polar interactions in proteins. AdV. Protein Chem. 39, 125-189.
31. Jackson, M. R., Beahm, R., Duvvuru, S., Narasimhan, C., Wu, J., Wang, H. N., Philip, V. M., Hinde, R. J., and Howell, E. E. (2007) A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions. J. Phys. Chem. B 111, 8242-8249.
32. Gallivan, J. P., and Dougerty, D. A. (1999) Cation-pi interactions in structural biology. Proc. Nat. Acad. Sci. U.S.A. 96, 9459-9464.
33. Ma, J. C., and Dougherty, D. A. (1997) The cation-π interaction. Chem. Rev. 97, 1303-1324.
34. Neidigh, J. W., Fesinmeyer, R. M., Prickett, K. S., and Andersen, N. H. (2001) Exendin-4 and glucagon-like peptide-1: NMR structural comparisons in the solution and micelle-associated states. Biochemistry 40, 13188-13200.
35. Terwilliger, T. C., and Eisenberg, D. (1982) The structure of melittin. II. Interpretation of the structure. J. Biol. Chem. 257, 6016-6022.
36. Hashimoto, S., Obata, K., Takeuchi, H., Needleman, R., and Lanyi, J. K. (1997) Ultraviolet resonance Raman spectra of Trp-182 and Trp-189 in bacteriorhodopsin: novel information on the structure of Trp-182 and its steric interaction with retinal. Biochemistry 36, 11583-11590.
37. Marvin, D. A., Welsh, L. C., Symmons, M. F., Scott, W. R., and Straus, S. K. (2006) Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane. J. Mol. Biol. 355, 294-309.
38. Welsh, L. C., Symmons, M. F., Sturtevant, J. M., Marvin, D. A., and Perham, R. N. (1998) Structure of the capsid of Pf3 filamentous phage determined from x-ray fibre diffraction data at 3.1 Å resolution. J. Mol. Biol. 283, 155-177.
39. Blanch, E. W., Hecht, L., Day, L. A., Pederson, D. M., and Barron, L. D. (2001) Tryptophan absolute stereochemistry in viral coat proteins from Raman optical activity. J. Am. Chem. Soc. 123, 4863-4864.
40. Tsuboi, M., Overman, S. A., and Thomas, G. J., Jr. (1996) Orientation of tryptophan-26 in coat protein subunits of the filamentous virus Ff by polarized Raman microspectroscopy. Biochemistry 35, 10403-10410.
41. Marvin, D. A., Hale, R. D., Nave, C., and Citterich, M. H. (1994) Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages: Ff (fd, f1, M13), If1 and IKe. J. Mol. Biol. 235, 260-286.
42. Jordan, T., Eads, J. C., and Spiro, T. G. (1995) Secondary and tertiary structure of the A-state of cytochrome c from resonance Raman spectroscopy. Protein Sci. 4, 716-728.
43. Wen, Z. Q., and Thomas, G. J., Jr. (2000) Ultraviolet-resonance Raman spectroscopy of the filamentous virus Pf3: interactions of Trp 38 specific to the assembled virion subunit. Biochemistry 39, 146-152.
44. Juszczak, L. J., Zhang, Z. Y., Wu, L., Gottfried, D. S., and Eads, D. D. (1997) Rapid loop dynamics of Yersinia protein tyrosine phosphatases. Biochemistry 36, 2227-2236.
45. Austin, J. C., Wharton, C. W., and Hester, R. E. (1989) An ultraviolet resonance Raman study of dehydrogenase enzymes and their interactions with coenzymes and substrates. Biochemistry 28, 1533-1538.
46. Couling, V. W., Fischer, P., Klenerman, D., and Huber, W. (1998) Ultraviolet resonance Raman study of drug binding in dihydrofolate reductase, gyrase, and catechol O-methyltransferase. Biophys. J. 75, 1097-1106.
47. Rodgers, K. R., Su, C., Subramanian, S., and Spiro, T. G. (1992) Hemoglobin R → T structural dynamics from simultaneous monitoring of tyrosine and tryptophan time-resolved UV resonance Raman signals. J. Am. Chem. Soc. 114, 3697-3709.
48. Skarznski, T., Moody, P. C., and Wonacott, A. J. (1987) Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. J. Mol. Biol. 193, 171- 187.
49. Lamour, V., Hoermann, L., Jeltsch, J. M., Oudet, P., and Moras, D. (2002) Crystallization of the 43 kDa ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 1376-1378.
50. Lafitte, D., Lamour, V., Tsvetkov, P. O., Makarov, A. A., Klich, M., Deprez, P., Moras, D., Briand, C., and Gilli, R. (2002) DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5′-methyl group of the noviose. Biochemistry 41, 7217-7223.
51. Grigorieff, N., Ceska, T. A., Downing, K. H., Baldwin, J. M., and Henderson, R. (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259, 393-421.
52. Stuckey, J. A., Schubert, H. L., Fauman, E. B., Zhang, Z. Y., Dixon, J. E., and Saper, M. A. (1994) Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 Å and the complex with tungstate. Nature 370, 571-575.
53. Fauman, E. B., Yuvaniyama, C., Schubert, H. L., Stuckey, J. A., and Saper, M. A. (1996) The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications. J. Biol. Chem. 271, 18780-18788.
54. Safo, M. K., Burnett, J. C., Musayev, F. N., Nokuri, S., and Abraham, D. J. (2002) Structure of human carbonmonoxyhemo-globin at 2.16 Å: a snapshot of the allosteric transition. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 2031-2037.
55. Fermi, G., Perutz, M. F., Shaanan, B., and Fourme, R. (1984) The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution. J. Mol. Biol. 175, 159-174.
56. Bushnell, G. W., Louie, G. V., and Brayer, G. D. (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J. Mol. Biol. 214, 585-595.
57. Denu, J. M., Lohse, D. L., Vijayalakshmi, J., Saper, M. A., and Dixon, J. E. (1996) Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis. Proc. Natl. Acad. Sci. U.S.A. 93, 2493-2498.
58. Marvin, D. A., Hale, R. D., Nave, C., and Helmer-Citterich, M. (1994) Molecular models and structural comparisons of native and mutant class 1 filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe. J. Mol. Biol. 235, 260-286.