Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins

Analytical Biochemistry

Volumn 507, Issue , 2016, Pages 74-78

  Mukherjee, Debopreeti ^a   Gai, Feng ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

5 Cyanotryptophan; CD spectroscopy; Exciton coupling; p Cyanophenylalanine; Protein structure

Indexed keywords

AMINO ACIDS; AROMATIC COMPOUNDS; CHROMOPHORES; CIRCULAR DICHROISM SPECTROSCOPY; DICHROISM; EXCITONS; RED SHIFT; SPECTRUM ANALYSIS;

5-CYANOTRYPTOPHAN; CD SPECTROSCOPY; CONFORMATIONAL CHANGE; ELECTRONIC TRANSITION; EXCITON COUPLING; EXTINCTION COEFFICIENTS; PROTEIN STRUCTURES; QUANTITATIVE ASSESSMENTS;

PROTEINS;

5 CYANOTRYPTOPHAN; ALANINE; AROMATIC AMINO ACID; CYANOPHENYLALANINE; NITRILE; PEPTIDE; PHENYLALANINE; TRYPTOPHAN; UNCLASSIFIED DRUG; PROTEIN;

ABSORPTION SPECTROSCOPY; ALPHA HELIX; ARTICLE; CHROMATOPHORE; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; DIPOLE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY;

CIRCULAR DICHROISM; MOLECULAR STRUCTURE; NITRILES; PROTEINS;

EID: 84975106843     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2016.05.017     Document Type: Article

References (29)

1. P. Bayley The analysis of circular dichroism of biomolecules Prog. Biophys. Mol. Biol. 27 1973 1 76
2. S.W. Provencher, and J. Gloeckner Estimation of globular protein secondary structure from circular dichroism Biochemistry 20 1981 33 37
3. A. Rodger Far UV protein circular dichroism G.C.K. Roberts, Encyclopedia of Biophysics 2013 Springer New York 726 730
4. J. Jiang, D. Abramavicius, B.M. Bulheller, J.D. Hirst, and S. Mukamel Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: Combined QM and MM simulations J. Phys. Chem. B 114 2010 8270 8277
5. I.B. Grishina, and R.W. Woody Contributions of tryptophan side chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators Faraday Discuss. 99 1994 245 262
6. J. Hudecová, J. Horníček, M. Buděšínský, J. Šebestík, M. Šafařík, G. Zhang, T.A. Keiderling, and P. Bouř Three types of induced tryptophan optical activity compared in model dipeptides: theory and experiment ChemPhysChem 13 2012 2748 2760
7. A.G. Cochran, N.J. Skelton, and M.A. Starovasnik Tryptophan zippers: stable, monomeric β-hairpins Proc. Natl. Acad. Sci. U. S. A. 98 2001 5578 5583
8. L. Wu, D. McElheny, R. Huang, and T.A. Keiderling Role of tryptophan-tryptophan interactions in Trpzip ß-hairpin formation, structure, and stability Biochemistry 48 2009 10362 10371
9. L. Wu, D. McElheny, T. Takekiyo, and T.A. Keiderling Geometry and efficacy of cross-strand Trp/Trp, Trp/Tyr, and Tyr/Tyr aromatic interaction in a ß-hairpin peptide Biochemistry 49 2010 4705 4714
10. O.K. Gasymov, A.R. Abduragimov, and B.J. Glasgow Double tryptophan exciton probe to gauge proximal side chains in proteins: augmentation at low temperature J. Phys. Chem. B 119 2015 3962 3968
11. M. Adil Khan, C. Neale, C. Michaux, R. Pomès, G.G. Privé, R.W. Woody, and R.E. Bishop Gauging a hydrocarbon ruler by an intrinsic exciton probe Biochemistry 46 2007 4565 4579
12. N. Berova, L. Di Bari, and G. Pescitelli Application of electronic circular dichroism in configurational and conformational analysis of organic compounds Chem. Soc. Rev. 36 2007 914 931
13. M.P. Heyn Dependence of exciton circular dichroism amplitudes on oscillator strength J. Phys. Chem. 79 1975 2424 2426
14. Z. Getahun, C.-Y. Huang, T. Wang, B. De León, W.F. DeGrado, and F. Gai Using nitrile-derivatized amino acids as infrared probes of local environment J. Am. Chem. Soc. 125 2003 405 411
15. M.M. Waegele, M.J. Tucker, and F. Gai 5-Cyanotryptophan as an infrared probe of local hydration status of proteins Chem. Phys. Lett. 478 2009 249 253
16. W. Zhang, B.N. Markiewicz, R.S. Doerksen, A.B. Smith III, and F. Gai CN stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: What determines its frequency? Phys. Chem. Chem. Phys. 18 2016 7027 7034
17. B.N. Markiewicz, D. Mukherjee, T. Troxler, and F. Gai Utility of 5-cyanotryptophan fluorescence as a sensitive probe of protein hydration J. Phys. Chem. B 120 2016 936 944
18. M.R. Mintzer, T. Troxler, and F. Gai p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides Phys. Chem. Chem. Phys. 17 2015 7881 7887
19. C.L. Friedrich, A. Rozek, A. Patrzykat, and R.E. Hancock Structure and mechanism of action of an indolicidin peptide derivative with improved activity against gram-positive bacteria J. Biol. Chem. 276 2001 24015 24022
20. J.M. Anderson, B.L. Kier, B. Jurban, A. Byrne, I. Shu, L.A. Eidenschink, A.A. Shcherbakov, M. Hudson, R.M. Fesinmeyer, and N.H. Andersen Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization Biopolymers 105 2016 337 356
21. C. Subbalakshmi, V. Krishnakumari, R. Nagaraj, and N. Sitaram Requirements for antibacterial and hemolytic activities in the bovine neutrophil derived 13 residue peptide indolicidin FEBS Lett. 395 1996 48 52
22. M.L. Finnegan, and B.E. Bowler Propensities of aromatic amino acids versus leucine and proline to induce residual structure in the denatured-state ensemble of iso-1-cytochrome c J. Mol. Biol. 403 2010 495 504
23. N. Ferguson, C.M. Johnson, M. Macias, H. Oschkinat, and A. Fersht Ultrafast folding of WW domains without structured aromatic clusters in the denatured state Proc. Natl. Acad. Sci. U. S. A. 98 2001 13002 13007
24. E.K. Koepf, H.M. Petrassi, M. Sudol, and J.W. Kelly WW: An isolated three-stranded antiparallel β-sheet domain that unfolds and refolds reversibly: Evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state Protein Sci. 8 1999 841 853
25. B.E. Bowler, K. May, T. Zaragoza, P. York, A. Dong, and W.S. Caughey Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: implications for the denatured state Biochemistry 32 1993 183 190
26. D. Shortle Denatured states of proteins and their roles in folding and stability Curr. Opin. Struct. Biol. 3 1993 66 74
27. A.L. Serrano, T. Troxler, M.J. Tucker, and F. Gai Photophysics of a fluorescent non-natural amino acid: p-Cyanophenylalanine Chem. Phys. Lett. 487 2010 303 306
28. D.D. Young, T.S. Young, M. Jahnz, I. Ahmad, G. Spraggon, and P.G. Schultz An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity Biochemistry 50 2011 1894 1900
29. P. Talukder, S. Chen, B. Roy, P. Yakovchuk, M.M. Spiering, M.P. Alam, M.M. Madathil, C. Bhattacharya, S.J. Benkovic, and S.M. Hecht Cyanotryptophans as novel fluorescent probes for studying protein conformational changes and DNA-protein interaction Biochemistry 54 2015 7457 7469