Azido homoalanine is a useful infrared probe for monitoring local electrostatistics and side-chain solvation in proteins

Journal of Physical Chemistry Letters

Volumn 2, Issue 17, 2011, Pages 2158-2162

  Choi, Jun Ho ^a   Raleigh, Daniel ^b   Cho, Minhaeng ^a,c  

^a Korea University   (South Korea)

^b STONY BROOK UNIVERSITY   (United States)

^c Korea Basic Science Institute (KBSI)   (South Korea)

Author keywords

Biophysical Chemistry

Indexed keywords

BIOPHYSICAL CHEMISTRY; ENZYME CATALYSIS; H-BONDED; INFRARED PROBES; IR SPECTRUM; LOCAL ELECTRIC FIELD; PEPTIDE BONDS; PROTEIN STRUCTURES; QM/MM MD SIMULATIONS; SIDE-CHAINS; WATER MOLECULE;

ELECTRIC FIELDS; PROTEIN FOLDING; PROTEINS;

PROBES;

EID: 80052352163     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz200980g     Document Type: Article

References (32)

1. Getahun, Z.; Huang, C.-Y.; Wang, T.; De Leon, B.; DeGrado, W. F.; Gai, F. Using Nitrile-Derivatized Amino Acids as Infrared Probes of Local Environment J. Am. Chem. Soc. 2003, 125, 405-411 (Pubitemid 36077861)
2. Mukherjee, S.; Chowdhury, P.; DeGrado, W. F.; Gai, F. Site-Specific Hydration Status of an Amphipathic Peptide in AOT Reverse Micelles Langmuir 2007, 23, 11174-11179 (Pubitemid 350069343)
3. Suydam, I. T.; Boxer, S. G. Vibrational Stark Effects Calibrate the Sensitivity of Vibrational Probes for Electric Fields in Proteins Biochemistry 2003, 42, 12050-12055 (Pubitemid 37280655)
4. Oh, K.-I.; Lee, J.-H.; Joo, C.; Han, H.; Cho, M. β-Azidoalanine as an IR Probe: Application to Amyloid Aβ(16-22) Aggregation J. Phys. Chem. B 2008, 112, 10352-10357
5. Schultz, K. C.; Supekova, L.; Ryu, Y.; Xie, J.; Perera, R.; Schultz, P. G. A Genetically Encoded Infrared Probe J. Am. Chem. Soc. 2006, 128, 13984-13985 (Pubitemid 44657464)
6. Fang, C.; Bauman, J. D.; Das, K.; Remorino, A.; Arnold, E.; Hochstrasser, R. M. Two-Dimensional Infrared Spectra Reveal Relaxation of the Nonnucleoside Inhibitor TMC278 Complexed with HIV-1 Reverse Transcriptase Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1472-1477 (Pubitemid 351346538)
7. Bagchi, S.; Nebgen, B. T.; Loring, R. F.; Fayer, M. D. Dynamics of a Myoglobin Mutant Enzyme: 2D IR Vibrational Echo Experiments and Simulations J. Am. Chem. Soc. 2010, 132, 18367-18376
8. Suydam, I. T.; Snow, C. D.; Pande, V. S.; Boxer, S. G. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory Science 2006, 313, 200-204 (Pubitemid 44066246)
9. Lin, Y. S.; Shorb, J. M.; Mukherjee, P.; Zanni, M. T.; Skinner, J. L. Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles J. Phys. Chem. B 2008, 113, 592-602
10. Kinnaman, C. S.; Cremeens, M. E.; Romesberg, F. E.; Corcelli, S. A. Infrared Line Shape of an α-Carbon Deuterium-Labeled Amino Acid J. Am. Chem. Soc. 2006, 128, 13334-13335 (Pubitemid 44582999)
11. Lindquist, B. A.; Furse, K. E.; Corcelli, S. A. Nitrile Groups As Vibrational Probes of Biomolecular Structure and Dynamics: An Overview Phys. Chem. Chem. Phys. 2009, 11, 8119-8132
12. Krummel, A. T.; Zanni, M. T. Evidence for Coupling between Nitrile Groups Using DNA Templates: A Promising New Method for Monitoring Structures with Infrared Spectroscopy J. Phys. Chem. B 2008, 112, 1336-1338 (Pubitemid 351288198)
13. Koziński, M.; Garrett-Roe, S.; Hamm, P. 2D-IR Spectroscopy of the Sulfhydryl Band of Cysteines in the Hydrophobic Core of Proteins J. Phys. Chem. B 2008, 112, 7645-7650
14. Jansen, T. l. C.; Knoester, J. Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy Acc. Chem. Res. 2009, 42, 1405-1411
15. Jansen, T. L.; Dijkstra, A. G.; Watson, T. M.; Hirst, J. D.; Knoester, J. Modeling the Amide I Bands of Small Peptides J. Chem. Phys. 2006, 125, 044312
16. Fafarman, A. T.; Webb, L. J.; Chuang, J. I.; Boxer, S. G. Site-Specific Conversion of Cysteine Thiols into Thiocyanate Creates an IR Probe for Electric Fields in Proteins J. Am. Chem. Soc. 2006, 128, 13356-13357 (Pubitemid 44583010)
17. Taskent-Sezgin, H.; Chung, J.; Banerjee, P. S.; Nagarajan, S.; Dyer, R. B.; Carrico, I.; Raleigh, D. P. Azidohomoalanine: A Conformationally Sensitive IR Probe of Protein Folding, Protein Structure, and Electrostatics Angew. Chem., Int. Ed. 2010, 49, 7473-7475
18. Kiick, K. L.; Saxon, E.; Tirrell, D. A.; Bertozzi, C. R. Incorporation of Azides into Recombinant Proteins for Chemoselective Modification by the Staudinger Ligation Proc. Natl. Acad. Sci. U.S.A 2002, 99, 19-24 (Pubitemid 34060308)
19. Ye, S.; Zaitseva, E.; Caltabiano, G.; Schertler, G. F. X.; Sakmar, T. P.; Deupi, X.; Vogel, R. Tracking G-Protein-Coupled Receptor Activation Using Genetically Encoded Infrared Probes Nature 2010, 464, 1386-1389
20. Wang, A.; Nairn, N. W.; Johnson, R. S.; Tirrell, D. A.; Grabstein, K. Processing of N-Terminal Unnatural Amino Acids in Recombinant Human Interferon-β in Escherichia coli ChemBioChem 2008, 9, 324-330 (Pubitemid 351196801)
21. Oh, K.-I.; Choi, J.-H.; Lee, J.-H.; Han, J.-B.; Lee, H.; Cho, M. Nitrile and Thiocyanate IR Probes: Molecular Dynamics Simulation Studies J. Chem. Phys. 2008, 128, 154504
22. Choi, J.-H.; Oh, K.-I.; Cho, M. Azido-Derivatized Compounds as IR Probes of Local Electrostatic Environment: Theoretical Studies J. Chem. Phys. 2008, 129, 174512
23. Oh, K.-I.; Kim, W.; Joo, C.; Yoo, D.-G.; Han, H.; Hwang, G.-S.; Cho, M. Azido Gauche Effect on the Backbone Conformation of β-Azidoalanine Peptides J. Phys. Chem. B 2010, 114, 13021-13029
24. Kuhlman, B.; Boice, J. A.; Fairman, R.; Raleigh, D. P. Structure and Stability of the N-Terminal Domain of the Ribosomal Protein L9: Evidence for Rapid Two-State Folding Biochemistry 1998, 37, 1025-1032 (Pubitemid 28100604)
25. Anil, B.; Sato, S.; Cho, J.-H.; Raleigh, D. P. Fine Structure Analysis of a Protein Folding Transition State; Distinguishing Between Hydrophobic Stabilization and Specific Packing J. Mol. Biol. 2005, 354, 693-705 (Pubitemid 41628286)
26. Cho, J.-H.; Raleigh, D. P. Electrostatic Interactions in the Denatured State and in the Transition State for Protein Folding: Effects of Denatured State Interactions on the Analysis of Transition State Structure J. Mol. Biol. 2006, 359, 1437-1446 (Pubitemid 43903498)
27. Kuhlman, B.; Luisi, D. L.; Evans, P. A.; Raleigh, D. P. Global Analysis of the Effects of Temperature and Denaturant on the Folding and Unfolding Kinetics of the N-Terminal Domain of the Protein L9 J. Mol. Biol. 1998, 284, 1661-1670 (Pubitemid 28566094)
28. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M., Jr.; Pearlman, D. A.; Crowley, M. AMBER 9; University of California: San Francisco, 2006.
29. Jeon, J.; Yang, S.; Choi, J.-H.; Cho, M. Computational Vibrational Spectroscopy of Peptides and Proteins in One and Two Dimensions Acc. Chem. Res. 2009, 42, 1280-1289
30. Choi, J.-H.; Oh, K.-I.; Lee, H.; Lee, C.; Cho, M. Nitrile and Thiocyanate IR Probes: Quantum Chemistry Calculation Studies and Multivariate Least-Square Fitting Analysis J. Chem. Phys. 2008, 128, 134506
31. Cho, M. Coherent Two-Dimensional Optical Spectroscopy Chem. Rev. 2008, 108, 1331-1418 (Pubitemid 351662365)
32. Kwac, K.; Cho, M. Molecular Dynamics Simulation Study of N -Methylacetamide in Water. I. Amide I Mode Frequency Fluctuation J. Chem. Phys. 2003, 119, 2247-2255