Advertisement

Ultrafast Time-Resolved IR Studies of Protein-Ligand Interactions

  • Manho Lim
  • Philip A. Anfinrud
Part of the Methods in Molecular Biology™ book series (MIMB, volume 305)

Abstract

Time-resolved mid-IR spectroscopy combines molecular sensitivity with ultrafast capability to incisively probe protein-ligand interactions in model heme proteins. Highly conserved residues near the heme binding site fashion a ligand-docking site that mediates the transport of ligands to and from the binding site. We employ polarization anisotropy measurements to probe the orientation and orientational distribution of CO when bound to and docked near the active binding site, as well as the dynamics of ligand trapping in the primary docking site. In addition, we use more conventional transient absorption methods to probe the dynamics of ligand escape from this site, as well as the ultrafast dynamics of NO geminate recombination with the active binding site. The systems investigated include myoglobin, hemoglobin, and microperoxidase.

Key Words

Time-resolved femtosecond mid-IR spectroscopy photoselection anisotropy heme-pocket myoglobin hemoglobin NO CO 

References

  1. 1.
    Ansari A., Berendzen J., Bowne S. F., Frauenfelder H., Iben I. E. T., Sauke T. B., Shyamsunder E., and Young R. D. (1985) Protein states and proteinquakes. Proc. Natl. Acad. Sci. USA 82, 5000–5004.PubMedCrossRefGoogle Scholar
  2. 2.
    Moller J. K. S. and Skibsted L. H. (2002) Nitric Oxide and Myoglobins. Chem. Rev. 102, 1167–1178.PubMedCrossRefGoogle Scholar
  3. 3.
    Maxwell J. C. and Caughey W. S. (1978) Infrared spectroscopy of ligands, gases, and other groups in aqueous solutions and tissues. Methods Enzymol. 54, 302–323.PubMedCrossRefGoogle Scholar
  4. 4.
    Kim S., Jin G., and Lim M. (2003) Structural dynamics of myoglobin probed by femtosecond infrared spectroscopy of the amide band. Bull. Kor. Chem. Soc. 24, 1470–1474.CrossRefGoogle Scholar
  5. 5.
    Lim M., Wolford M. F., Hamm P., and Hochstrasser R. M. (1998) Chirped wavepacket dynamics of HgBr from the photolysis of HgBr2 in solution. Chem. Phys. Lett. 290, 355–362.CrossRefGoogle Scholar
  6. 6.
    Hamm P., Lim L., and Hochstrasser R. M. (1998) The Structure of the Amide I Band of Peptides Measured by Femtosecond Nonlinear IR Spectroscopy. J. Phys. Chem. B. 102, 6123–6138.CrossRefGoogle Scholar
  7. 7.
    Hamm P., Kaindl R. A., and Stenger J. (2000) Noise suppression in femtosecond mid-infrared light sources. Opt. Lett. 25, 1798–1800.PubMedCrossRefGoogle Scholar
  8. 8.
    Kaindl R. A., Wurm M., Reimann K., Hamm P., Weiner A. M., and Woerner M. (2000) Generation, shaping, and characterization of intense femtosecond pulses tunable from 3 to 20 µm. J. Opt. Soc. Am. B. 17, 2086–2094.CrossRefGoogle Scholar
  9. 9.
    Moore J. N., Hansen P. A., and Hochstrasser R. M. (1988) Iron-carbonyl bond geometries of carboxymyoglobin and carboxyhemoglobin in solution determined by picosecond time-resolved infrared spectroscopy. Proc. Natl. Acad. Sci. USA 85, 5062–5066.PubMedCrossRefGoogle Scholar
  10. 10.
    Ansari A. and Szabo A. (1993) Theory of photoselection by intense light pulses. Biophys. J. 64, 838–851.PubMedCrossRefGoogle Scholar
  11. 11.
    Eaton W. A. and Hofrichter J. (1981) Polarized absorption and linear dichroism spectroscopy of hemoglobin. Methods Enzymol. 76, 175–261.PubMedCrossRefGoogle Scholar
  12. 12.
    Lim M., Jackson T. A., and Anfinrud P. A. (2004) The orientational distribution of CO before and after photolysis of MbCO and HbCO: A determination using time-resolved polarized mid-IR spectroscopy. J. Am. Chem. Soc. 126, 7946–7957.PubMedCrossRefGoogle Scholar
  13. 13.
    Augspurger J. D., Dykstra C. E., and Oldfield E. (1991) Correlation of carbon-13 and oxygen-17 chemical shifts and the vibrational frequency of electrically perturbed carbon monoxide: a possible model for distal ligand effects in carbonmonoxyheme proteins. J. Am. Chem. Soc. 113, 2447–2451.CrossRefGoogle Scholar
  14. 14.
    Ma J., Huo S., and Straub J. E. (1997) Molecular dynamics simulation study of the B-states of solvated carbon monoxymyoglobin. J. Am. Chem. Soc. 119, 2541–2551.CrossRefGoogle Scholar
  15. 15.
    Park E. S. and Boxer S. G. (2002) Origins of the sensitivity of molecular vibrations to electric fields: Carbonyl and nitrosyl stretches in model compounds and proteins. J. Phys. Chem. B. 106, 5800–5806.CrossRefGoogle Scholar
  16. 16.
    Reimers J. R. and Hush N. S. (1999) Vibrational Stark spectroscopy 3. Accurate benchmark ab initio and density functional calculations for CO and CN-. J. Phys. Chem. A 103, 10,580–10,587.CrossRefGoogle Scholar
  17. 17.
    Andrews S. S. and Boxer S. G. (2002) Vibrational Stark effects of nitriles II. Physical orgins of Stark effects from experiment and perturbation models. J. Phys. Chem. A 10, 469–477.CrossRefGoogle Scholar
  18. 18.
    Park E. S., Andrews S. S., Hu R. B., and Boxer S. G. (1999) Vibrational Stark Spectroscopy in Proteins: A Probe and Calibration for Electrostatic Fields. J. Phys. Chem. B. 103, 9813–9817.CrossRefGoogle Scholar
  19. 19.
    Lim M., Jackson T. A., and Anfinrud P. A. (1997) Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. Nature Struct. Biol. 4, 209–214.PubMedCrossRefGoogle Scholar
  20. 20.
    Alben J. O., Beece D., Browne S. F., Eisenstein L., Frauenfelder H., Good D., Marden M. C., Moh P. P., Reinisch L., Reynolds A. H., and Yue K. T. (1980) Isotope effect in molecular tunneling. Phys. Rev. Lett. 44, 1157–1163.CrossRefGoogle Scholar
  21. 21.
    Alben J. O., Beece D., Bowne S. F., Doster W., Eisenstein L., Frauenfelder H., Good D., McDonald J. D., Marden M. C., Mo P. P., Reinisch L., Reynolds A. H., Shyamsunder E., and Yue K. T. (1982) Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures. Proc. Natl. Acad. Sci. USA 79, 3744–3748.PubMedCrossRefGoogle Scholar
  22. 22.
    Schotte F., Lim M., Jackson T. A., Smirnov A. V., Soman J., Olson J. S., Phillips G. N., Jr., Wulff M., and Anfinrud P. A. (2003) Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science 300, 1944–1947.PubMedCrossRefGoogle Scholar
  23. 23.
    Ansari A., Berendzen J., Braunstein D. K., Cowen B. R., Frauenfelder H., Hong M. K., Iben I. E. T., Johnson J. B., Ormos P., Sauke T. B., Scholl R., Schulte A., Steinbach P. J., Vittitow J., and Young R. D. (1987) Rebinding and relaxation in the myoglobin pocket. Biophys. Chem. 26, 337–355.PubMedCrossRefGoogle Scholar
  24. 24.
    Balasubramanian S., Lambright D. G., and Boxer S. G. (1993) Perturbation of the distal heme pocket in human myoglobin mutants probed by infrared spectroscopy of bound CO: correlation with ligand binding kinetics. Proc. Natl. Acad. Sci. USA 90, 4718–4722.PubMedCrossRefGoogle Scholar
  25. 25.
    Tian W. D., Sage J. T., Srajer V., and Champion P. M. (1992) Relaxation dynamics of myoglobin in solution. Phys. Rev. Lett. 68, 408–411.PubMedCrossRefGoogle Scholar
  26. 26.
    Kim S., Jin G., and Lim M. (2004) Dynamics of geminate recombination of NO with myoglobin in aqueous solution probed by femtosecond mid-IR spectroscopy. J. Phys. Chem. B., in press.Google Scholar
  27. 27.
    Petrich J. W., Lambry J. C., Kuczera K., Karplus M., Poyart C., and Martin J. L. (1991) Ligand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombination. Biochemistry 30, 3975–3987.PubMedCrossRefGoogle Scholar
  28. 28.
    Petrich J. W., Lambry J.-C., Balasubramanian S., Lambright D. G., Boxer S. G., and Martin J. L. (1994) Ultrafast measurements of geminate recombination of NO with site-specific mutants of human myoglobin. J. Mol. Biol. 238, 437–444.PubMedCrossRefGoogle Scholar
  29. 29.
    Lim M., Jackson T. A., and Anfinrud P. A. (1993) Nonexponential protein relaxation: dynamics of conformational change in myoglobin. Proc. Natl. Acad. Sci. USA 90, 5801–5804.PubMedCrossRefGoogle Scholar
  30. 30.
    Venyaminov S. Y. and Prendergast F. G. (1997) Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions. Anal. Biochem. 248, 234–245.PubMedCrossRefGoogle Scholar
  31. 31.
    Suhre D. R., Singh N. B., Balakrishna V., Fernelius N. C., and Hopkins F. K. (1997) Improved crystal quality and harmonic generation in GaSe doped with indium. Opt. Lett. 22, 775–777.PubMedCrossRefGoogle Scholar
  32. 32.
    Locke B., Lian T., and Hochstrasser R. M. (1995) Erratum of Chemical Physics 158 (1991) 409-419. Chem. Phys. 190, 155.CrossRefGoogle Scholar
  33. 33.
    Lim M. (2002) The orientation of CO in heme proteins determined by time-resolved mid-IR spectroscopy: anisotropy correction for finite photolysis of an optically thick sample. Bull. Kor. Chem. Soc. 23, 865–871.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Manho Lim
    • 1
  • Philip A. Anfinrud
    • 2
  1. 1.Department of ChemistryPusan National UniversityBusanSouth Korea
  2. 2.Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda

Personalised recommendations