Infrared methods with appropriate time resolution are being developed to measure: (i) The overall protein rotation, based on intrinsic probes; (ii) The motion of the chromophore as a whole relative to the protein; (iii) The orientational motion of the particular IR active bond; (iv) Both the order parameters and time constants for these motions; (v) correlations between infrared absorptions and chromophore absorptions; (vi) correlations between different IR transitions of the same species (e.g. amino acid); (vii) Probing the Amide-I substructure by dynamic holeburning and (viii) infrared photon echo measurements. (see also Scientific Subproject- Transient Infrared Spectroscopy). The RLBL has proved the principle of an important experiment aimed at using molecular vibrational transitions to study molecular reorientation. The basic idea is to excide a bond vibration with a polarized IR pulse and probe it with another polarized IR pulse at a later time. The ensemble average of the projection of the initial dipole onto itself at later time is the orientational correlation function of the bond. A principal result of molecular dynamics simulations are these functions. The experimental plan underway involves the construction of an IR pump/IR probe device capable of accessing vibrations of the protein backbone and the residues. Much work remains to be done to perfect this technique which could have significant effect on understanding the detailed vibrational spectra of proteins and enlarging the time range within which molecular dynamics and environmental fluctuations can be evaluated.
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