Using Resonance Raman Spectroscopy to Study the Structure and Dynamics of Enzyme-Bound Substrates

Abstract

The chemical nature of the enzyme-substrate intermediates studied by resonance Raman (RR) spectroscopy is defined. The information available on these intermediates from RR spectroscopy is compared to that obtained from absorption and fluorescence techniques. Two major classes of substrates useful for RR studies are discussed. The first class involves the use of substrates which are chromophoric by virtue of the fact that they have acyl groups, e.g. cinnamoyl, based on delocalised π-systems. Their use to probe the effect on the substrate’s C=0 group of going to active-pH in serine proteases, and to probe the strong electron polarisation forces available in cysteine proteases, is detailed. The second class of substrate involves thionoesters RC(=S)OCH, which form chromophoric dithioester intermediates, RC(=S)S-enzyme, with cysteine proteases, HS-enzyme. Because the dithioester RR spectrum is sensitive to conformational changes in the R-C(=S)-S-C bonds it is used to characterise conformational activation in the scissile linkages which occur for substrates specific for the cysteine protease papain. In addition RR spectra of these dithio-intermediates have been obtained under cryoenzymological conditions at 77°K and offer the opportunity to characterise such dynamical events as the thermal activation of the substrate in the active-site.