Enzyme Specificity and Mechanisms
F. M. Richards · 2015
AbstractThe solvent is considered to play a critical role in the structure of macromolecules and in their association with a variety of ligands. Competition between self-association and solvent-association is presumed to control the equilibria involved in macromolecular structures. From the known structures of some globular proteins quantitative estimates can be made of the changes in solvent contacts that occur during defined conformational changes.Somewhat arbitrarily all carbon and sulfur atoms are considered nonpolar and all oxygen and nitrogen atoms polar. In comparing the accessibility to solvent of both the hypothetical fully extended chain and the native folded conformation it is found that solvent contact, or accessibility, decreases by about a factor of 3 in going from the extended to the folded conformation for both classes of atoms. This result is essentially the same for ribonuclease-S, lysozyme and myoglobin. The estimated energetic consequences of this change in geometry will depend intimately on 1) the assumptions made about the unit free energy changes for the different atom types and, 2) the extent of internal pairing of polar atoms that occur in the native structure. One such case has been examined in detail, the association of the 20 residue peptide, S-peptide, with the 104 residue protein, S-protein to give the enzymatically active complex RNase-S. The thermodynamics of this interaction have been examined in detail by direct calorimetry [HEARN et al.: Biochemistry 10: 806, 1971]. The structure of the complex is known, the structure of free S-peptide is close to a random coil. Only the structure of free S-protein is uncertain. Tentative correlations can be made between the geometrical changes and the observed thermodynamic changes.The association of substrates or inhibitors with enzymes must follow essentially the same rules as those related to protein structure directly. Diffraction studies at the moment can only deal with stable complexes so that true Michaelis complexes cannot be observed. Substrate analogues can, however, serve to define the probable geometry of complexes related to the catalytic path. In this sense, the direct structural data can provide severe restrictions for proposed catalytic mechanisms. The complex of the dinucleotide analog UpcA with RNase-S will be used as an example.