Form and Function in Biological Macromolecules: Kinetic Stability is Key, with Oblique Roles for Intramolecularity and Hydrophobicity in Enzyme Catalysis

Abstract

Certain structure-reactivity aspects of biological macromolecules, with particular emphasis on protein folding and enzyme catalysis, are discussed herein. Furthermore, the role played by the hydrophobic effect and intramolecularity in enzymic reactivity are evaluated afresh, with new insights of much importance in chemical biology. Thus, the sum of the energies of the hydrogen bonds constituting the tertiary structures of proteins, determines the overall Gibbs energy of activation for loss of conformational integrity. As protein molecules of even modest size consist of a relatively large number of intramolecular hydrogen bonding interactions, the activation barrier to even partial unfolding of the α-helices and β-sheets forming the tertiary structure would be prohibitively high under normal conditions. The resulting kinetic stability conserves the natural conformation of a protein molecule established at the ribosomal site of synthesis, carrying the molecule through the thick-and-thin of a range of metabolic pathways during its ‘journey of life’. However, protein molecules also acquire flexibility via ‘strain delocalization’ (Ramachandran plots being relevant), thus enabling stabilization of multiple transition states along a pathway (particularly in case of covalent enzyme-substrate complexes). Two mechanistic features of enzyme catalysis that have been exhaustively studied are intramolecularity and the hydrophobic effect. Although intramolecularity has for long been touted as the origin of enzymic reactivity, this can be challenged on fundamental physical-organic grounds. Intriguingly, however, the collapse of the classical Michaelis-Menten mechanism for enzyme catalysis leads to a reconsideration of the role of intramolecularity, although not as hitherto envisaged. Thus, a majority of enzymes apparently form covalent enzyme-substrate complexes—possibly also exergonically—so the subsequent reactions at the active site may well benefit from the traditional propinquity effect: The critical caveat would be the highly exergonic formation of final products. It is argued that the hydrophobic effect—although intuitively reasonable—is difficult to pin down quantitatively, model systems (including micelles) leading to inconsistent and debatable results. However, the hydrophobic effect likely contributes to enzymic reactivity along with charge-relay via the proteinic backbone.