Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis

Abstract

The question of the nature of the proton bridge involved in general acid-base catalysis in both enzymic and non-enzymic systems is considered in the light of long-known but insufficiently appreciated work of Jencks and his coworkers and of more recent results from neutron-diffraction crystallography and NMR spectroscopic studies, as well as results from isotope-effect investigations. These lines of inquiry lead toward the view that the bridging proton, when between electronegative atoms, is in a stable potential at the transition state, not participating strongly in the reaction-coordinate motion. Furthermore they suggest that bond order is well-conserved at unity for bridging protons, and give rough estimates of the degree to which the proton will respond to structural changes in its bonding partners. Thus if a center involved in general-catalytic bridging becomes more basic, the proton is expected to move toward it while maintaining a unit total bond order. For a unit increase in the pK of a bridging partner, the other partner is expected to acquire about 0.06 units of negative charge. The implications are considered for charge distribution in enzymic transition states as the basicity of catalytic residues changes in the course of molecular evolution or during progress along a catalytic pathway.

Revisitation of the βCl-Elimination Reaction of d-Amino Acid Oxidase

“…The absorbance increase at 320 nm reflects formation of pyruvate (Ⅺ), the absorbance at 450 nm reflects the oxidation state of the enzyme (E), and that at 540 nm reflects the presence of CT complexes I1-CT and I2-CT (224). arising from a single site and a single hydrogen being involved (25). Similarly, at pH 6.5 the conversion of I1-CT into I2-CT in H 2 O versus D 2 O shows a solvent KIE Ϸ 1.5, whereas the decay of I2-CT exhibits a larger solvent KIE Ϸ 5 (supplemental Fig.…”

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

“…Hydrogen bonding [1][2][3][4] plays a key role in various biological processes, including pairing of nucleobases [4,6], protein folding [7,8], enzyme catalysis [9,10], and other interactions in biosystems. Hydrogen bonding influences the solubility of biologically active ligands and the way they bind to bioreceptors [11].…”

Concerted Asynchronous Proton Transfer in H-Bonding Relay Model: An Implication of Green Fluorescent Protein

“…[1][2][3] There are many proteins that have H-bonded networks to serve the function of proton transport, where green fluorescent protein is included. In recent decades, the green fluorescent protein (GFP) has been widely used in imaging studies of protein folding, gene expression, protein trafficking and cell development from a nearly unknown protein.…”