Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

Challenges and advances in the computational modeling of biological phosphate hydrolysis

“…93 Globally, our calculations suggested that the promiscuity of this enzyme arises due to ''electrostatic flexibility'', 63 i.e., the ability of individual amino acids to take on more than one catalytic role during transition state stabilization and to compensate for each other upon binding of different substrates with different requirements for efficient catalysis. This is in agreement with experimental work on the organophosphate hydrolase serum paraoxonase 1 (PON1), [94][95][96] which has also pointed to catalytic versatility of individual active site residues, and is further supported by our subsequent computational work on different PMHs. 63 Finally, a comparison of structural and physico-chemical properties of the active sites of different alkaline phosphatases vs. the number of known activities for these enzymes shows a This journal is © The Royal Society of Chemistry 2018 correlation between larger active site volume and polar solvent accessible surface area with a greater number of promiscuous activities.…”

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

“…Overall, it was found that the catalysis requires less flexibility rather than more flexibility. This is supported by recent studies 129 of interfacial activation of serum paraoxonase 1 by association with highdensity lipoprotein (HDL), where it was demonstrated that the activity stimulation of this enzyme upon association with HDL is due to rigidification of a hydrogen bonding network that spans over 20 Å from the surface of the protein through to the catalytic core of the enzyme, and keeps the key catalytic residues in place. This work also discussed the "dark side" of excessive dynamics in enzyme design studies.…”

“…In addition, there is a "dark side" to excess enzyme dynamics, in that floppiness impairs catalytic efficiency and promotes futile encounters. 129,181 Therefore, if anything, rational design efforts are best directed towards reducing excessive conformational flexibility in de novo enzymes.…”

Using experimental evolution to probe molecular mechanisms of protein function

“…Identification of key activity‐determining residues by directed evolution can allow more targeted subsequent investigation of sequence‐function relationships. For example combining previous findings from directed evolution with structural information and computer simulations has provided fundamental insights into mechanisms regulating activity and stability of the lipophilic lactonase paraoxonase‐1, with important wider implications for other membrane‐associated enzymes …”

“…For example combining previous findings from directed evolution 21 with structural information and computer simulations has provided fundamental insights into mechanisms regulating activity and stability of the lipophilic lactonase paraoxonase-1, with important wider implications for other membraneassociated enzymes. 22 Whilst directed evolution experiments reveal key activity-determining residues there are some instances where additional non activity-modulating positions also appear as mutated positions within the selected population, giving rise to a false positive background. An example of this is the six residue positions initially identified during a directed evolution of a lipase from Pseudomonas aeruginosa for enantioselectivity.…”