Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification

TLDR

The study aims to explain how ionic strength influences the activity of native and chemically modified Cu‑Zn superoxide dismutase by linking the size of the positively charged region at the active site and the surrounding negative potential barrier to electrostatic focusing effects. The authors implemented a finite‑difference solver for the linearized Poisson‑Boltzmann equation, microcoded on an ST‑100 array processor, to generate electrostatic potential maps of proteins—including ionic strength effects—in about 30 minutes, and applied it to a Cu‑Zn superoxide dismutase dimer. The calculations show that the protein’s shape and ionic strength strongly influence electrostatic potentials, with a positively charged cluster at the active‑site channel producing a highly focused positive potential that cannot be reproduced by uniform dielectric models, while the surrounding protein exhibits a weak negative potential, suggesting the enzyme’s electrostatics are tuned to maximize productive collisions and explain its ionic‑strength‑dependent activity.

Abstract

Abstract In this paper we report the implementation of a finite‐difference algorithm which solves the linearized Poisson‐Boltzmann equation for molecules of arbitrary shape and charge distribution and which includes the screening effects of electrolytes. The microcoding of the algorithm on an ST‐100 array processor allows us to obtain electrostatic potential maps in and around a protein, including the effects of ionic strength, in about 30 minutes. We have applied the algorithm to a dimer of the protein Cu‐Zn superoxide dismutase (SOD) and compared our results to those obtained from uniform dielectric models based on coulombic potentials. We find that both the shape of the protein‐solvent boundary and the ionic strength of the solvent have a profound effect on the potentials in the solvent. For the case of SOD, the cluster of positive charge at the bottom of the active site channel produces a strongly enhanced positive potential due to the focusing of field lines in the channel—a result that cannot be obtained with any uniform dielectric model. The remainder of the protein is surrounded by a weak negative potential. The electrostatic potential of the enzyme seems designed to provide a large cross‐sectional area for productive collisions. Based on the ionic strength dependence of the size of the positive potential region emanating from the active site and the repulsive negative potential barrier surrounding the protein, we are able to suggest an explanation for the ionic strength dependence of the activity of the native and chemically modified forms of the enzyme.