The Active Site Loop Modulates the Reorganization Energy of Blue Copper Proteins by Controlling the Dynamic Interplay with Solvent

Abstract

Understanding the factors governing the rate of electron transfer processes in proteins is crucial not only to a deeper understanding of redox processes in living organisms but also for the design of efficient devices featuring biological molecules. Here, molecular dynamics simulations performed on native azurin and four chimeric cupredoxins allow for the calculation of the reorganization energy and of structure-related quantities that were used to clarify the molecular determinants to the dynamics/function relationship in blue copper proteins. We find that the dynamics of the small, metal-binding loop region controls the outer-sphere reorganization energy not only by determining the exposure of the active site to solvent but also through the modulation of the redox-dependent rearrangement of the whole protein scaffold and of the surrounding water molecules.

Protein electron transfer: Dynamics and statistics

“…A good study case to illustrate the origin of discrepancies is electron transfer in a family of azurin mutants for which both experimental activation enthalpies 114 115 Getting a near-unity slope between H † and F † requires χ G 7, which is taken as a constant value. This value is consistent with χ G 7.8 calculated from MD simulations of plastocyanin, 11 a blue copper protein from the same family and with a similar structure.…”

“…The value of χ G can be extracted from the dependence of the rate on the electrode overpotential, 113 which in the current description is given by the following equation: (21) with λ St from MD simulations 115 and a constant χ G = 7. The latter choice of χ G produces a unity slope of the linear regression (shown by the dashed line) and a non-zero intercept, nominally corresponding to the activation entropy.…”

Surface-enhanced infrared absorption spectroscopy and electrochemistry reveal the impact of nanoparticles on the function of protein immobilized on mimic biointerface

“…This means the oxidized cyt c is more hydrophilic or the reduced cyt c is more hydrophobic. From the energy point of view, the redox-dependent water rearrangement is the major determinant of the total reorganization energy (λ), the energy required to distort the equilibrium nuclear configuration of reactants toward the equilibrium configuration of products before electron transfer [39]. Herein, the smaller change in the degree of hydration of cyt c treated with SiO2 NPs inevitably decreases the λ of its redox process, and finally results in the decrease in ΔEp and the increase of reversibility of cyt c relative to those of native cyt c. residues 37~39 and 57~59 also shows strong electropositivity in addition to the region around the electrostatic interaction sites.…”

“…For a partially unfolded cyt c [39,47], its oxidized form always opens the heme crevice due to the change of ligand so as to have a large solvent accessibility of the heme, while its reduced form possesses a relatively compact conformation, which determines the negative shift of its formal potential relative to native cyt c. Since the structure and related heme microenvironment of cyt c treated with SiO2 NPs were changed in the oxidized form while were kept in the reduced form relative to those of native cyt c as shown in Fig. 6d, a similar hydration degree could be proposed for both cyt c (Fe 2+ ) and a more hydrophilic microenvironment for cyt c (Fe 3+ ) treated by SiO2 NPs, and thus a higher dielectric constant environment, which could result in the slight negative shift of the formal potential relative to that of native cyt c. In addition, the adsorption of negatively charged SiO2 NPs could compensate the surface charge of cyt c/MUA/Au, which could induce the change of surface potential, resulting in slight negative shift in the formal potential of adsorbed cyt c [43].…”

Probing redox reaction of azurin protein immobilized on hydroxyl-terminated self-assembled monolayers with different lengths

“…Previously, the role of surface residues in determining the ET process in azurin protein has been considered by molecular dynamics simulation [38]. In this study, to explore the effect of hydrophobicity of the SAM functional groups on the redox potential and ET of azurin, present amino acids in the azurin protein have been categorized in 3 groups including hydrophobic, hydrophilic and neutral groups [39].…”