The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin

Abstract

he has been an associate professor of Montana State University. His research interests are computational chemistry, inorganic chemistry, and X-ray spectroscopy. AbstractThe co-existence of "axial" and "rhombic" coordination environments has been demonstrated in a "Type 1" copper site of Pseudoazurin. This observation opens up previously not considered interpretations for the relationship between geometry and electronic structure of the four coordinate copper site. The Met16 variants of pseudoazurin were considered as model systems for investigating the effect of weak interactions from the second coordination sphere. The correlation between geometric and electronic structures of "Type 1" copper site was evaluated by the multi-edge (Cu K-edge and S K-edge) X-ray absorption spectroscopy (XAS) of Met16 variants of pseudoazurin. The co-existing axial and rhombic sites in pseudoazurin were characterized by Culigand distances, effective nuclear charge, and CuS(Cys) covalency from XAS. The XAS results were correlated with DFT calculations for investigating the effect of protein environment from the inner-sphere and beyond around the Cu site. The combined experimental and theoretical results support the presence of a close correlation between outer sphere environment and inner sphere coordination environment. This is achieved in pseudoazurin by a previously undisclosed allosteric effect that involves a rearrangement of the protein tertiary structure.

X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling

“…Generally, the Cu-S(Cys) distance in the axial site is expected to be shorter than the rhombic site from the higher Cu-S(Cys) frequency in resonance Raman spectra, 19 and the increased Cu-S bond covalency from S K-edge XAS. 21 Highly similar bond lengths for the oxidized axial and rhombic Cu sites in AcPAz were also observed by Cu K-edge extended X-ray absorption fine structure (EXAFS) analysis.…”

Computational Modelling Study on the Pseudoazurin Type 1 Cu Site

“…The inner coordination sphere of "Type-1" Cu site can be described with the Cu-S(Cys78) 2.16 Å, Cu-S(Met86) 2.48 Å and the average Cu-N(His40, His81) 1.95 Å distances, which were obtained from the analysis of the Cu K-edge EXAFS [21] (Table I.). Furthermore, the S(Cys78) 3p contribution to the Cu-S(Cys) bond were determined also from the pre-edge region of S K-edge XANES spectra which were 38% ± 3% [21] (Table II.).…”

“…The inner coordination sphere of "Type-1" Cu site can be described with the Cu-S(Cys78) 2.16 Å, Cu-S(Met86) 2.48 Å and the average Cu-N(His40, His81) 1.95 Å distances, which were obtained from the analysis of the Cu K-edge EXAFS [21] (Table I.). Furthermore, the S(Cys78) 3p contribution to the Cu-S(Cys) bond were determined also from the pre-edge region of S K-edge XANES spectra which were 38% ± 3% [21] (Table II.). Significant differences couldn't be observed between the two basis sets (def2SVP and mixed basis set) for geometry and electronic structure, therefore we will just discuss the results obtained by the def2SVP basis set and furthermore the computational time is also more efficient with the smaller def2SVP basis set.…”

Non-innocent ground state electronic structure of a polynuclear copper complex with picolinate bridges

“…The employed computational approach has recently been successfully utilized for describing the ground state of a trinuclear Cu II complex with biomimetic catecholase function [13]. The level of theory was selected to be a hybrid density functional that gives experimentally sound ground-state description for Cu II /Cu I complexes [14][15][16][17]. Validation for the given complexes was carried out using the electronically and structural well-defined complex 1 with a formally Cu II site.…”

“…These Cu oxidation and spin states, and their various ferro-and antiferromagnetic spin coupling schemes give a range of combinations that we explored using broken-symmetry, density functional theory electronic structure calculations and structural optimizations. The selected level of theory was the spectroscopically calibrated B(38HF)P86 set of functionals with saturated basis set that has been shown to perform well for both ground and excited states of Cu complexes [14] and bioinorganic compounds [13], metalloprotein [17] and metalloenzyme Cu sites [14,16]. For all models (Figs.14A-C) except the asymmetric unit (Fig.14D), the all electron def2TZVP [34,35] triple-ζ quality basis set with polarization functions were utilized.…”