Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

Abstract

The ground and excited state properties of copper proteins are studied and analyzed using hybrid quantum mechanics/molecular mechanics technique. Wildtype plastocyanin, characterized by an intense blue color, and wild-type nitrosocyanin, a red protein, are considered. These proteins differ from some ligands of the copper containing chromophore; we also studied the effects of selective mutations of one of the active site residue in plastocyanin. It is shown that this mutation is able to strongly modify the UV/VIS spectrum continuously modifying the absorption spectrum of the protein that from blue becomes red. Electrostatic and polarization effects of the macromolecular environment on the chromophore are taken into account using original techniques. Principal transitions are analyzed by mean of natural transition orbitals.

Charge‐Transfer versus Charge‐Separated Triplet Excited States of [ReI(dmp)(CO)3(His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

“…Our results are not directly comparable with those obtained experimentally for the full protein because we neglect to account for the copper center, which is responsible for a very bright red absorption. However, previous computational studies have shown how time‐dependent (TD) DFT is able to provide a good representation of such transitions . An analysis of the convergence of the simulated absorption spectrum with the number of snapshots is presented in Figure S1 in the Supporting Information.…”

Hybrid QM/MM Methods: Treating Electronic Phenomena in Very Large Molecular Systems

“…The QM-MM absorption spectrum obtained at TDDFT level putting only the copper ion and the ligating aminoacids in the QM part is also reported in Fig. 1.3 and one can notice the very good agreement with the experimental values, providing that the PE effect is taken into account, on the contrary ME gives totally unreliable results indicating an important effects of electrostatic and polarization effects [57]. Note also that more in detail the PE spectrum is composed of a large tail in the near infrared region while the visible part is constituted by the huge absorption band peaking at 600 nm and of a much less intense band appearing close to 490 nm.…”

“…1.3) are metallo-protein present in superior plants were they assure electron-transfer during the photosynthetic process [57,58]. The active site of the protein is constituted by a copper ion complexed by four aminoacids residues: one deprotonated cysteine, one methionine and two hystidines.…”

“…Notice that the electron-transfer is assured by the copper atoms that can reversibly convert between the + II and + I form. QM-MM calculations have allowed us to show that the protein environment regulates the necessary high rate of electron-transfer by constraining the copper environment in a geometry that is somehow mid-way between the ones of the + II and + I complex in gas phase [57] (i.e. copper coordinated by the lateral chains of the previous cited aminoacids, only), moreover in the protein geometrical differences between the oxidized and reduced form are extremely small, thus minimizing the reorganization energy of the redox process.…”

“…By analyzing the single excitation in terms of orbital contribution, and in particular in terms of natural transition orbitals (NTO) [57,58] we have been able to correctly interpret the spectral features. In particular the band at 450 nm is dominated by metal-to-ligand charge-transfer (MLCT) transition, while the band at 350 nm is much more complex and is composed of MLCT as well as of intra-and inter-ligand charge transfer transitions.…”