A Quantum‐mechanical Study of the Binding Pocket of Proteorhodopsin: Absorption and Vibrational Spectra Modulated by Analogue Chromophores

Abstract

Proteorhodopsin is a light-driven proton pumping membrane protein related to bacteriorhodopsin. It contains an all-trans retinal A1 chromophore covalently bound to a lysine residue via a protonated Schiff base. In this study, we exploited density functional theory (DFT) calculations to investigate the retinal binding pocket in the dark state and after mimicking photoisomerization. The model of the binding pocket is constructed incrementally by adding the residues near the retinal that are necessary to ensure a stable protonated Schiff base. The presence of a few water molecules near the Schiff base turns out to be an essential feature of the model. The absorption properties are then studied using time-dependent DFT (TDDFT) and compared to experimental data to further validate the structural model and to assess the accuracy of the computational setting. It is shown that TDDFT is able to reproduce the main absorption peak accurately and to quantitatively determine the spectral shift induced by substituting the native all-trans retinal A1 chromophore with different retinal analogues. Moreover, ab initio molecular dynamics simulations are performed to investigate the vibrational spectra of our models before and after isomerization. Specific differences in the vibrational spectra are identified that provide further insight into experimental FTIR difference spectra.

A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin

“…The long-range corrected functional CAM-B3LYP produces a slightly higher excitation energy of 2.56 eV. These results are in agreement with a recent study by Buda et al 31 where B3LYP (2.43 eV) and CAM-B3LYP (2.72 eV) were employed as well. However, it should be noted that instead of a full QM/MM protein model a reduced cluster model was used in that study which contained rpSb with lysine, the counterion complex D97, D227, H75 and three water molecules which were treated at the DFT level and TZP basis set.…”

“…Furthermore, the crystal structure of BPR served as a starting point to investigate ground state properties via classical MD. 30 Finally, Buda et al 31 have also used cluster models to calculate the properties of excited states based on TDDFT and to perform ab initio molecular dynamics. For this purpose, they have relied on a previously reported homology model 32 and extracted the positions of the retinal atoms and its nearest neighbours.…”

Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin

“…The high energetic cost of proton transfer from the retinal Schiff base to D292 in wild-type C1C2 ensures that the protein avoids unproductive deprotonation of the Schiff base prior to photoisomerization. Since the energetics of proton transfer computed without a protein environment strongly favours the transfer of the proton from the retinal Schiff base to a nearby carboxylate side chain [ 54 , 100 ], the important question that arises is that of the molecular interactions that stabilize the protonated retinal Schiff base state in all- trans C1C2. We addressed this question by calculating proton transfer pathways for the wild type and for the K132A mutant using different amounts of active site water molecules, different protonation states of E162 and performing our computations with and without a lipid membrane.…”

Energetic Effects of a Closed System Approach Including Explicit Proton and Electron Acceptors as Demonstrated by a Mononuclear Ruthenium Water Oxidation Catalyst

“…However, in this trajectory bonds are formed and broken, and therefore one cannot assume that the change in zero‐point energy will be negligible. For this reason the vibrational density of states was obtained from the CPMD trajectory files,, as shown in Figure S5. The zero‐point energy contribution from the changed Ru−O bond, the broken O−H bond, and the formed H + solv /[H 5 O 2 ] + complex would amount to a correction of only −0.04 eV, which is small in comparison to the uncertainty in the change in KS energy.…”

“…However, in this trajectory bonds are formed and broken, and therefore one cannot assume that the change in zero-point energy will be negligible. For this reason the vibrational density of states was obtained from the CPMD trajectory files, [37,38] as shown in Figure S5 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57…”