Entwicklung und Evaluation von effizienten und genauen theoretischen Methoden zur Berechnung Raman Spektren von Kofaktoren in Proteinen
Final Report Abstract
Vibrational spectroscopy is an essential experimental technique for investigating the structure and dynamics of molecular systems. In particular, resonance Raman (RR) spectroscopy is becoming very popular for selectively probing the vibrational signature of chromophores embedded in complex environments, such as a protein matrix. Since these techniques can be operated in a time-resolved mode, covering a dynamic range from femtoseconds to seconds, they can also provide insight into molecular dynamics and reaction mechanism. The analysis and interpretation of the complex vibrational signature often requires the assistance of accurate and efficient theoretical calculations. The main goal of this project was to test, compare and improve different formalism and approaches within a QM/MM framework for the computation of Raman spectra of protein cofactors using two different photoreceptors as targets: the phytochrome photoreceptor carrying a tetrapyrrole molecule as cofactor and the rhodopsin photoreceptor with a retinal Schiff base as active site. The computational methods which were tested include the conventional Normal Mode Analysis (NMA) approach and its variant, the Instantaneous Normal Mode Analysis (INMA); as well as of Fourier Transform of Time Correlation Function (FTTCF) method. The FTTCF approach, although computationally demanding, formally incorporates dynamics effects of the protein in the calculation of Raman spectra, in principle, making it possible to describe the vibrational signature of flexible systems. However, the accuracy of FTTCF-based Raman spectra calculations depends on two critical factors: a thorough sampling of the molecular phase space and the evaluation of polarizability derivatives. Within the funding period, the Mroginski group devoted its effort on testing the NMA and INMA approaches on the M-state- and the reduced M-state- of Bacteriorhodopsin (BR) and on the Pr-state of Bacteriophytochrome Cph1. The QM/MM calculations demonstrated that the spectral quality obtained with the conventional NMA approach is high enough that allows not only the extraction of structural information but also, the identification of environmental effects on the Raman spectra of a chromophore. This property was used to determine the structure and the protonation state of titrable side chains in the chromophore binding pocket of Cph1 and Cph2 as well as the elucidation of the structure of the retinal Shiff base in the reduced M- state of BR. The description of the environment by polarizable force fields slightly improves the results of the QM/MM calculation. However, the efforts associated to the generation and implementation of polarized force fields does not justify the minor increase in accuracy of calculated spectra. In parallel, the Elstner group worked on the improvement of the SCCDFTB approach for computing Raman spectra. Successful reparametrization of DFTB3, led to the new 3OB and 3OB-f parameter sets. In particular, the 3OB-f was generated to specifically reproduce C=O stretching frequencies. This parameter set was shown to be very sensitive to changes in protonation state of proteins. Furthermore, two approximations to correct for the minimal basis set error in DFTB were tested: the chemical potential equalization and the variational approach. Although these two new implementations provide improved molecular polarizabilities, the derivatives of the molecular polarizabilities with respect to atomic displacement, required for computing Raman intensities, are not corrected. The lack of personal and the low accuracy of polarizability derivatives provided by the DFTB method, hindered the realization of the work package dealing with the computation of QM/MM Raman spectra of the retinal and the tetrapyrrole chromophores in BR and in Cph1, respectively, using the FTTCF formalism.
Publications
- “Elucidating Photoinduced Structural Changes in Phytochromes by the Combined Application of Resonance Raman Spectroscopy and Theoretical Methods” J. Mol. Struc., 993, 15-25 (2011)
Mroginski, M. A.; von Stetten, D.; Kaminski, S.; Escobar, F. V.; Michael, N.; Daminelli-Widany, G.; Hildebrandt, P.
- “Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization” J. Phys. Chem. A 116 (2012) 9131
Kaminski S., Giese, T., York, D. Elstner, M.
(See online at https://doi.org/10.1021/jp306239c) - “Improved Electronic Properties from 3rd Order SCC-DFTB with Cost Efficient Post-SCF Extensions” J. Phys. Chem. A 116 (2012) 11927
Kaminski S.,M. Gaus, Elstner, M.
(See online at https://doi.org/10.1021/jp307264f) - “Parametrization and Benchmark of DFTB3 for Organic Molecules” J. Chem. Theor. Comput. (2012) 9, 338
Gaus, M., Goez, A., and Elstner, M.
(See online at https://doi.org/10.1021/ct300849w) - "QM/MM Simulations of Vibrational Spectra in Bacteriorhodopsin and Channelrhodopsin-2” Phys. Chem. Chem. Phys., (2013) 15, 6651-6659
K. Welke, H. C. Watanabe, T. Wolter, M. Gaus and M. Elstner
(See online at https://doi.org/10.1039/c3cp44181d) - „Structure of a Cph2-like phytochrome”. J. Biol. Chem .288 35714-35725 (2014)
Anders,K., Daminelli Widany, G., Mroginski, M.A., von Stetten, D., Essen, L.-O.
(See online at https://doi.org/10.1074/jbc.M113.510461) - “Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States” J. Phys. Chem. B (2015) 119, 2229
T. Wolter, M. Elstner, S. Fischer, J. C. Smith and N. Bondar
(See online at https://doi.org/10.1021/jp505818r) - Protonation-dependent structural heterogeneity in the chromophore binding site of cyanobacterial phytochrome Cph1. Journal Phys. Chem. B, 2017, 121 (1), pp 47–57
Francisco Velazquez Escobar, Christina Lang, Aref Takiden, Constantin Schneider, Jens Balke, Jon Hughes, Ulrike Alexiev, Peter Hildebrandt and Maria Andrea Mroginski
(See online at https://doi.org/10.1021/acs.jpcb.6b09600)
