TY - JOUR A1 - Götze, Jan A1 - Saalfrank, Peter T1 - Serine in BLUF domains displays spectral importance in computational models N2 - The BLUF (blue-light sensing using flavine) domain of the AppA photoreceptor protein from Rhodobacter sphaeroides was modelled by using quantum chemical chromophore plus amino acid models at the (TD-)B3LYP/6-31G* level of theory. The models were based on NMR structures, and further refined by CHARM force field molecular dynamics simulations. The goal is to explain the total redshift by about 10 nm in the UV/Vis spectra of BLUF domains after illumination, and to relate it to structural changes. For this purpose UV/Vis spectra of the available NMR structures were calculated and related to geometrical features. In particular, the hydrogen network embedding the central chromophore is discussed. Specifically, the position of a conserved glutamine, Q63, is found to be important in agreement with findings from previous works. Additionally, however, we find a systematic dependence also on the geometry of a conserved serine, S41. Based on a series of calculations with known structures and with artificial structural models, we argue that indeed the light-induced switching of both Q63 and S41 is necessary to explain the full similar to 10 nm redshift in the light (signalling) state of serine containing BLUF domains. Following or accompanying the double switching, two structurally highly important residues W104 and M106 exchange places, but do not affect the overall UV/ Vis properties of the chromophore. Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/10111344 U6 - https://doi.org/10.1016/j.jphotobiol.2008.10.003 SN - 1011-1344 ER - TY - THES A1 - Götze, Jan Philipp T1 - Influence of protein and solvent environments on quantum chemical properties of photosynthesis enzymes and photoreceptors T1 - Einfluss von Protein- und Lösungsmittelumgebungen auf quantenchemische Eigenschaften von Photosynthese-Enzymen und -Photorezeptoren N2 - This thesis contains quantum chemical models and force field calculations for the RuBisCO isotope effect, the spectral characteristics of the blue-light sensor BLUF and the light harvesting complex II. The work focuses on the influence of the environment on the corresponding systems. For RuBisCO, it was found that the isotopic effect is almost unaffected by the environment. In case of the BLUF domain, an amino acid was found to be important for the UV/vis spectrum, but unaccounted for in experiments so far (Ser41). The residue was shown to be highly mobile and with a systematic influence on the spectral shift of the BLUF domain chromophore (flavin). Finally, for LHCII it was found that small changes in the geometry of a Chlorophyll b/Violaxanthin chromophore pair can have strong influences regarding the light harvesting mechanism. Especially here it was seen that the proper description of the environment can be critical. In conclusion, the environment was observed to be of often unexpected importance for the molecular properties, and it seems not possible to give a reliable estimate on the changes created by the presence of the environment. N2 - Diese Arbeit beinhaltet quantenchemische und molekularmechanische Modelle zum Isotopeneffekt des Enzyms RuBisCO, der spektralen Charakterisierung des Blaulicht-Rezeptors BLUF und dem Lichtsammelkomplex II (LHCII). Es wurden vor allem die Einflüsse der Umgebung auf die entsprechenden Systeme untersucht. Für RuBisCO wurde gefunden, dass der Isotopeneffekt nur marginal von der Umgebung abhängt. Im Falle der BLUF Domäne wurde eine Aminosäure charakterisiert (Ser41), die bis dato experimentell noch nicht beschrieben war. Es wurde festgestellt, dass Ser41 hochmobil ist und einen systematischen Einfluss auf die spektrale Verschiebung des BLUF Chromophors (Flavin) hat. Schließlich wurde bei LHCII festgestellt, dass kleine Veränderungen in der Geometrie eines Chlorophyll b/Violaxanthin Chromophorenpaares bereits massive Einflüsse auf den Mechanismus des Lichtsammelprozesses haben können. Insbesondere hier zeigt sich, wie kritisch die genaue Beschreibung der Umgebung ist. Zusammenfassend wurde beobachtet, dass sich die Umgebung in oft unerwarteter Weise auf die molekularen Eigenschaften auswirken kann und es daher nicht möglich zu sein scheint, die entsprechenden Effekte vorher abzuschätzen. KW - Photosynthese KW - Molekülmodelle KW - RuBisCO KW - LHCII KW - Blaulichtsensoren KW - Photosynthesis KW - molecular modeling KW - RuBisCO KW - LHCII KW - Blue-light sensors Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-51135 ER - TY - JOUR A1 - Kröner, Dominik A1 - Götze, Jan Philipp T1 - Modeling of a violaxanthin-chlorophyll b chromophore pair in its LHCII environment using CAM-B3LYP JF - Journal of photochemistry and photobiology : B, Biology N2 - Collecting energy for photosystem II is facilitated by several pigments, xanthophylls and chlorophylls, embedded in the light harvesting complex II (LHCII). One xanthophyll, violaxanthin (Vio), is loosely bound at a site close to a chlorophyll b (Chl). No final answer has yet been found for the role of this specific xanthophyll. We study the electronic structure of Vio in the presence of Chl and under the influence of the LHCII environment, represented by a point charge field (PCF). We compare the capability of the long range corrected density functional theory (DFT) functional CAM-B3LYP to B3LYP for the modeling of the UV/vis spectrum of the Vio + Chl pair. CAM-B3LYP was reported to allow for a very realistic reproduction of bond length alternation of linear polyenes, which has considerable impact on the carotenoid structure and spectrum. To account for the influence of the LHCII environment, the chromophore geometries are optimized using an ONIOM(DFT/6-31G(d):PM6) scheme. Our calculations show that the energies of the locally excited states are almost unaffected by the presence of the partner chromophore or the PCF. There are, however, indications for excitonic coupling of the Chl Soret band and Vio. We propose that Vio may accept energy from blue-light excited Chl. KW - CAM-B3LYP KW - Density functional theory KW - Light-harvesting complex II KW - Photosynthesis KW - Violaxanthin KW - Chlorophyll b Y1 - 2012 U6 - https://doi.org/10.1016/j.jphotobiol.2011.12.007 SN - 1011-1344 VL - 109 IS - 2 SP - 12 EP - 19 PB - Elsevier CY - Lausanne ER - TY - JOUR A1 - Götze, Jan Philipp A1 - Saalfrank, Peter T1 - Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO JF - Journal of molecular modeling N2 - Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO2 carbon atom. This kinetic isotope effect alpha = k (12)/k (13) for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of (CO2)-C-12 compared to (CO2)-C-13. The latter is the dominant mode for the product formation at the transition state. KW - Cluster model KW - Dark reactions KW - Densityfunctional theory KW - Isotope effect KW - Photosynthesis KW - Quantum chemistry KW - RuBisCO Y1 - 2012 U6 - https://doi.org/10.1007/s00894-011-1207-0 SN - 1610-2940 VL - 18 IS - 5 SP - 1877 EP - 1883 PB - Springer CY - New York ER -