@article{HuegeGoetzeSchwarzetal.2011,
  author    = {Huege, Jan and Goetze, Jan and Schwarz, Doreen and Bauwe, Hermann and Hagemann, Martin and Kopka, Joachim},
  title     = {Modulation of the major Paths of Carbon in photorespiratory mutants of synechocystis},
  series = {PLoS one},
  volume    = {6},
  journal   = {PLoS one},
  number    = {1},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0016278},
  pages     = {12},
  year      = {2011},
  abstract  = {Background: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration. Methodology/Principal Findings: The (13)C labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO(2) (5\%, HC) or limited CO(2) (0.035\%, LC) conditions were pulse-labelled under very high (2\% w/w) (13)C-NaHCO(3) (VHC) conditions followed by treatment with ambient (12)C at HC and LC conditions, respectively. The (13)C enrichment, relative changes in pool size, and (13)C flux of selected metabolites were evaluated. We demonstrate two major paths of CO(2) assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, (13)C labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating Delta glcD1 mutant, we demonstrate enhanced (13)C partitioning into the glycolate pool under conditions favouring photorespiration and enhanced (13)C partitioning into the glycine pool of the glycine-accumulating Delta gcvT mutant. Under LC conditions, the photorespiratory mutants Delta glcD1 and Delta gcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway. Conclusions/Significance: With our approach of non-steady-state (13)C labelling and analysis of metabolite pool sizes with respective (13)C enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies.},
  language  = {en}
}
@article{TitovGranucciGoetzeetal.2016,
  author    = {Titov, Evgenii and Granucci, Giovanni and Goetze, Jan Philipp and Persico, Maurizio and Saalfrank, Peter},
  title     = {Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects},
  series = {The journal of physical chemistry letters},
  volume    = {7},
  journal   = {The journal of physical chemistry letters},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1948-7185},
  doi       = {10.1021/acs.jpciett.6b01401},
  pages     = {3591 -- 3596},
  year      = {2016},
  abstract  = {While azobenzenes readily photoswitch in solution, their photoisomerization in densely packed self-assembled monolayers (SAMs) can be suppressed. Reasons for this can be steric hindrance and/or electronic quenching, e.g., by exciton coupling. We address these possibilities by means of nonadiabatic molecular dynamics with trajectory surface hopping calculations, investigating the trans -> cis isomerization of azobenzene after excitation into the pi pi* absorption band. We consider a free monomer, an isolated dimer and a dimer embedded in a SAM-like environment of additional azobenzene molecules, imitating in this way the gradual transition from an unconstrained over an electronically coupled to an electronically coupled and sterically hindered, molecular switch. Our simulations reveal that in comparison to the single molecule the quantum yield of the trans -> cis photoisomerization is similar for the isolated dimer, but greatly reduced in the sterically constrained situation. Other implications of dimerization and steric constraints are also discussed.},
  language  = {en}
}
@article{WitzelGoetzeEbenhoeh2010,
  author    = {Witzel, Franziska and Goetze, Jan and Ebenhoeh, Oliver},
  title     = {Slow deactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase elucidated by mathematical models},
  issn      = {1742-464X},
  doi       = {10.1111/j.1742-4658.2009.07541.x},
  year      = {2010},
  abstract  = {Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme of the Calvin cycle, catalyzing the fixation of inorganic carbon dioxide to organic sugars. Unlike most enzymes, RuBisCO is extremely slow, substrate unspecific, and catalyzes undesired side-reactions, which are considered to be responsible for the slow deactivation observed in vitro, a phenomenon known as fallover. Despite the fact that amino acid sequences and the 3D structures of RuBisCO from a variety of species are known, the precise molecular mechanisms for the various side reactions are still unclear. In the present study, we investigate the kinetic properties of RuBisCO using mathematical models. Initially, we formulate a minimal model that quantitatively reflects the kinetic behavior of RuBisCOs from different organisms. By relating rate parameters for single molecular steps to experimentally determined K-m and V-max values, we can examine mechanistic differences among species. The minimal model further demonstrates that two inhibitor producing side reactions are sufficient to describe experimentally determined fallover kinetics. To explain the observed kinetics of the limited capacity of RuBisCO to accept xylulose 1,5-bisphosphate as substrate, the inclusion of other side reactions is necessary. Our model results suggest a yet undescribed alternative enolization mechanism that is supported by the molecular structure. Taken together, the presented models serve as a theoretical framework to explain a wide range of observed kinetic properties of RuBisCOs derived from a variety of species. Thus, we can support hypotheses about molecular mechanisms and can systematically compare enzymes from different origins.},
  language  = {en}
}
@article{GoetzeKroenerBanerjeeetal.2014,
  author    = {Goetze, Jan P. and Kr{\"o}ner, Dominik and Banerjee, Shiladitya and Karasulu, Bora and Thiel, Walter},
  title     = {Carotenoids as a shortcut for chlorophyll Soret-to-Q band energy flow},
  series = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  volume    = {15},
  journal   = {ChemPhysChem : a European journal of chemical physics and physical chemistry},
  number    = {15},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1439-4235},
  doi       = {10.1002/cphc.201402233},
  pages     = {3391 -- 3400},
  year      = {2014},
  abstract  = {It is proposed that xanthophylls, and carotenoids in general, may assist in energy transfer from the chlorophyll Soret band to the Q band. Ground-state (1A(g)) and excited-state (1B(u)) optimizations of violaxanthin (Vx) and zeaxanthin (Zx) are performed in an environment mimicking the light-harvesting complex II (LHCII), including the closest chlorophyll b molecule (Chl). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) is used in combination with a semi-empirical description to obtain the excited-state geometries, supported by additional DFT/multireference configuration interaction calculations, with and without point charges representing LHCII. In the ground state, Vx and Zx show similar properties. At the 1B(u) minimum, the energy of the Zx 1Bu state is below the Chl Q band, in contrast to Vx. Both Vx and Zx may act as acceptors of Soret-state energy; transfer to the Q band seems to be favored for Vx. These findings suggest that carotenoids may generally mediate Soret-to-Q energy flow in LHCII.},
  language  = {en}
}
@article{GoetzeGrecoMitricetal.2012,
  author    = {Goetze, Jan P. and Greco, Claudio and Mitric, Roland and Bonacic-Koutecky, Vlasta and Saalfrank, Peter},
  title     = {BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study},
  series = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  volume    = {33},
  journal   = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
  number    = {28},
  publisher = {WILEY-BLACKWELL},
  address   = {HOBOKEN},
  issn      = {0192-8651},
  doi       = {10.1002/jcc.23056},
  pages     = {2233 -- 2242},
  year      = {2012},
  abstract  = {Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.},
  language  = {en}
}