@article {26388,
	title = {Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR},
	journal = {Biophysical Journal},
	volume = {119},
	number = {3},
	year = {2020},
	note = {Cited By :1Export Date: 30 January 2022},
	month = {2020},
	pages = {705 - 716},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088223349\&doi=10.1016\%2fj.bpj.2020.06.031\&partnerID=40\&md5=eb1dd08eaac581eda4cbcceeefc25d95},
	author = {Kaufmann, J.C.D. and Krause, B.S. and Adam, S. and Ritter, E. and Schapiro, I. and Hegemann, P. and Bartl, F.J.}
}
@article {26387,
	title = {NeoR, a near-infrared absorbing rhodopsin},
	journal = {Nature Communications},
	volume = {11},
	number = {1},
	year = {2020},
	note = {Cited By :11Export Date: 30 January 2022},
	month = {2020},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85095766677\&doi=10.1038\%2fs41467-020-19375-8\&partnerID=40\&md5=3b0e15225ed6d978ab1d6f478f64e005},
	author = {Broser, M. and Spreen, A. and Konold, P.E. and Peter, E. and Adam, S. and Borin, V. and Schapiro, I. and Seifert, R. and Kennis, J.T.M. and Bernal Sierra, Y.A. and Hegemann, P.}
}
@article {26389,
	title = {Tuning Quantum Dots Coupling Using Organic Linkers with Different Vibrational Modes},
	journal = {Journal of Physical Chemistry C},
	volume = {124},
	number = {29},
	year = {2020},
	note = {Cited By :1Export Date: 30 January 2022},
	month = {2020},
	pages = {16159 - 16165},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089818416\&doi=10.1021\%2facs.jpcc.0c03703\&partnerID=40\&md5=1cd1111443f3d9fce2f3bca66ab43ac1},
	author = {Kolodny, Y. and Fererra, S. and Borin, V. and Yochelis, S. and Dibenedetto, C.N. and Mor, M. and Dehnel, J. and Remmenik, S. and Fanizza, E. and Striccoli, M. and Schapiro, I. and E. Lifshitz and Paltiel, Y.}
}
@article {24766,
	title = {The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2020},
	month = {2020/06/26},
	pages = {201921706},
	abstract = {Bilin-binding photoreceptors are light-signaling proteins that mediate various processes from photomorphogenesis, phototaxis, chromatic acclimation, to photosynthesis. They are also promising tunable optical agents for use in optogenetics and superresolution microscopy. Using an integrated approach of crystallography, spectroscopy, and QM/MM calculations, this work examines the ultrafast dynamics of a photoactive single-domain phytochrome. Our work reveals in detail the critical role of the protein environment in defining the excited state lifetime and thereby the quantum efficiency of the bilin photoisomerization. This insight provides design principles for engineering of bilin-based photoreceptors for biotechnological and medical applications.Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇄ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (Pr) and far red-absorbing (Pfr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the Pr form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at \~{}300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.},
	url = {http://www.pnas.org/content/early/2020/06/25/1921706117.abstract},
	author = {Slavov, Chavdar and Fischer, Tobias and Barnoy, Avishai and Shin, Heewhan and Aditya G. Rao and Wiebeler, Christian and Zeng, Xiaoli and Sun, Yafang and Xu, Qianzhao and Gutt, Alexander and Zhao, Kai-Hong and Wolfgang G{\"a}rtner and Yang, Xiaojing and Schapiro, Igor and Wachtveitl, Josef}
}
@article {24685,
	title = {Spin-chemical effects on intramolecular photoinduced charge transfer reactions in bisphenanthroline copper(i)-viologen dyad assemblies},
	journal = {Chemical Science},
	volume = {11},
	number = {21},
	year = {2020},
	month = {2020},
	pages = {5511 - 5525},
	publisher = {The Royal Society of Chemistry},
	abstract = {Two covalently linked donor{\textendash}acceptor copper phenanthroline complexes (C{\textendash}A dyads) of interest for solar energy conversion/storage schemes, [Cu(i)(Rphen(OMV)24+)2]9+ = RC+A48+ with RC+ = [Cu(i)Rphen2]+ involving 2,9-methyl (R = Me) or 2,9-phenyl (R = Ph)-phenanthroline ligands that are 5,6-disubstituted by 4-(n-butoxy) linked methylviologen electron acceptor groups (A2+ = OMV2+), have been synthesized and investigated via quantum chemical calculations and nanosecond laser flash spectroscopy in 1,2-difluorobenzene/methanol (dfb/MeOH) mixtures. Upon photoexcitation, charge transfer (CT) states RC2+A+A36+ are formed in less than one ns and decay by charge recombination on a time scale of 6{\textendash}45 ns. The CT lifetime of RC2+A+A36+ has a strong dependence on MeOH solvent fraction when R = Me, but is unaffected if R = Ph. This solvent effect is due to coordination of MeOH solvent in MeC+A48+ (i.e. exciplex formation) allowed by conformational flattening of the ligand sphere, which cannot occur in PhC+A48+ having bulkier Phphen ligand framework. Interestingly, the decay time of the CT state increases for both species at low magnetic fields with a maximum increase of ca. 30\% at ca. 150 mT, then decreases as the field is increased up to 1500 mT, the highest field investigated. This magnetic field effect (MFE) is due to magnetic modulation of the spin dynamics interconverting 3CT and 1CT states. A quantitative modeling according to the radical pair mechanism involving ab initio multireference calculations of the complexes revealed that the spin process is dominated by the effect of Cu hyperfine coupling. The external magnetic field suppresses the hyperfine coupling induced spin state mixing thereby lengthening the CT decay time. This effect is counteracted by the field dependent processes of T0{\textendash}S mixing through the Δg-mechanism and by a local mode spin{\textendash}orbit mechanism. Further, the maximum MFE is limited by a finite rate of direct recombination of 3CT states and the spin-rotational mechanism of spin relaxation. This study provides a first comprehensive characterization of Cu(ii)-complex spin chemistry and highlights how spin chemistry can be used to manipulate solar energy harvesting and storage materials.},
	isbn = {2041-6520},
	url = {http://dx.doi.org/10.1039/D0SC00830C},
	author = {Lazorski, Megan S. and Schapiro, Igor and Gaddie, Ross S. and Lehnig, Ammon P. and Atanasov, Mihail and Neese, Frank and Steiner, Ulrich E. and Elliott, C. Michael}
}
@article {24684,
	title = {Modern quantum chemistry with [Open]Molcas},
	journal = {The Journal of Chemical Physics},
	volume = {152},
	number = {21},
	year = {2020},
	pages = {214117},
	doi = {10.1063/5.0004835},
	url = {https://aip.scitation.org/doi/abs/10.1063/5.0004835},
	author = {Aquilante, Francesco and Autschbach, Jochen and Alberto Baiardi and Stefano Battaglia and Borin, Veniamin A. and Chibotaru, Liviu F. and Irene Conti and De Vico, Luca and Micka{\"e}l Delcey and Fdez. Galv{\'a}n, Ignacio and Ferr{\'e}, Nicolas and Freitag, Leon and Garavelli, Marco and Xuejun Gong and Knecht, Stefan and Ernst D. Larsson and Lindh, Roland and Lundberg, Marcus and Malmqvist, Per {\r A}ke and Nenov, Artur and Norell, Jesper and Michael Odelius and Olivucci, Massimo and Thomas B. Pedersen and Laura Pedraza-Gonz{\'a}lez and Quan M. Phung and Pierloot, Kristine and Reiher, Markus and Schapiro, Igor and Segarra-Mart{\'\i}, Javier and Francesco Segatta and Luis Seijo and Sen, Saumik and Dumitru-Claudiu Sergentu and Stein, Christopher J. and Ungur, Liviu and Vacher, Morgane and Valentini, Alessio and Veryazov, Valera}
}
@article {24683,
	title = {Femtosecond-to-millisecond structural changes in a light-driven sodium pump},
	year = {2020},
	month = {2020},
	abstract = {Light-driven sodium pumps actively transport small cations across cellular membranes1. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved2,3, it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser4, we have collected serial crystallographic data at ten pump{\textendash}probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.},
	isbn = {1476-4687},
	url = {https://doi.org/10.1038/s41586-020-2307-8},
	author = {Skopintsev, Petr and Ehrenberg, David and Weinert, Tobias and James, Daniel and Kar, Rajiv K. and Johnson, Philip J. M. and Ozerov, Dmitry and Furrer, Antonia and Martiel, Isabelle and Dworkowski, Florian and Nass, Karol and Knopp, Gregor and Cirelli, Claudio and Arrell, Christopher and Gashi, Dardan and Mous, Sandra and Wranik, Maximilian and Gruhl, Thomas and Kekilli, Demet and Br{\"u}nle, Steffen and Deupi, Xavier and Schertler, Gebhard F. X. and Benoit, Roger M. and Panneels, Valerie and Nogly, Przemyslaw and Schapiro, Igor and Milne, Christopher and Heberle, Joachim and Standfuss, J{\"o}rg}
}
@article {24415,
	title = {Dynamic Properties of the Photosensory Domain of Deinococcus radiodurans Bacteriophytochrome},
	journal = {The Journal of Physical Chemistry BThe Journal of Physical Chemistry B},
	volume = {124},
	number = {9},
	year = {2020},
	month = {2020},
	pages = {1740 - 1750},
	publisher = {American Chemical Society},
	abstract = {Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.},
	isbn = {1520-6106},
	url = {https://doi.org/10.1021/acs.jpcb.0c00612},
	author = {Battocchio, Giovanni and Gonz{\'a}lez, Ronald and Aditya G. Rao and Schapiro, Igor and Mroginski, Maria Andrea}
}
@article {24414,
	title = {Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein},
	year = {2020},
	month = {2020},
	abstract = {ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation\&nbsp;in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.},
	keywords = {ABC transporter, Arabinan utilization system, arabinose, substrate-binding protein},
	isbn = {0022-2836},
	url = {http://www.sciencedirect.com/science/article/pii/S0022283620301078},
	author = {Lansky, Shifra and Salama, Rachel and Shulami, Smadar and Lavid, Noa and Sen, Saumik and Schapiro, Igor and Shoham, Yuval and Shoham, Gil}
}
@article {24413,
	title = {Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump\&mdash;IR-Probe Spectroscopy and Computational Methods},
	journal = {Molecules},
	volume = {25},
	number = {4},
	year = {2020},
	abstract = {Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.\&nbsp;},
	author = {Stensitzki, Till and Adam, Suliman and Schlesinger, Ramona and Schapiro, Igor and Heyne, Karsten}
}
@article {24412,
	title = {Intramolecular Proton Transfer Controls Protein Structural Changes in Phytochrome},
	journal = {BiochemistryBiochemistry},
	volume = {59},
	number = {9},
	year = {2020},
	note = {doi: 10.1021/acs.biochem.0c00053},
	month = {2020},
	pages = {1023-1037},
	publisher = {American Chemical Society},
	abstract = {Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.},
	isbn = {0006-2960},
	url = {https://doi.org/10.1021/acs.biochem.0c00053},
	author = {Kraskov, Anastasia and Nguyen, Anh Duc and Goerling, Jan and Buhrke, David and Velazquez Escobar, Francisco and Fernandez Lopez, Maria and Michael, Norbert and Sauthof, Luisa and Schmidt, Andrea and Piwowarski, Patrick and Yang, Yang and Stensitzki, Till and Adam, Suliman and Bartl, Franz and Schapiro, Igor and Heyne, Karsten and Siebert, Friedrich and Scheerer, Patrick and Mroginski, Maria Andrea and Hildebrandt, Peter}
}
@article {24350,
	title = {Structural elements regulating the photochromicity in a cyanobacteriochrome},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {117},
	number = {5},
	year = {2020},
	month = {2020/01/20},
	pages = {2432-2440},
	abstract = {Phytochromes and related photoreceptors distinguish themselves for their long-wavelength absorption and large spectral shift between parental state and photoproduct. Both features are not well understood, partly due to lack of high-resolution structural data and insufficient support from quantum-chemical calculations. The red{\textendash}green switching cyanobacteriochrome Slr1393g3 shows an absorption shift larger than 110 nm. Both parental state and photoproduct could be crystallized with high resolution, together with a {\textquotedblleft}hybrid{\textquotedblright} form carrying the chromophore in parental state geometry, whereas the protein remained in the photoproduct conformation. The crystal structures reveal how chromophore and protein mutually regulate their conformational changes, yielding the observed spectral shift. Quantum-chemical calculations, based on these structures, provide a deeper understanding of the spectral tuning mechanisms.The three-dimensional (3D) crystal structures of the GAF3 domain of cyanobacteriochrome Slr1393 (Synechocystis PCC6803) carrying a phycocyanobilin chromophore could be solved in both 15-Z dark-adapted state, Pr, λmax = 649 nm, and 15-E photoproduct, Pg, λmax = 536 nm (resolution, 1.6 and 1.86 {\r A}, respectively). The structural data allowed identifying the large spectral shift of the Pr-to-Pg conversion as resulting from an out-of-plane rotation of the chromophore{\textquoteright}s peripheral rings and an outward movement of a short helix formed from a formerly unstructured loop. In addition, a third structure (2.1-{\r A} resolution) starting from the photoproduct crystals allowed identification of elements that regulate the absorption maxima. In this peculiar form, generated during X-ray exposition, protein and chromophore conformation still resemble the photoproduct state, except for the D-ring already in 15-Z configuration and tilted out of plane akin the dark state. Due to its formation from the photoproduct, it might be considered an early conformational change initiating the parental state-recovering photocycle. The high quality and the distinct features of the three forms allowed for applying quantum-chemical calculations in the framework of multiscale modeling to rationalize the absorption maxima changes. A systematic analysis of the PCB chromophore in the presence and absence of the protein environment showed that the direct electrostatic effect is negligible on the spectral tuning. However, the protein forces the outer pyrrole rings of the chromophore to deviate from coplanarity, which is identified as the dominating factor for the color regulation.},
	url = {http://www.pnas.org/content/early/2020/01/17/1910208117.abstract},
	author = {Xu, Xiuling and Port, Astrid and Wiebeler, Christian and Zhao, Kai-Hong and Schapiro, Igor and Wolfgang G{\"a}rtner}
}
