Armon AM, Bedi A, Borin V, Schapiro I, Gidron O. Bending versus Twisting Acenes – A Computational Study. European Journal of Organic Chemistry [Internet]. 2021;2021 (39) :5424 - 5429. Publisher's Version
Riebe S, Adam S, Roy B, Maisuls I, Daniliuc CG, Dubbert J, Strassert CA, Schapiro I, Voskuhl J. Bridged Aromatic Oxo- and Thioethers with Intense Emission in Solution and the Solid State. Chemistry - An Asian Journal [Internet]. 2021;16 (16) :2307 - 2313. Publisher's Version
Rao AG, Wiebeler C, Sen S, Cerutti DS, Schapiro I. Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2. Physical Chemistry Chemical Physics [Internet]. 2021;23 (12) :7359 - 7367. Publisher's Version
Lahav Y, Noy D, Schapiro I. Spectral tuning of chlorophylls in proteins - electrostaticsvs.ring deformation. Physical Chemistry Chemical Physics [Internet]. 2021;23 (11) :6544 - 6551. Publisher's Version
Adam S, Wiebeler C, Schapiro I. Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2. Journal of Chemical Theory and Computation [Internet]. 2021;17 (10) :6302 - 6313. Publisher's Version
Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen H-Y, Vial A, et al. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nature Communications [Internet]. 2021;12 (1). Publisher's Version
Asido M, Kar RK, Kriebel CN, Braun M, Glaubitz C, Schapiro I, Wachtveitl J. Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration. Journal of Physical Chemistry Letters [Internet]. 2021;12 (27) :6284 - 6291. Publisher's Version
Sokolovski SG, Zherebtsov EA, Kar RK, Golonka D, Stabel R, Chichkov NB, Gorodetsky A, Schapiro I, Möglich A, Rafailov EU. Two-photon conversion of a bacterial phytochrome. Biophysical Journal [Internet]. 2021;120 (5) :964 - 974. Publisher's Version
Han Y, Wang Z, Wei Z, Schapiro I, Li J. Binding affinity and mechanisms of SARS-CoV-2 variants. Computational and Structural Biotechnology Journal [Internet]. 2021;19 :4184 - 4191. Publisher's Version
Church JR, Rao AG, Barnoy A, Wiebeler C, Schapiro I. Computational Studies of Photochemistry in Phytochrome Proteins.; 2021 pp. 197 - 226. Publisher's Version
Mroginski M-A, Adam S, Amoyal GS, Barnoy A, Bondar A-N, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, et al. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology [Internet]. 2021;97 (2) :243 - 269. Publisher's Version
Sen S, Kar RK, Borin VA, Schapiro I. Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science [Internet]. 2021. Publisher's Version
Kaufmann JCD, Krause BS, Adam S, Ritter E, Schapiro I, Hegemann P, Bartl FJ. Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR. Biophysical Journal [Internet]. 2020;119 (3) :705 - 716. Publisher's Version
Broser M, Spreen A, Konold PE, Peter E, Adam S, Borin V, Schapiro I, Seifert R, Kennis JTM, Bernal Sierra YA, et al. NeoR, a near-infrared absorbing rhodopsin. Nature Communications [Internet]. 2020;11 (1). Publisher's Version
Kolodny Y, Fererra S, Borin V, Yochelis S, Dibenedetto CN, Mor M, Dehnel J, Remmenik S, Fanizza E, Striccoli M, et al. Tuning Quantum Dots Coupling Using Organic Linkers with Different Vibrational Modes. Journal of Physical Chemistry C [Internet]. 2020;124 (29) :16159 - 16165. Publisher's Version
Slavov C, Fischer T, Barnoy A, Shin H, Rao AG, Wiebeler C, Zeng X, Sun Y, Xu Q, Gutt A, et al. The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome. Proceedings of the National Academy of Sciences [Internet]. 2020 :201921706. Publisher's VersionAbstract
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.
Lazorski MS, Schapiro I, Gaddie RS, Lehnig AP, Atanasov M, Neese F, Steiner UE, Elliott CM. Spin-chemical effects on intramolecular photoinduced charge transfer reactions in bisphenanthroline copper(i)-viologen dyad assemblies. Chemical Science [Internet]. 2020;11 (21) :5511 - 5525. Publisher's VersionAbstract
Two covalently linked donor–acceptor copper phenanthroline complexes (C–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 6–45 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–S mixing through the Δg-mechanism and by a local mode spin–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.
Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez. Galván I, et al. Modern quantum chemistry with [Open]Molcas. The Journal of Chemical Physics [Internet]. 2020;152 (21) :214117. Publisher's Version
Skopintsev P, Ehrenberg D, Weinert T, James D, Kar RK, Johnson PJM, Ozerov D, Furrer A, Martiel I, Dworkowski F, et al. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. [Internet]. 2020. Publisher's VersionAbstract
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–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.