Article
Chemistry, Physical
Partha Malakar, Ishita Das, Sudeshna Bhattacharya, Andrew Harris, Mordechai Sheves, Leonid S. Brown, Sanford Ruhman
Summary: Decades of research on microbial retinal proteins, ion pumps, and sensory photoreceptors have not yielded structure-function indicators for predicting photoisomerization dynamics. However, a new indicator has emerged in this study.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Rodrigo A. Vargas-Hernandez, Chern Chuang, Paul Brumer
Summary: This passage discusses the use of multi-objective optimization to find the best model for multiple target observables, as well as the approximation of predicted errors using Gaussian process models to reduce computational costs.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Chun-Fu Chang, Masae Konno, Keiichi Inoue, Tahei Tahara
Summary: Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily that functions as an unusual inward-proton pump upon absorbing light. The unique chromophore-protein interactions resulting from two major protein structural differences around the chromophore may be responsible for its unusual function. Therefore, it is crucial to understand how these differences affect the primary photoreaction dynamics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Leonardo Barneschi, Danil Kaliakin, Miquel Huix-Rotllant, Nicolas Ferre, Michael Filatov(Gulak), Massimo Olivucci
Summary: This study compares the performance of different electronic structure methods and implementation of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The results show that REKS method behaves differently in some systems compared to other methods, which can be attributed to the effect of the employed density functional approximation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Baptiste Demoulin, Margherita Maiuri, Tetyana Berbasova, James H. Geiger, Babak Borhan, Marco Garavelli, Giulio Cerullo, Ivan Rivalta
Summary: The study shows that modifying the electrostatic environment of the chromophore through protein point mutations can affect its excited state properties, allowing control of its photophysics with the same power as chemical modifications of the chromophore. This fine control is essential for the design of bio-mimetic opto-electronic and photonic devices.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Xuchun Yang, Madushanka Manathunga, Samer Gozem, Jeremie Leonard, Tadeusz Andruniow, Massimo Olivucci
Summary: This study demonstrates the degeneracy between the reactive excited state and a neighboring state in rhodopsin, which causes the splitting of the rhodopsin population into subpopulations after 15 femtoseconds of light absorption. These subpopulations propagate with different velocities and contribute differently to the quantum efficiency. Furthermore, the study reveals that protein electrostatics modulate this splitting and link amino acid sequence variations to quantum efficiency modulation.
Article
Chemistry, Multidisciplinary
Kouhei Hayashi, Misao Mizuno, Hideki Kandori, Yasuhisa Mizutani
Summary: Recent discoveries of light-driven inward proton-pumping rhodopsins have provided new insights into the mechanism of unidirectional transport. By studying Schizorhodopsin, it was found that cis-trans thermal reisomerization precedes reprotonation at the Schiff base, shedding light on the mechanism of proton uptake during inward proton pumping.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Kota Horiuchi, Chiasa Uragami, Ruohan Tao, Daisuke Kosumi, Richard J. Cogdell, Hideki Hashimoto
Summary: This study investigates the roles of cis isomers of carotenoids in light harvesting and photoprotection in photosynthetic bacteria. Carotenoids containing carbonyl groups exhibit efficient energy transfer and their intramolecular charge-transfer (ICT) excited states are crucial in this process. By using spectroscopy techniques, correlations are observed between the decay rate constant of the S1 excited state and the S-0-S-1 energy gap, as well as between the position of the cis-bend and the stabilization of the ICT excited state.
Article
Chemistry, Physical
Taito Urui, Ishita Das, Misao Mizuno, Mordechai Sheves, Yasuhisa Mizutani
Summary: Photoreceptor proteins, such as rhodopsin, play a critical role in light utilization and environmental sensing. The structure of the retinal chromophore in rhodopsins determines the wavelengths of light absorbed. Resonance Raman spectroscopy is an effective tool for studying chromophore structures in proteins. Recent studies on heliorhodopsins, a rhodopsin family, revealed a unique double-band feature in the ethylenic C=C stretching modes, which is attributed to the linear structure of the retinal polyene chain. This linear structure is different from the bent all-trans chromophore found in type-1 rhodopsins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Ramprasad Misra, Ishita Das, Andras Der, Gabor Steinbach, Jin-gon Shim, Wayne Busse, Kwang-Hwan Jung, Laszlo Zimanyi, Mordechai Sheves
Summary: The presence of highly conserved tryptophan residues in microbial rhodopsins is crucial for the charge distribution, quantum yield, photocycle, and absorption properties of the retinal chromophore. Mutations of these residues to non-aromatic leucine or phenylalanine result in increased sensitivity to photobleaching, lower trans-cis photoisomerization yield, and altered photocycle kinetics. These findings suggest that protein-retinal interactions mediated by these tryptophan residues play a key role in achieving efficient light-induced retinal isomerization.
Article
Chemistry, Physical
Seung Noh Lee, Jungsoo Ahn, Taiha Joo
Summary: Time-resolved fluorescence is a powerful tool for identifying emitting states and investigating molecular dynamics in excited states. This study reports the coherent vibrational spectrum of a Schiff base salicylaldehyde azine and demonstrates the use of quantum chemical calculations in identifying emitting species and their states.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Physics, Multidisciplinary
I Tutunnikov, K. Rajitha, A. Yu Voronin, V. V. Nesvizhevsky, I. Sh Averbukh
Summary: The study theoretically examines the behavior of an impulsively excited quantum bouncer, revealing a wave-packet echo effect and suggesting a potential method for investigating ground gravitational quantum states.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Sang Jin Lee, Tae Wu Kim, Jong Goo Kim, Cheolhee Yang, So Ri Yun, Changin Kim, Zhong Ren, Indika Kumarapperuma, Jane Kuk, Keith Moffat, Xiaojing Yang, Hyotcherl Ihee
Summary: This study investigates the light-induced structural transitions of bacteriophytochromes in a liquid solution phase using time-resolved x-ray solution scattering. It reveals the kinetic analysis of the structural species and provides mechanistic insights into how these photoreceptors transmit structural signals and regulate downstream biological responses.
Article
Chemistry, Multidisciplinary
Jin Feng, Baofeng Li, Xinlu Wang, Xinlong Mao, Tengfei Ma, Dapeng Zhang, Siwei Bi
Summary: We studied the relationship between visual function and structural characteristics, focusing on the C=O terminal group, N = 6 conjugation length, and CH3 saturated group. The presence of C=O in the conjugated chain is determined by N = 6, which prevents its occurrence in shorter carotenoids. N = 6 ensures the high stability of retinal and sensitivity to the growth of conjugation length. The electron-withdrawing ability of the saturated group determines its oxidation-reduction ability. Among them, the CH3-saturated retinal has electronic properties closest to H-saturated derivatives. We provide a new perspective on the specificity of retinal structure, contributing to the understanding of the visual mechanism and serving as a foundation for structural improvement and functional expansion of retinal.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Astronomy & Astrophysics
Zhi Qin, Tianrui Bai, Linhua Liu
Summary: Photodissociation processes play a crucial role in interstellar chemistry modeling. A detailed ab initio study of AlH photodissociation was conducted, revealing the pathways and cross sections under different conditions. Applications of the findings in computing photodissociation rates in various radiation fields were discussed.
ASTROPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Juan F. Bada Juarez, Peter J. Judge, Suliman Adam, Danny Axford, Javier Vinals, James Birch, Tristan O. C. Kwan, Kin Kuan Hoi, Hsin-Yung Yen, Anthony Vial, Pierre-Emmanuel Milhiet, Carol V. Robinson, Igor Schapiro, Isabel Moraes, Anthony Watts
Summary: The study reveals significant differences between the ground and dark-adapted states of Archaerhodopsin-3 (AR3), with dynamics of water molecules and internal water networks playing key roles in this desensitization process.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Marvin Asido, Rajiv K. Kar, Clara Nassrin Kriebel, Markus Braun, Clemens Glaubitz, Igor Schapiro, Josef Wachtveitl
Summary: A transient near-UV absorption signature was identified in Krokinobacter eikastus rhodopsin 2 (KR2) which could serve as a marker for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations revealed that this signature corresponds to S-0 -> S-3 and/or S-0 -> S-5 transitions, and these transitions show negligible spectral shift with changes in the protein environment. The study also explored potential optogenetic applications through near-UV quenching experiments, demonstrating ultrafast regeneration of the parent state of KR2.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Saumik Sen, Rajiv K. Kar, Veniamin A. Borin, Igor Schapiro
Summary: The photoisomerization of retinal is a crucial primary event in the rhodopsin protein family, highly optimized in the protein for ultrafast, selective, and efficient reactions. Space saving mechanisms based on the rotation of multiple double bonds have been proposed to elucidate the highly complex process inside the protein.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Physical
Partha Malakar, Veniamin Borin, Anjan Bedi, Igor Schapiro, Ori Gidron, Sanford Ruhman
Summary: This study investigates the effect of twisting on the photophysics of acenes, revealing that twisting can influence the rate of intersystem crossing. Quantum chemical calculations explain this effect as an increase in spin-orbit coupling. Additionally, the study observes structural reorganization and coherent vibrational wave packet motions in S-1, reflected in transient spectral changes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Jonathan R. Church, Gil S. Amoyal, Veniamin A. Borin, Suliman Adam, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. By substituting glutamine with leucine, the absorption wavelength of PR can be tuned, allowing it to adapt to different depths in the ocean. Our study reveals the tuning mechanism and provides guidance for rational design of spectral shifts.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Ya-Nan Hou, Astrid Hoeppner, Aditya G. Rao, Yigal Lahav, Prabir Kumar Das, Wen-Long Ding, Xiang-Xiang Jiang, Ji-Ling Hu, Igor Schapiro, Dror Noy, Kai-Hong Zhao
Summary: The molecular structure of mBDFP, a far-red fluorescent protein, was analyzed and found to have a unique attachment of its biliverdin chromophore. Spectral shifts can be induced by modifying a single residue, allowing for the rational design of far-red and near-infrared FPs which are important for bioimaging.
Article
Multidisciplinary Sciences
Riccardo Palombo, Leonardo Barneschi, Laura Pedraza-Gonzalez, Daniele Padula, Igor Schapiro, Massimo Olivucci
Summary: This study presents a computational model for the highly fluorescent Neorhodopsin protein, explaining its fluorescence enhancement through charge confinement during the isomerization process. The model successfully replicates the experimental observables, providing insights into the design of more effective optogenetic tools.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Yonatan Sukhran, Israel Alshanski, Ofer Filiba, Megan J. Mackintosh, Igor Schapiro, Mattan Hurevich
Summary: Designing and synthesizing orthogonally protected monosaccharide building blocks is important for the controlled preparation of defined oligosaccharides. This study investigates the selective introduction of protecting groups and the unexpected reactivity of a conformationally restricted galactoside. The insights gained from this research offer a new strategy for acylation reactions and can be applied in the synthesis of key monomeric building blocks.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tzuriel S. Metzger, Harikrishna Batchu, Anil Kumar, Daniil A. Fedotov, Naama Goren, Deb Kumar Bhowmick, Israa Shioukhi, Shira Yochelis, Igor Schapiro, Ron Naaman, Ori Gidron, Yossi Paltiel
Summary: Chirality is a fundamental property in nature, and chiral molecules exist in two forms, each being a mirror image of the other. The chirality of molecules is related to their optical activity, and circular dichroism is often used to determine the chirality of chiral molecules. Recently, the chiral induced spin selectivity (CISS) effect was discovered, showing that electron transfer within chiral molecules depends on the electron's spin. This study found that the CISS properties are similar for the two enantiomers when adsorbed on a metal substrate, while on a nonmetallic surface, the preferred spin depends on the molecule's chirality. The correlation between optical activity and CISS effect suggests a relation to the global polarizability of the molecule.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
David Buhrke, Yigal Lahav, Aditya Rao, Jeannette Ruf, Igor Schapiro, Peter Hamm
Summary: In this study, the researchers explored a cyanobacteriochrome called Slr1393-g3, which can switch between red-absorbing and green-absorbing forms. They used advanced IR spectroscopic methods to track the intermediates during the photocycle and discovered a new intermediate with distinct spectroscopic features. Additionally, they measured the vibrational couplings and structural disorder in these intermediate states using stationary and transient 2D IR experiments. Anharmonic QM/MM calculations were also performed to predict the spectra and suggest structural changes of the intermediates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Jonathan R. Church, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: Multiscale simulations have been used to calculate excitation energies in complex systems, with the chromophore treated quantum mechanically and the protein and environment described classically. Electrostatic embedding and polarizable embedding were compared for their effect on excitation energies in two different proteins. Results showed that polarizable embedding produces absorption maxima closer to experimental values and recovers a significant portion of the quantum mechanical improvement in excitation energies. A detailed analysis revealed that aromatic residues have the largest influence on excitation energy.
BIOPHYSICS AND PHYSICOBIOLOGY
(2023)
Article
Chemistry, Physical
Aditya G. G. Rao, Igor Schapiro
Summary: Phytochromes are photoreceptors that undergo photoisomerization upon light illumination, and this study focused on the photoisomerization of chromophore models based on phycocyanobilin. By introducing substitutions into the model, it was found that the isomerization mechanism and preference can be changed.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ofer Filiba, Veniamin A. Borin, Igor Schapiro
Summary: In this study, the possible involvement of triplet states in the photoisomerization of retinaloids was investigated using the extended multistate (XMS) version of CASPT2. The calculation results of energy positions, spin-orbit coupling matrix elements, etc. revealed differences in the characteristics of different retinaloids during the photoisomerization process.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Jonathan R. Church, Jogvan Magnus Haugaard Olsen, Igor Schapiro
Summary: This study analyzes the absorption spectra and structural changes of jumping spider rhodopsin-1 (JSR1) through hybrid QM/MM simulations, revealing that the distance of a nearby tyrosine residue plays a significant role in predicting the absorption maximum.
Article
Chemistry, Physical
Yigal Lahav, Dror Noy, Igor Schapiro
Summary: In photosynthetic complexes, the tuning of chlorophyll light-absorption spectra by the protein environment is crucial. Analysis shows that geometric distortions like chlorophyll ring deformation and direct polarization of electron density are the main factors contributing to the spectral shift. Protein electrostatics is easier to manipulate than chlorophyll conformations, making it more readily implementable in designing artificial protein-chlorophyll complexes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Brandon P. Russell, David J. Vinyard
Summary: The Mn4CaO5 oxygen-evolving complex in Photosystem II is crucial for water oxidation. D1 residue R334 participates in proton release and interacts with PsbO. A D1-R334G mutant destabilizes the OEC but stabilizes the S2 intermediate.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Alexander A. Bulychev, Tatiana S. Strelets
Summary: Excitable cells of higher plants and characean algae respond to stressful stimuli by generating action potentials that influence chlorophyll fluorescence and photosynthesis for an extended period of time. While plant leaves exhibit a reversible depression in the efficiency of photosystem II reaction after an individual action potential, characean algae show long-lasting oscillations of photosystem II reaction efficiency after firing an action potential. This study investigates the possible mechanisms behind these oscillations and suggests that they are a result of metabolic rearrangements in chloroplasts and the cyclosis cessation-recovery cycle induced by calcium influx during action potentials. The findings also indicate that fluidic communications between different cell regions play a role in these oscillations, and the inhibition of oscillations occurs when these communications are restricted or eliminated.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Dmitry Zlenko, Elena A. Protasova, Georgy Tsoraev, Nikolai N. Sluchanko, Dmitry A. Cherepanov, Thomas Friedrich, Baosheng Ge, Song Qin, Eugene G. Maksimov, Andrew B. Rubin
Summary: The conformation of chromophores in isolated phycobiliproteins is heterogeneous, but not in the entire phycobilisome (PBS). Under low-energy excitation, there is no significant uphill energy transfer from the core to the peripheral rods of the PBS, while transfer from the terminal emitters to bulk allophycocyanin chromophores is highly probable.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
Article
Biochemistry & Molecular Biology
Makio Yokono, Chiyo Noda, Jun Minagawa
Summary: This paper investigates the energy transfer between Photosystem II and Photosystem I in Arabidopsis thaliana, and finds that the fast spillover is reversibly regulated depending on pH.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2024)
