Article
Multidisciplinary Sciences
Se-Hwan Kim, Kimleng Chuon, Shin-Gyu Cho, Ahreum Choi, Seanghun Meas, Hyun-Suk Cho, Kwang-Hwan Jung
Summary: Microbial rhodopsins, including the newly discovered heliorhodopsins, have similar structural features but different spectral characteristics. By studying and mutating various heliorhodopsins, researchers identified key residues that influence spectral changes. Homology modeling was used to predict the 3D structure of Thermoplasmatales heliorhodopsin, and the color-tuning mechanism of type-I rhodopsin was found to be applicable to understanding heliorhodopsin color-tuning.
SCIENTIFIC REPORTS
(2021)
Article
Biophysics
Gaoshang Li, Yongnan Hu, Sizhu Pei, Jiajia Meng, Jiayu Wang, Ju Wang, Shuai Yue, Zhuan Wang, Shufeng Wang, Xinfeng Liu, Yuxiang Weng, Xubiao Peng, Qing Zhao
Summary: By recording ultrafast transient absorption spectra of three mutants of a rhodopsin mimic based on cellular retinoic acid-binding protein II in an acidic environment, this study investigates the excited-state dynamics of the all-trans protonated RSB. The experimental results suggest that aromatic residues near the b-ionone ring structure may help stabilize the AT-PRSB and slow down its isomerization rate, providing implications for designing rhodopsin-like proteins with significant infrared fluorescence.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Masuzu Kikuchi, Keiichi Kojima, Shin Nakao, Susumu Yoshizawa, Shiho Kawanishi, Atsushi Shibukawa, Takashi Kikukawa, Yuki Sudo
Summary: Microbial rhodopsins are photoswitchable seven-transmembrane proteins found in archaea, bacteria, and eukarya. Eukaryotic rhodopsin OmR2 from the dinoflagellate Oxyrrhis marina was successfully expressed in E. coli cells, exhibiting outward proton-pumping activity. Spectroscopic characterization revealed similarities between OmR2 and known eukaryotic proton pump rhodopsins, potentially advancing our understanding and utilization of eukaryotic rhodopsins.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
R. Astashkin, K. Kovalev, S. Bukhdruker, S. Vaganova, A. Kuzmin, A. Alekseev, T. Balandin, D. Zabelskii, I Gushchin, A. Royant, D. Volkov, G. Bourenkov, E. Koonin, M. Engelhard, E. Bamberg, V Gordeliy
Summary: This study presents the high-resolution structures of the SyHR protein from the cyanobacterial anion pumps family, providing insights into the molecular mechanisms of SyHR and cyanobacterial anion pumps in general.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Jasmine N. Tutol, Jessica Lee, Hsichuan Chi, Farah N. Faizuddin, Sameera S. Abeyrathna, Qin Zhou, Faruck Morcos, Gabriele Meloni, Sheel C. Dodani
Summary: The power of protein engineering was demonstrated by converting the fluorescent proton-pumping rhodopsin GR into GR1, a red-shifted, turn-on fluorescent sensor for chloride. GR1 provides a pH-dependent response in detergent micelles and live Escherichia coli, offering a reversible, ratiometric readout of changes in extracellular chloride.
Article
Biochemistry & Molecular Biology
Kirill Kovalev, Fedor Tsybrov, Alexey Alekseev, Vitaly Shevchenko, Dmytro Soloviov, Sergey Siletsky, Gleb Bourenkov, Michael Agthe, Marina Nikolova, David von Stetten, Roman Astashkin, Sergey Bukhdruker, Igor Chizhov, Antoine Royant, Alexander Kuzmin, Ivan Gushchin, Riccardo Rosselli, Francisco Rodriguez-Valera, Nikolay Ilyinskiy, Andrey Rogachev, Valentin Borshchevskiy, Thomas R. Schneider, Ernst Bamberg, Valentin Gordeliy
Summary: By studying a bacterial inward proton-pumping rhodopsin, researchers have uncovered its molecular mechanism and revealed how proton wires mediate ion selectivity and proton transport through cell membrane. Proton transport is essential for cell life and understanding the mechanisms behind it is a challenge. The study presents a comprehensive function-structure analysis of a light-driven bacterial inward proton pump, providing insights into proton translocation and the use of synchrotron source for rhodopsin studies. The results also have implications for optogenetics.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Gustavo Cardenas, Vincent Ledentu, Miquel Huix-Rotllant, Massimo Olivucci, Nicolas Ferre
Summary: The ARM+MEM protocol incorporates all relevant protonation microstates to provide a more accurate modeling of rhodopsins' absorption spectrum. By simulation on a toy model and Anabaenasensory rhodopsin, it is confirmed that considering multiple microstates improves the description of the absorption spectrum.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Yuya Ohki, Tsukasa Shinone, Sayo Inoko, Miu Sudo, Makoto Demura, Takashi Kikukawa, Takashi Tsukamoto
Summary: Previous research on anion channelrhodopsins (ACRs) overlooked the native functions of full-length ACRs and the potential role of the cytoplasmic domain (CPD). In this study, we expressed the full-length Guillardia theta ACR1 (GtACR1_full) and found that the CPD enhanced NO3- transport, suggesting its natural function in algal cells.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
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
Biochemistry & Molecular Biology
Sijin Chen, Xiaoyan Ding, Chao Sun, Anthony Watts, Xiao He, Xin Zhao
Summary: The study investigated the dynamic coupling of Y185 with the bR photocycle through calculations and simulations, revealing its significant role in regulating thermal equilibrium, stabilizing H-bond networks, participating in orientation switch, and opening the channel gate. These findings provide a detailed molecular mechanism of the dynamic couplings of Y185 and the bR photocycle from a structural perspective, with potential applications to other microbial photoreceptors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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, Physical
Vinicius Manzoni, Rogerio Gester, Antonio R. da Cunha, Tarciso Andrade-Filho, Rodrigo Gester
Summary: The analysis of solvent effects on the fluorescence and NLO response of thieno[3,4-b]pyrazine was done using s-MC/QM method, showing potential applications in solar cells and biological markers. EC plays a key role in the first hyperpolarizability, with solvent effects being negligible.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Multidisciplinary Sciences
Jessica E. Besaw, Jorg Reichenwallner, Paolo De Guzman, Andrejs Tucs, Anling Kuo, Takefumi Morizumi, Koji Tsuda, Adnan Sljoka, R. J. Dwayne Miller, Oliver P. Ernst
Summary: In this study, the crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) was determined under low pH conditions. The structure revealed the accommodation of a chloride anion in the hydrophilic Schiff base cavity (SBC), stabilizing the protonated retinal Schiff base. Computational studies further supported an intramolecular signaling transduction pathway, with allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space. These findings suggest the potential sensory role of TaHeR as a rhodopsin.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Orawan Jakdetchai, Peter Eberhardt, Marvin Asido, Jagdeep Kaur, Clara Nassrin Kriebel, Jiafei Mao, Alexander J. Leeder, Lynda J. Brown, Richard C. D. Brown, Johanna Becker-Baldus, Christian Bamann, Josef Wachtveitl, Clemens Glaubitz
Summary: This study on the functional mechanism of the light-driven sodium pump KR2 uses solid-state nuclear magnetic resonance spectroscopy to reveal the interconversion of photointermediates and the perturbation caused by the nearby bound sodium ion. The findings suggest a mechanism different from traditional principles, highlighting the importance of understanding the role of sodium ion in retinal conformation changes.
Article
Chemistry, Multidisciplinary
Cui Liu, Yang Ren, Xiao-qin Gao, Xue Du, Zhong-zhi Yang
Summary: This study developed a new simulation method to accurately simulate the mechanism of DNA glycosylase removing damaged bases. The results confirm that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. This research provides a theoretical basis for the study of DNA glycosylase excising damaged bases.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Monja Sokolov, Beatrix M. Bold, Julian J. Kranz, Sebastian Hofener, Thomas A. Niehaus, Marcus Elstner
Summary: The study reports the derivation and implementation of analytical nuclear gradients for TD-LC-DFTB in the DFTB+ program, showing high accuracy in benchmark tests. The application of seminumerical second derivatives allows for simulation of vibrationally resolved UV/vis spectra.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Claudia L. Gomez-Flores, Denis Maag, Mayukh Kansari, Van-Quan Vuong, Stephan Irle, Frauke Graeter, Tomas Kubar, Marcus Elstner
Summary: This paper investigates the generation of free energy surfaces in complex reactions using the semiempirical method DFTB and improves its accuracy by developing a specific reaction parametrization (SRP). Through the implementation of an artificial neural network (ANN), the authors successfully generate highly accurate free energy surfaces for thiol-disulfide exchange in two molecular complexes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Sara Roosta, Farhad Ghalami, Marcus Elstner, Weiwei Xie
Summary: The present study systematically examines the performance of two approximations in the simulations of charge transport in organic semiconductors. The results show that the proposed methods can achieve consistent results with standard simulations at reduced computational cost. The study also highlights the importance of the reorganization energy in determining the charge carrier mobility and its sensitivity to the choice of DFT functionals.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Samaneh Inanlou, Rodrigo Cortes-Mejia, Ali Deniz Oezdemir, Sebastian Hoefener, Wim Klopper, Wolfgang Wenzel, Weiwei Xie, Marcus Elstner
Summary: In this study, the absorption spectra of CBP in gas and condensed phases were simulated using the TD-LC-DFTB method. The accuracy of the computed spectra was verified by comparing with experimental results. Static and dynamic disorders play a crucial role in accurately calculating absorption spectra, and a reasonable structural model is important for representing these disorders.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ziwei Pang, Monja Sokolov, Tomas Kubar, Marcus Elstner
Summary: In this study, molecular dynamics simulations were used to investigate the mechanism of glucose binding in GGBP mutant and wild-type proteins. The simulations provided insights into changes in the hydrogen-bonding network and chromophore conformations upon glucose binding, which can help optimize the design of glucose sensors.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Bastian Kraft, Susanne Wagner, Karl G. Schell, Michael J. Hoffmann
Summary: The electrical conductivity of Nb-Al2O3 composite materials prepared using the Field-assisted sintering technique (FAST) was investigated. The study found that the percolation threshold is influenced by the particle size of the starting powders and the volume contents of the refractory metal. The microstructure was also found to affect the resulting material properties at the macroscopic scale.
ADVANCED ENGINEERING MATERIALS
(2022)
Correction
Chemistry, Physical
B. Hourahine, B. Aradi, V. Blum, F. Bonafe, A. Buccheri, C. Camacho, C. Cevallos, M. Y. Deshaye, T. Dumitrica, A. Dominguez, S. Ehlert, M. Elstner, T. van der Heide, J. Hermann, S. Irle, J. Jakowski, J. J. Kranz, C. Koehler, T. Kowalczyk, T. Kubar, I. S. Lee, V. Lutsker, R. J. Maurer, S. K. Min, I. Mitchell, C. Negre, T. A. Niehaus, A. M. N. Niklasson, A. J. Page, A. Pecchia, G. Penazzi, M. P. Persson, J. Rezac, C. G. Sanchez, M. Sternberg, M. Stohr, F. Stuckenberg, A. Tkatchenko, V. W. -Z. Yu, T. Frauenheim
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Julian Boeser, Tomas Kubar, Marcus Elstner, Denis Maag
Summary: This study investigates the mechanism of glutaredoxin catalyzed oxidation and reduction of protein disulfide bonds through both experimental and computational approaches. Molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical metadynamics simulations were used to obtain the free energy profiles of the reactions. The results confirm the proposed pathway and provide insights into the regiospecificity of the reactions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Lisa Ross, Julius Reitemeier, Farhad Ghalami, Wen-Shan Zhang, Jurgen H. Gross, Frank Rominger, Sven M. Elbert, Rasmus Schroeder, Marcus Elstner, Michael Mastalerz
Summary: In this study, the solution and solid-state behavior of two-dimensionally triptycene end-capped QPPs were investigated. QPPs were synthesized through condensation reactions with pyrene-based tetraketone and ortho-diamines, resulting in the formation of dimers in solution, supported by MALDI-TIMS-TOF-MS analysis. Single-crystal X-ray analysis showed a short p-p distance of 3.3-3.4 angstrom and a perfect shape match during the dimerization of triptycene end-capped QPPs, indicating its potential as a synthon for crystal engineering.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Review
Biophysics
T. Kubar, M. Elstner, Q. Cui
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are essential for studying biomolecules. This article reviews the methodology of QM/MM approaches and their application to energy transduction in biomolecular machines. The importance of balancing efficiency and accuracy is emphasized, and examples showcase the value and limitations of QM/MM methodologies. Suggestions for further development in making QM/MM analyses more quantitative and applicable to complex biological problems are discussed.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Chemistry, Physical
Denis Maag, Josua Boeser, Henryk A. Witek, Ben Hourahine, Marcus Elstner, Tomas Kubar
Summary: Coupled-perturbed equations for degenerate orbitals were implemented to study proton-coupled electron transfer reactions. The method was tested for both QM and QM/MM setups and showed stable enhanced sampling simulations. The obtained potentials of the mean force successfully described the thermodynamic and kinetic features of the reactions, making it a promising tool for investigating more complex systems like proteins.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Philipp M. Dohmen, Mila Kramer, Patrick Reiser, Pascal Friederich, Marcus Elstner, Weiwei Xie
Summary: In this study, the surface hopping method is used to simulate charge transport in organic semiconductors. Nonadiabatic molecular dynamics simulations are performed to study hole transport in anthracene and pentacene. Neural network based Hamiltonians are employed in two different nuclear relaxation schemes, and their performance in reproducing hole mobilities and inverse participation ratios is evaluated. The results show that the neural network models are able to accurately reproduce the desired properties with significantly reduced computational cost compared to traditional methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Ali Deniz Ozdemir, Samaneh Inanlou, Franz Symalla, Weiwei Xie, Wolfgang Wenzel, Marcus Elstner
Summary: This paper investigates the impact of structural disorder in amorphous organic semiconductors (OSCs) on the transfer parameters and charge mobilities. A sampling strategy for incorporating static and dynamic structural disorder is developed using QM/MM methods and extensive MD sampling. The results show that dynamic disorder causes an order of magnitude difference in the calculated mobility between morphologies of the same material. The method allows for the sampling of disorder in HOMO energies and couplings, and the statistical analysis characterizes the relevant time scales for charge transfer in these complex materials.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Hematology
Fabian Kutzki, Diego Butera, Angelina J. Lay, Denis Maag, Joyce Chiu, Heng-Giap Woon, Tomas Kubar, Marcus Elstner, Camilo Aponte-Santamaria, Philip J. Hogg, Frauke Graeter
Summary: This study revealed the oxidation state of disulfide bridges in the VWF-C4 domain and its implications for VWF's platelet binding function. It was found that two major force-bearing disulfide bonds are partially reduced in human blood, leading to conformational changes within C4 that affect the accessibility of the integrin-binding motif and impair integrin-mediated platelet binding. Additionally, specific thiol/disulfide exchanges between the reduced species and the remaining disulfide bridges were observed, with mechanical force potentially enhancing the proximity of reactant cysteines and further affecting integrin binding propensity.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2023)
Article
Materials Science, Multidisciplinary
Niklas J. Herrmann, Nadine von Coelln, Robin M. Teichgreber, Sebastian Hoefener, Christian Huck, Farhad Ghalami, Simon Settele, Manuel Hertzog, Marcus Elstner, Petra Tegeder, Eva M. Herzig, Jana Zaumseil
Summary: In this study, meniscus-guided zone-casting was used to selectively deposit two different polymorphs of PDIF-CN2 from solution. The two polymorphs can be distinguished by their characteristic low-wavenumber Raman modes and distinctive photoluminescence spectra, reflecting different intermolecular coupling. Despite having different crystalline structures, field-effect transistors based on thin films of both polymorphs show similar electron mobilities.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)