Review
Biotechnology & Applied Microbiology
Natalie Chia, Sang Yup Lee, Yaojun Tong
Summary: Optogenetics technique provides a solution to chemical induction with dynamic control and low cost. It utilizes genetically encodable light-sensing modules to fine tune gene expression and protein activity. Recent advancements in microbial synthetic biology have been achieved, but more portable optogenetic tools need to be developed.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Physiology
Fei Lin, Ruijing Tang, Chong Zhang, Nicole Scholz, Georg Nagel, Shiqiang Gao
Summary: Researchers developed a novel optogenetic toolkit by combining light-gated anion channel GtACR1 with either light-gated K+ channel HcKCR1 or the new Na+ channelrhodopsin HcNCR1, allowing non-invasive manipulation of water transport in Xenopus oocytes. Water efflux was achieved by activating K+ and Cl- efflux through HcKCR1 and GtACR1, while water influx was triggered by inward movement of Na+ and Cl- through GtACR1 co-expressed with HcNCR1.
PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY
(2023)
Article
Ecology
Alexander L. Jaffe, Masae Konno, Yuma Kawasaki, Chihiro Kataoka, Oded Beja, Hideki Kandori, Keiichi Inoue, Jillian F. Banfield
Summary: This study found that Saccharibacteria Type-1 rhodopsins function as outward proton pumps and can rapidly uptake the chromophore retinal. The co-occurring microorganisms with Saccharibacteria showed evidence of the ability to produce retinal from beta-carotene, suggesting a potential association between them.
Review
Biochemistry & Molecular Biology
Xiao Min Zhang, Tatsushi Yokoyama, Masayuki Sakamoto
Summary: Membrane potential, a critical parameter reflecting neuron excitability, is traditionally measured invasively by electrodes, but new fluorescent probe technologies offer high spatiotemporal resolution for individual cell activity. Genetically encoded voltage indicators show superior performance in accurately targeting genetic populations and revealing neuronal dynamics. Microbial rhodopsins, commonly used in optogenetics to manipulate neuronal activities, can also serve as fluorescent voltage indicators, with recent advances in their design and application summarized in this review.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Leonid S. Brown
Summary: In the past twenty years, there have been significant breakthroughs in understanding the rules and mechanisms of proton transport in microbial rhodopsins, transitioning from atomic-level understanding to a confounding variety of new homologs. This review summarizes and discusses experimental data obtained on new microbial rhodopsin variants, with a focus on the vectoriality of proton transport and their structural determinants.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Multidisciplinary Sciences
Sandra Mous, Guillaume Gotthard, David Ehrenberg, Saumik Sen, Tobias Weinert, Philip J. M. Johnson, Daniel James, Karol Nass, Antonia Furrer, Demet Kekilli, Pikyee Ma, Steffen Bruenle, Cecilia Maria Casadei, Isabelle Martiel, Florian Dworkowski, Dardan Gashi, Petr Skopintsev, Maximilian Wranik, Gregor Knopp, Ezequiel Panepucci, Valerie Panneels, Claudio Cirelli, Dmitry Ozerov, Gebhard F. X. Schertler, Meitian Wang, Chris Milne, Joerg Standfuss, Igor Schapiro, Joachim Heberle, Przemyslaw Nogly
Summary: By combining time-resolved crystallography, spectroscopy, and multiscale simulations, we have elucidated the molecular mechanism and structural dynamics of a chloride-pumping rhodopsin throughout the transport cycle. We identified transient anion-binding sites, provided evidence for the use of light energy in the pumping mechanism, and discovered molecular gates that ensure unidirectional transport. These findings reveal key mechanistic features that enable finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.
Article
Biochemistry & Molecular Biology
Jikang Xu, Qifan Yang, Baofu Ma, Longjie Li, Fei Kong, Lan Xiao, Deliang Chen
Summary: This study presents a novel approach to evaluate K+ uptake and demonstrates the K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called NdR2. Unlike previous studies, this research shows that NdR2 is able to uptake intracellular K+ without requiring structural modifications. This discovery expands the options for future K+ pump designs and provides a valuable reference for the development of optogenetic tools and other applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Qifan Yang, Deliang Chen
Summary: This review focuses on the importance of Na+ pump research, particularly on the structural and functional studies of the light-driven Na+-pumping rhodopsin (NaR). Key areas of investigation include uncovering the translocation pathway of Na+, examining the role of structural changes in the photocycle for Na+ transport, and investigating the timing of Na+ uptake/release.
Article
Biochemistry & Molecular Biology
Julia Dietler, Roman Schubert, Tobias G. A. Krafft, Simone Meiler, Stephanie Kainrath, Florian Richter, Kristian Schweimer, Michael Weyand, Harald Janovjak, Andreas Moeglich
Summary: Sensory photoreceptors can regulate the physiology, behavior, and development of organisms in response to light, making them useful in optogenetics for controlling diverse cellular processes. This study demonstrates that certain LOV modules can modulate protein expression by light, and some photoreceptors can also function as temperature sensors, potentially impacting their applications in optogenetics and biotechnology.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Neurosciences
Jessica McNeill, Christopher Rudyk, Michael E. Hildebrand, Natalina Salmaso
Summary: Astrocytes are electrically dynamic cells with diverse electrophysiological properties, including polarization, ion channel expression, and intracellular Ca2+ signaling. They play crucial roles in regulating K+ and expressing various types of Na+ channels, with different functional properties at regional and cellular levels.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Shigekazu Oda, Emi Sato-Ebine, Akinobu Nakamura, Koutarou D. Kimura, Kazuhiro Aoki
Summary: Optogenetic techniques responsive to red/near-infrared light were successfully implemented in C. elegans, allowing manipulation of cell signaling and induction of defecation motor program. These tools will greatly contribute to elucidating the molecular mechanisms underlying C. elegans behaviors.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biology
Jong S. Park, Austin M. Gabel, Polina Kassir, Lois Kang, Prableen K. Chowdhary, Afia Osei-Ntansah, Neil D. Tran, Soujanya Viswanathan, Bryanna Canales, Pengfei Ding, Young-Sam Lee, Rachel Brewster
Summary: Lack of oxygen can be detrimental to cell function and survival, and this study demonstrates the role of the ndrg1a gene in hypoxia adaptation in zebrafish embryos. ndrg1a is involved in degrading ATPase, which helps maintain cellular energy homeostasis.
Review
Materials Science, Biomaterials
Armin Baumschlager, Mustafa Khammash
Summary: Light has become an established tool in biology for visualizing, investigating, and steering biological systems. This review discusses the unique features of light in biology, its progression in control mechanisms, and focuses on the application of transcriptional light regulators in synthetic biology.
Review
Agricultural Engineering
Hao Gao, Clarisse Manishimwe, Lu Yang, Hanxiao Wang, Yujia Jiang, Wankui Jiang, Wenming Zhang, Fengxue Xin, Min Jiang
Summary: Synthetic microbial consortia offer a versatile platform for biochemicals production, but their unmatched growing conditions, low stability, and low production efficiency hinder their further applications. This review comprehensively summarizes the progress of synthetic light-driven microbial consortia for chemicals production and discusses the potential of space efficient synthetic light-driven microbial consortia in hydrogel systems.
BIORESOURCE TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Kai Xiao, Paolo Giusto, Fengxiang Chen, Ruotian Chen, Tobias Heil, Shaowen Cao, Lu Chen, Fengtao Fan, Lei Jiang
Summary: The study demonstrates the use of a TiO2/C3N4 semiconductor heterojunction nanotube membrane for light-driven directional ion transport, showing similar performance to biological systems. This system can also be used for enhanced osmotic energy generation and holds potential for applications such as water desalination.
NATIONAL SCIENCE REVIEW
(2021)
Article
Biochemistry & Molecular Biology
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, Valentin Gordeliy, Ivan Gushchin
Summary: This study utilized molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope protein in its monomeric form, identifying the orientation of its different components and their influence by factors like palmitoylation and glycosylation. The protein was found to localize at curved regions of the membrane, potentially aiding in oligomer assembly. These results contribute to a better understanding of the function of the coronaviral E protein and viroporins in general, and may help in combating the ongoing SARS-CoV-2 pandemic.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Review
Chemistry, Multidisciplinary
Philipp S. Orekhov, Marine E. Bozdaganyan, Natalia Voskoboynikova, Armen Y. Mulkidjanian, Maria G. Karlova, Anna Yudenko, Alina Remeeva, Yury L. Ryzhykau, Ivan Gushchin, Valentin I. Gordeliy, Olga S. Sokolova, Heinz-Juergen Steinhoff, Mikhail P. Kirpichnikov, Konstantin V. Shaitan
Summary: Amphiphilic copolymers with alternating hydrophilic and hydrophobic units can extract membrane proteins directly from lipid membranes, forming nanoparticles suitable for various spectroscopy and biophysical techniques. Copolymer-encased nanolipoparticles have proven to be important in structural biology applications such as cryo-electron microscopy.
Review
Biochemistry & Molecular Biology
Alexey V. Vlasov, Stepan D. Osipov, Nikolay A. Bondarev, Vladimir N. Uversky, Valentin Borshchevskiy, Mikhail F. Yanyushin, Ilya Manukhov, Andrey Rogachev, Anastasiia D. Vlasova, Nikolay S. Ilyinsky, Alexandr Kuklin, Norbert A. Dencher, Valentin Gordeliy
Summary: ATP synthases are unique molecular machines that synthesize ATP and play important roles in cellular bioenergetics. Understanding their structure and function can lead to the development of new therapies and tools for controlling cellular energy.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Valentin Borshchevskiy, Kirill Kovalev, Ekaterina Round, Rouslan Efremov, Roman Astashkin, Gleb Bourenkov, Dmitry Bratanov, Taras Balandin, Igor Chizhov, Christian Baeken, Ivan Gushchin, Alexander Kuzmin, Alexey Alekseev, Andrey Rogachev, Dieter Willbold, Martin Engelhard, Ernst Bamberg, Georg Buldt, Valentin Gordeliy
Summary: High-resolution structures of bacteriorhodopsin reveal the important roles of hydrogen bond chains and low-barrier hydrogen bonds in proton transport and storage, as well as long-range communication and signaling in proteins.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biology
Igor Melnikov, Philipp Orekhov, Maksim Rulev, Kirill Kovalev, Roman Astashkin, Dmitriy Bratanov, Yury Ryzhykau, Taras Balandin, Sergei Bukhdruker, Ivan Okhrimenko, Valentin Borshchevskiy, Gleb Bourenkov, Christoph Mueller-Dieckmann, Peter van der Linden, Philippe Carpentier, Gordon Leonard, Valentin Gordeliy, Alexander Popov
Summary: This work examines the molecular-level interactions between small hydrophobic molecules and membrane proteins (MPs), particularly focusing on noble gases and their potential role in anesthesia.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elena L. Bolkhovitina, Julia D. Vavilova, Andrey O. Bogorodskiy, Yuliya A. Zagryadskaya, Ivan S. Okhrimenko, Alexander M. Sapozhnikov, Valentin Borshchevskiy, Marina A. Shevchenko
Summary: In this study, it was found that induction of RBD-specific antibodies stimulates the activation of mature neutrophils in response to RBD-coated particles without triggering excessive inflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Elizaveta Lyapina, Egor Marin, Anastasiia Gusach, Philipp Orekhov, Andrey Gerasimov, Aleksandra Luginina, Daniil Vakhrameev, Margarita Ergasheva, Margarita Kovaleva, Georgii Khusainov, Polina Khorn, Mikhail Shevtsov, Kirill Kovalev, Sergey Bukhdruker, Ivan Okhrimenko, Petr Popov, Hao Hu, Uwe Weierstall, Wei Liu, Yunje Cho, Ivan Gushchin, Andrey Rogachev, Gleb Bourenkov, Sehan Park, Gisu Park, Hyo Jung Hyun, Jaehyun Park, Valentin Gordeliy, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov
Summary: This study reports the crystal structure of the S1P(5) receptor in complex with a selective inverse agonist, revealing an allosteric subpocket and shedding light on inverse agonism in S1P receptors.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Marina Goncharuk, Nadezhda S. Baleeva, Dmitry E. Nolde, Alexey S. Gavrikov, Alexey Mishin, Alexander S. Mishin, Andrey Y. Sosorev, Alexander S. Arseniev, Sergey A. Goncharuk, Valentin Borshchevskiy, Roman G. Efremov, Konstantin S. Mineev, Mikhail S. Baranov
Summary: This study describes the rational design of enhanced FAST mutants optimized for the N871b fluorogen. Through structural analysis, NMR relaxation analysis, and computer simulations, the study identifies mobile regions in the complex and suggests mutations that could stabilize both the protein and the ligand. The experimental results show that the mutants exhibit higher brightness and provide up to 35% enhancement for several other fluorogens of similar structure, both in vitro and in vivo.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Physical
Noora Aho, Pavel Buslaev, Anton Jansen, Paul Bauer, Gerrit Groenhof, Berk Hess
Summary: Molecular dynamics simulations are widely used for computing atomistic trajectories of complex systems. However, considering constant pH in simulations is more challenging. To overcome this limitation, researchers have implemented an alternative scheme for interpolating the Hamiltonians of protonation states and a simpler scheme for modeling side chains with multiple titratable sites.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Business, Finance
V. Borshchevskiy, V. Chemeris, N. Khomyuk, V. Lyublin
Summary: The purpose of this research is to identify the priority directions for enhancing the financial and investment potential of Ukrainian regions amidst the challenges of globalization and security threats. The study focuses on various components of financial and investment potential, including the financial and budgetary capacity of the regions, market potential for investment, and the ability to attract resources through co-financing and lending. The research highlights the importance of institutional processes, cooperation with businesses and investors, human and social capital, and regional infrastructure development in shaping the financial and investment potential at the regional level. The study also categorizes Ukrainian regions based on the impact of modern wartime challenges, and proposes mechanisms such as institutional and organizational optimization, information and communication tools, and formation of clusters to enhance financial and investment potential. Recommendations are provided for state authorities and local self-government bodies, emphasizing the support for entrepreneurship, development of the domestic energy industry, and modernization of the military-industrial complex at the state and regional levels.
FINANCIAL AND CREDIT ACTIVITY-PROBLEMS OF THEORY AND PRACTICE
(2022)
Article
Biochemistry & Molecular Biology
Andrey Nikolaev, Anna Yudenko, Anastasia Smolentseva, Andrey Bogorodskiy, Fedor Tsybrov, Valentin Borshchevskiy, Siarhei Bukhalovich, Vera V. Nazarenko, Elizaveta Kuznetsova, Oleg Semenov, Alina Remeeva, Ivan Gushchin
Summary: Researchers have developed a palette of 22 fluorescent tags based on the LOV domain, allowing for fine tuning of the emission wavelength range from 486 to 512 nm. They have demonstrated the applications of these tags in multi-color imaging of bacteria and mammalian cells, highlighting their potential in fluorescence microscopy.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Andrei Gilep, Tatsiana Varaksa, Sergey Bukhdruker, Anton Kavaleuski, Yury Ryzhykau, Sviatlana Smolskaya, Tatsiana Sushko, Kouhei Tsumoto, Irina Grabovec, Ivan Kapranov, Ivan Okhrimenko, Egor Marin, Mikhail Shevtsov, Alexey Mishin, Kirill Kovalev, Alexander Kuklin, Valentin Gordeliy, Leonid Kaluzhskiy, Oksana Gnedenko, Evgeniy Yablokov, Alexis Ivanov, Valentin Borshchevskiy, Natallia Strushkevich
Summary: In this study, the structures of 3Fe-4S ferredoxins from M. tuberculosis and their complexes with CYP143 were solved. The high-affinity binding of FdxE to CYP143 was demonstrated. The results reveal the diversity of electron transfer complexes and the conformational changes induced by FdxE binding.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Pavel V. Natashin, Ludmila P. Burakova, Margarita I. Kovaleva, Mikhail B. Shevtsov, Daria A. Dmitrieva, Elena V. Eremeeva, Svetlana V. Markova, Alexey V. Mishin, Valentin I. Borshchevskiy, Eugene S. Vysotski
Summary: The bioluminescence of hydromedusan photoproteins, responsible for marine jellyfish and hydroid, is a unique biochemical system consisting of apoprotein and preoxygenated coelenterazine. The role of water molecule and dioxetanone intermediate in the bioluminescence reaction is still under discussion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Egor Marin, Daniil A. Kornilov, Sergey S. Bukhdruker, Vladimir A. Aleksenko, Valentin A. Manuvera, Egor V. Zinovev, Kirill V. Kovalev, Mikhail B. Shevtsov, Anna A. Talyzina, Pavel A. Bobrovsky, Pavel K. Kuzmichev, Alexey V. Mishin, Ivan Y. Gushchin, Vassili N. Lazarev, Valentin I. Borshchevskiy
Summary: Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes and has two different enzymatic activities. The crystal structures reveal the location of a sodium ion and provide insights into the inhibition mechanism of the muramidase activity. The study suggests revising the hypothesis of isopeptidase activity and highlights the ambiguity of destabilase catalytic residue identification.
SCIENTIFIC REPORTS
(2023)
Article
Biology
Ivan Maslov, Oleksandr Volkov, Polina Khorn, Philipp Orekhov, Anastasiia Gusach, Pavel Kuzmichev, Andrey Gerasimov, Aleksandra Luginina, Quinten Coucke, Andrey Bogorodskiy, Valentin Gordeliy, Simon Wanninger, Anders Barth, Alexey Mishin, Johan Hofkens, Vadim Cherezov, Thomas Gensch, Jelle Hendrix, Valentin Borshchevskiy
Summary: Single-molecule FRET experiments with human A2A adenosine receptor in lipid nanodiscs reveal its conformational dynamics and activation. This study establishes a general smFRET platform for GPCR investigations, which has potential applications in drug screening and mechanism-of-action studies.
COMMUNICATIONS BIOLOGY
(2023)