Article
Plant Sciences
Helena Sapeta, Makio Yokono, Atsushi Takabayashi, Yoshifumi Ueno, Andre M. Cordeiro, Toshihiko Hara, Ayumi Tanaka, Seiji Akimoto, M. Margarida Oliveira, Ryouichi Tanaka
Summary: Jatropha curcas responds to drought by increasing thermal dissipation of excitation energy in both photosystems, temporarily down-regulating the quantum yields of both PSII and PSI. This helps protect the photosynthetic machinery and enables rapid recovery of photosynthetic capacity when water is available.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Akihiro Saito, Kimika Hoshi, Yuna Wakabayashi, Takumi Togashi, Tomoki Shigematsu, Maya Katori, Takuji Ohyama, Kyoko Higuchi
Summary: The barley cultivar Sarab 1 can continue photosynthesis under low iron conditions through a reduction in P700 over-reduction and an increase in non-appressed thylakoid membranes. In contrast, another cultivar, Ehimehadaka-1, preferentially supplies iron to photosystem I to maintain photosynthetic activity. These findings highlight the multiple strategies that barley species have for acclimating photosynthesis to iron deficiency.
Article
Biochemistry & Molecular Biology
Wen-He Cai, Xin-Qiang Zheng, Yue-Rong Liang
Summary: The PSII of the light-sensitive albino tea plant is more vulnerable to high-light stress, which leads to the degradation of PSII subunits and disruption of light-harvesting chlorophyll-protein complexes, resulting in leaf bleaching. The de novo synthesis and repair of PSII subunits are involved in the impairment of PSII complexes, leading to the albino phenotype in the tea plant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mauro Bringas, Meike Luck, Peter Mueller, Holger A. Scheidt, Santiago Di Lella
Summary: The structure and dynamics of membranes are crucial for the proper functioning of cells. Two compounds used in therapeutics against COVID-19, remdesivir and favipiravir, were found to spontaneously bind to model lipid membranes in molecular dynamics simulation assays.
Article
Biology
Ido Caspy, Maria Fadeeva, Yuval Mazor, Nathan Nelson, David M. Kramer
Summary: High-resolution cryo-EM structures of eukaryotic PSII from Dunaliella salina revealed different conformations and demonstrated the role of CP29 in distinguishing the conformers. Additionally, the study discovered the flexibility of PSII in different orientations, providing a flexible stacking mechanism for grana arrangement in thylakoids.
Article
Biology
Josep Rizo, Levent Sari, Yife Qi, Wonpil Im, Milo M. Lin
Summary: Synaptic vesicles are prepared for fast neurotransmitter release upon calcium binding to Synaptotagmin-1. Molecular dynamics simulations suggest that SNARE complexes induce slow formation of membrane-membrane contact interfaces. The prepared state includes macromolecular assemblies of Synaptotagmin-1 and complexin bound to trans-SNARE complexes.
Article
Materials Science, Multidisciplinary
Murray S. Daw, Michael Chandross
Summary: We extend the parametric form of Embedded Atom Method interatomic potentials for FCC metals to treat alloys and study the dependence of alloy properties on model parameters. We introduce the concept of spread alloys, where constituent elements are defined as perturbations from an average FCC metal, and show that the model can describe the clustering and ordering tendencies of metal alloys. We prove a general theorem that alloy properties in random equimolar alloys differ from a simple rule of mixtures only based on the standard deviation among constituent parameters, independent of the number of constituents.
Article
Materials Science, Multidisciplinary
Murray S. Daw, Michael Chandross
Summary: We propose a simple parametric form for interatomic potentials of the Embedded Atom Method (EAM-X) for pure FCC metals and investigate the relationship between basic properties and input parameters. Instead of fitting a set of functions to experimental data or density functional theory calculations, we adopt an inside-out approach to understand how complex properties depend on the EAM-X parameters. This method enables the identification of desired parameter regions and the matching of those parameters to real elements.
Article
Biochemistry & Molecular Biology
Robert H. Calderon, Catherine de Vitry, Francis-Andre Wollman, Krishna K. Niyogi
Summary: This study found that rubredoxin 1 (RBD1) is not necessary for heme b559 assembly but may play a role in promoting the proper folding of D1 during PSII assembly.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Patrick Heasman, Aleksandar Y. Mehandzhiyski, Sarbani Ghosh, Igor Zozoulenko
Summary: Processing natural cellulose requires dissolution and regeneration. The crystallinity of re-generated cellulose does not match that of native cellulose, and the physical and mechanical properties of re-generated cellulose vary depending on the technique used. Molecular dynamics simulations were performed to simulate the regeneration of order in cellulose. The simulations show that cellulose chains have an affinity to align with each other on the nanosecond scale, but the end results still lack sufficient order. The time factor plays a major role in reclaiming the order of crystalline cellulose.
CARBOHYDRATE POLYMERS
(2023)
Article
Biochemistry & Molecular Biology
Ruiyuan Liu, Leng Wang, Yue Meng, Fang Li, Haiyu Nie, Huizhe Lu
Summary: A recent study confirmed that thylakoid lipids (TL) can activate LPOR. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. In this study, we used multiple computational approaches to explore potential cavities in Arabidopsis thaliana LPOR and identified a high-affinity binding site for phosphatidyl glycerol (PG) around the helix-G region. Through molecular dynamics simulations, we analyzed LPOR/PG and LPOR/NADPH/PG complexes and gained insights into their dynamics, energetics, and potential allosteric regulation. Our findings clarify the NADPH binding affinity for LPOR in the presence of PGs and suggest a mechanism involving lid opening upon binding of allosteric regulators to an allosteric hinge pocket.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Vasily V. Ptushenko, Dmitry D. Knorre, Elena S. Glagoleva
Summary: PsbS is a key photoprotective protein in plants that helps the photosynthetic apparatus adapt to changes in irradiance. Recently, it has been discovered that PsbS also plays a role in photoprotection in green algae. The amino acid sequence and structure of PsbS from the green algae species L. incisa were determined, and the pK(a) values of its protonatable residues were calculated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Yuan Gao, Weiqiang Chen, Yanming Liu, Jiangyu Wu, Hongwen Jing
Summary: The study reveals the potential of graphene kirigami (GK) as an ultra-permeable membrane for water desalination. The GK membrane demonstrates superior performance in water permeance, surpassing 103 L/m2/h/bar with complete salt rejection. The unique geometry of the kirigami structure reduces energy barrier and guides water molecules for more efficient filtration. Compared to nanoporous graphene and conventional reverse osmosis membranes, the theoretical efficiency of water permeance using GK membrane is significantly higher. Moreover, GK membranes can be mechanically deformed for practical applications.
Article
Physics, Multidisciplinary
Dayou Yang, Susana F. Huelga, Martin B. Plenio
Summary: Continuous monitoring of driven-dissipative quantum-optical systems is crucial for achieving highly precise measurements beyond the classical limit. We design a novel continuous-measurement strategy and develop a universal method to efficiently retrieve the quantum Fisher information. We also establish an effective formula for evaluating the quantum Fisher information of the emission field of driven-dissipative open sensors.
Article
Biochemistry & Molecular Biology
Matthew Carter Childers, Michael Geeves, Valerie Daggett, Michael Regnier
Summary: Researchers investigated whether the dynamics of the post-powerstroke state of the cross-bridge cycle are modulated in a nucleotide-dependent fashion, finding that different nucleotides interact with myosin in distinct ways and influence the flexibility and structure of the protein. Specifically, replacing ADP with dADP in the post-powerstroke state altered the conformation of the actin binding region in myosin heads. This study provides atomic level insights into allosteric communication networks in myosin and the nucleotide-dependent dynamics of the cross-bridge cycle.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Chemistry, Physical
Makoto Hatakeyama, Koji Ogata, Toshimasa Ishida, Kunihiro Kitamura, Shinichiro Nakamura
JOURNAL OF PHYSICAL CHEMISTRY A
(2015)
Article
Chemistry, Physical
Koji Ogata, Shinichiro Nakamura
JOURNAL OF PHYSICAL CHEMISTRY B
(2015)
Article
Chemistry, Medicinal
David Simoncini, Hiroya Nakata, Koji Ogata, Shinichiro Nakamura, Kam Y. J. Zhang
MOLECULAR INFORMATICS
(2015)
Article
Chemistry, Physical
Yuanqing Wang, Makoto Hatakeyama, Koji Ogata, Masamitsu Wakabayashi, Fangming Jin, Shinichiro Nakamura
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2015)
Article
Chemistry, Physical
Koji Ogata, Makoto Hatakeyama, Fangming Jin, Xu Zeng, Yuanqing Wang, Katsushi Fujii, Shinichiro Nakamura
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2015)
Article
Chemistry, Physical
Makoto Hatakeyama, Koji Ogata, Katsushi Fujii, Vittal K. Yachandra, Junko Yano, Shinichiro Nakamura
CHEMICAL PHYSICS LETTERS
(2016)
Article
Physics, Multidisciplinary
Hiromasa Sakaguchi, Koji Ogata, Tetsu Isomura, Shoko Utsunomiya, Yoshihisa Yamamoto, Kazuyuki Aihara
Article
Multidisciplinary Sciences
Osamu Kanie, Yuki Shioiri, Koji Ogata, Waka Uchida, Shusaku Daikoku, Katsuhiko Suzuki, Shinichiro Nakamura, Yukishige Ito
SCIENTIFIC REPORTS
(2016)
Article
Chemistry, Physical
Makoto Hatakeyama, Yuki Sakamoto, Koji Ogata, Yuto Sumida, Tomoe Sumida, Takamitsu Hosoya, Shinichiro Nakamura
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Biochemistry & Molecular Biology
Koji Ogata, Makoto Hatakeyama, Shinichiro Nakamura
Article
Chemistry, Physical
Koji Ogata, Makoto Hatakeyama, Yuki Sakamoto, Shinichiro Nakamura
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Chemistry, Physical
Koji Ogata
Summary: The study reveals that collective molecules exhibit cooperative principal component (PC) modes forming vorticial or torus-like structures, not only in water or methane molecules but also in proteins. Cooperative motions of proteins and surrounding water molecules strongly contribute to protein structure and function, influencing PC mode structures and indicating similarities in proteins with the same folds.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Kazuto Ikemoto, Yuki Sakamoto, Rikako Tanaka, Koji Ogata, Nobuyuki Matsushita, Shinichiro Nakamura
CRYSTAL GROWTH & DESIGN
(2017)
Proceedings Paper
Green & Sustainable Science & Technology
Shinichiro Nakamura, Makoto Hatakeyama, Yuanqing Wang, Koji Ogata, Katsushi Fujii
ADVANCES IN CO2 CAPTURE, SEQUESTRATION, AND CONVERSION
(2015)
Article
Chemistry, Multidisciplinary
Muhammad Imran, Saba Waqar, Koji Ogata, Mahmood Ahmed, Zobia Noreen, Sundus Javed, Nazia Bibi, Habib Bokhari, Asma Amjad, Muhammad Muddassar