Editorial Material
Chemistry, Physical
Guillaume Tcherkez, Nicolas Papon
Summary: The recent study by Chen et al. describes the structure of photosynthetic reaction centers in a green sulfur bacterium, contributing to our understanding of the evolution of reaction centers to modern plant photosystems and the production of oxygen from water.
Article
Plant Sciences
Juliany. M. T. Moura Barros, Vilma Marques Ferreira, Claudiana Moura dos Santos, Joao Correia de Araujo Neto, Andre L. Januario Silva, Jonatas Vieira dos Santos, Nathally Silva de Oliveira, Gilberto Costa Justino, Lauricio Endres
Summary: Foliar application of 24-epibrassinolide (EBL) can alleviate the adverse effects of water stress on soybean plants. EBL improves gas exchange,photosynthetic efficiency, chlorophyll synthesis, and biomass production of soybean plants. Additionally, EBL mitigates the damage caused by water stress, promotes post-stress recovery, and increases growth and yield.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Multidisciplinary Sciences
Lulu Wang, Jie Yan, Yuexian Hong, Zhihao Yu, Jitao Chen, Junrong Zheng
Summary: By utilizing the unique ultrafast proton conduction mechanism in vanadium oxide electrodes, a new aqueous battery with high rate capability up to 1000 C and extremely long life of 0.2 million cycles has been developed. The ultrafast kinetics and excellent cyclic stability are achieved through rapid 3D proton transfer in vanadium oxide via a special pair dance switching mechanism. This work provides insight into developing high-power and long-life electrochemical energy storage devices with nonmetal ion transfer through special pair dance top-ochemistry dictated by hydrogen bond.
Article
Plant Sciences
Vaclav Karlicky, Zuzana Kmecova Materova, Irena Kurasova, Jakub Nezval, Michal Stroch, Gyozo Garab, Vladimir Spunda
Summary: Light quality has a significant impact on plant metabolism, growth, and development. Recent research has shown that plants grown under monochromatic green light accumulate partially hydrogenated chlorophyll intermediates, affecting the structural-functional consequences of the photosynthetic apparatus. Accumulation of geranylgeranylated chlorophylls in pigment-protein complexes hampers the formation and stability of supercomplexes in thylakoid membranes, disrupting the photoprotective mechanism of non-photochemical quenching.
PHOTOSYNTHESIS RESEARCH
(2021)
Article
Crystallography
Maksym Golub, Miriam Koppel, Piret Pikma, Bernhard Frick, Joerg Pieper
Summary: A detailed understanding of protein function requires knowledge of the protein's spatial structure and conformational dynamics. This study investigated the molecular dynamics of Photosystem II membrane fragments in solution using quasielastic neutron scattering. The results showed that the dynamics of PSIImf are significantly activated at physiological temperatures, but restricted at low temperatures.
Article
Biochemistry & Molecular Biology
Juntaek Oh, Ji Shin, Ilona Christy Unarta, Wei Wang, Aaron W. Feldman, Rebekah J. Karadeema, Liang Xu, Jun Xu, Jenny Chong, Ramanarayanan Krishnamurthy, Xuhui Huang, Floyd E. Romesberg, Dong Wang
Summary: The study found that eukaryotic RNA polymerase II is capable of selectively recognizing unnatural base pairs with high fidelity, especially when the template strand contains dTPT3. Additionally, a novel 3'-RNA binding site termed the swing state was identified after rNaM addition. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Physical
Divya Kaur, Bryan Ferlez, Patrick Landry, Till Biskup, Stefan Weber, John H. Golbeck, K. V. Lakshmi, Art van der Est
Summary: This study confirms the functionality of the partially converted BChl g' / Chl a(F)' special pair in samples exposed to dioxygen. The energy of the charge-separated state increases significantly when both BChl g' molecules of the P-800 dimer are converted.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Mehar Fatma, Noushina Iqbal, Zebus Sehar, Mohammed Nasser Alyemeni, Prashant Kaushik, Nafees A. Khan, Parvaiz Ahmad
Summary: The study showed that application of MeJA during heat stress in wheat plants increased enzymatic antioxidant activity, reduced hydrogen peroxide and TBARS content, and enhanced photosynthetic efficiency.
Article
Biology
Stefania Viola, William Roseby, Stefano Santabarbara, Dennis Nurnberg, Ricardo Assuncao, Holger Dau, Julien Selles, Alain Boussac, Andrea Fantuzzi, A. William Rutherford
Summary: The study compares the turnover efficiency, electron transfer, reactions, and photodamage of different types of photosystem II (PSII). The results show that Chl-d-PSII is more sensitive to photodamage compared to Chl-a-PSII and Chl-f-PSII, but generates more singlet oxygen in the recombination via PD1+Phe repopulation. Chl-f-PSII avoids harmful reactions by adjusting energy gaps, making it more resilient to photodamage.
Article
Biochemistry & Molecular Biology
Mahir D. Mamedov, Georgy E. Milanovsky, Marco Malferrari, Liya A. Vitukhnovskaya, Francesco Francia, Alexey Yu Semenov, Giovanni Venturoli
Summary: The kinetics of flash-induced re-reduction of the Photosystem II primary electron donor P-680 was affected by different relative humidity levels and the presence of trehalose glassy matrices, with changes in lifetimes and contributions of kinetic components.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Review
Plant Sciences
Thomas Oliver, Tom D. Kim, Joko P. Trinugroho, Violeta Cordon-Preciado, Nitara Wijayatilake, Aaryan Bhatia, A. William Rutherford, Tanai Cardona
Summary: Recent advances in understanding the origin and evolution of photosystem II are reviewed and discussed, revealing that water oxidation occurred early in the history of life. Photosystem II has remained relatively unchanged for billions of years, but constant duplication of the D1 subunit has allowed the enzyme to adapt to different environments and even develop enzymatic functions beyond water oxidation. This adaptability could be utilized to develop novel light-powered enzymes for sustainable biocatalysis.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Chemistry, Physical
Wujie Wang, Zhenghao Wu, Johannes C. B. Dietschreit, Rafael Gomez-Bombarelli
Summary: In this study, a general stochastic method called DiffSim is proposed to learn pair interactions from data using differentiable simulations. The method uses molecular dynamics simulations and stochastic gradient descent to directly learn interaction potentials based on structural observables. DiffSim is flexible and can simultaneously simulate and optimize multiple systems, such as different temperatures or compositions. The results show that DiffSim can explore a wider functional space of pair potentials compared to traditional methods like iterative Boltzmann inversion. The methods can also be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve transferability.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Plant Sciences
Jure Zabret, Stefan Bohn, Sandra K. Schuller, Oliver Arnolds, Madeline Moller, Jakob Meier-Credo, Pasqual Liauw, Aaron Chan, Emad Tajkhorshid, Julian D. Langer, Raphael Stoll, Anja Krieger-Liszkay, Benjamin D. Engel, Till Rudack, Jan M. Schuller, Marc M. Nowaczyk
Summary: Auxiliary proteins play a crucial role in assisting the assembly of photosystems, as shown by the structure of a PSII assembly intermediate resolved by cryo-electron microscopy. This structure reveals mechanisms that protect against photodamage during vulnerable stages of biogenesis and prepare the active site for the unique water-splitting reaction catalyzed by the Mn4CaO5 cluster.
Article
Multidisciplinary Sciences
Makiko Kosugi, Masato Kawasaki, Yutaka Shibata, Kojiro Hara, Shinichi Takaichi, Toshio Moriya, Naruhiko Adachi, Yasuhiro Kamei, Yasuhiro Kashino, Sakae Kudoh, Hiroyuki Koike, Toshiya Senda
Summary: An Antarctic green alga called Prasiola crispa uses a ring-shaped protein structure to harness low-energy far-red light to excite photosystem II. This unique structure differs from the photosynthetic pigment structure of other algae.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Xiao-Ping Yi, He-Sheng Yao, Da-Yong Fan, Xin-Guang Zhu, Pasquale Losciale, Ya-Li Zhang, Wang-Feng Zhang, Wah Soon Chow
Summary: The study revealed that repairing PSII requires a substantial energy cost, with 24,000 ATP molecules needed to repair one entire PSII complex, and the ATP requirement for PSII repair was on average 4.6% of the ATP required for overall carbon assimilation. These values were found to be two to three times higher than previously calculated. Possible additional energy sinks in the PSII repair cycle are also discussed.
Article
Multidisciplinary Sciences
Daniele Narzi, Siri C. van Keulen, Ursula Rothlisberger
Summary: The conversion of ATP to cAMP is a crucial reaction in eukaryotes, catalyzed by adenylyl cyclase (AC) and regulated by G alpha(i) and G alpha(s) subunits. Crystal structures have been resolved showing the inhibition mechanism of AC by G alpha(i) remains not fully understood. Molecular dynamics simulations suggest that G alpha(i) inhibits AC activity by preventing the formation of a reactive ATP conformation.
Article
Biochemistry & Molecular Biology
Matteo Capone, Daniele Narzi, Leonardo Guidoni
Summary: This study characterized the events occurring in the last sector of the catalytic cycle of water oxidation in Photosystem II, revealing that oxygen release is the rate-limiting step and water insertion is coupled with proton transfer.
Article
Chemistry, Physical
Francesco Benfenati, Guglielmo Mazzola, Chiara Capecci, Panagiotis Kl Barkoutsos, Pauline J. Ollitrault, Ivano Tavernelli, Leonardo Guidoni
Summary: nu-VQE is a modified quantum computing algorithm for electronic structure optimization, using a nonunitary operator to simplify the wave function ansatz and achieve better results on noisy quantum computers. The method shows a significant improvement in accuracy compared to traditional VQE methods, with an order of magnitude reduction in absolute energy error.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Giovanna M. A. Rogati, Chiara Capecci, Enza Fazio, Scolastica Serroni, Fausto Puntoriero, Sebastiano Campagna, Leonardo Guidoni
Summary: The structure of a decanuclear dendrimer based on Ru(II) polypyridine subunits, suitable for artificial photosynthesis as a light-harvesting species, has been investigated through computer modeling. Molecular dynamics and quantum mechanics simulations were used to study the stability of possible isomers of each monomer, revealing a prevalence of MER isomerism in the central core. Additionally, the self-aggregation of the dendrimer and the distribution of counterions around the complexes were investigated using Molecular Dynamics in both implicit and explicit acetonitrile solution, suggesting a self-aggregation mechanism for the dendrimers.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Leonardo Ratini, Chiara Capecci, Francesco Benfenati, Leonardo Guidoni
Summary: The study introduces a modified VQE method named WAHTOR, which adapts the form of the molecular Hamiltonian to the circuit ansatz through an optimization procedure, making it more flexible. The method has been successfully applied to simulations of small molecules, demonstrating advantages over traditional VQE methods, being less dependent on circuit topology and less likely to be trapped in high-energy local minima.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Virology
Stefano Pascarella, Martina Bianchi, Marta Giovanetti, Daniele Narzi, Roberto Cauda, Antonio Cassone, Massimo Ciccozzi
Summary: The COVID-19 pandemic is still a global threat due to the emergence of new SARS-CoV-2 variants. The Mu variant, first identified in Colombia in January 2021, was classified as a variant of interest in August 2021. Despite lower infectivity compared to the Delta variant, this study examines the structural effect of Mu spike protein mutations and predicts their potential impact on infectivity compared to Delta and Delta plus spike protein.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Plant Sciences
Anna Scortica, Matteo Capone, Daniele Narzi, Mario Frezzini, Valentina Scafati, Moira Giovannoni, Francesco Angelucci, Leonardo Guidoni, Benedetta Mattei, Manuel Benedetti
Summary: This study demonstrates that plant cells secrete OGOX to protect themselves from pathogenic microorganisms during infection. The activity of OGOX is influenced by pH, with alkaline conditions promoting its oxidizing activity and enhancing the defense function of the plant cell wall by altering the hydrolyzing potential of OGs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Plant Sciences
Mario Frezzini, Anna Scortica, Matteo Capone, Daniele Narzi, Manuel Benedetti, Francesco Angelucci, Benedetta Mattei, Leonardo Guidoni
Summary: OGOX1 is an enzyme that oxidizes pectin fragments (OGs) and releases H2O2, thereby reducing the activity of OGs. Molecular dynamics simulations and enzyme kinetics studies have revealed the molecular determinants of OGOX1 that are responsible for binding OGs of different lengths. The results suggest that the binding between OGOX1 and OG5 is the most stable, with salt-bridge interactions stabilizing the optimal conformation of OG5 for efficient oxidation by the enzyme.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Paul Greife, Matthias Schoenborn, Matteo Capone, Ricardo Assuncao, Daniele Narzi, Leonardo Guidoni, Holger Dau
Summary: Photosynthesis stores solar energy in chemical form, which supports life on Earth. The splitting of water at the manganese cluster of photosystem II during photosynthesis has resulted in an oxygen-rich atmosphere. This study reveals the crucial stage of oxygen formation in photosynthesis and its mechanistic role.
Article
Chemistry, Physical
Gianluca Parisse, Daniele Narzi, Benny Danilo Belviso, Vito Capriati, Rocco Caliandro, Massimo Trotta, Leonardo Guidoni
Summary: Deep eutectic solvents (DESs) are versatile solvents that can be manipulated to improve the performance of biomolecules. A recent study has investigated the effects of hydrated DESs on protein dynamics using molecular dynamics simulations. The results show that DESs can restrict protein motion and increase the overall structural rigidity. Furthermore, specific interactions between DES components and protein residues have been identified, suggesting the potential for protein crystallization in the presence of hydrated DESs.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Daniele Narzi, Leonardo Guidoni
Summary: This study used classical Molecular Dynamics simulations to characterize the structural and dynamic features of apo PSII, revealing that not all residues acting as Mn ligands are pre-organized prior to Mn4Ca formation and previous local conformational changes are required to bind the first Mn ion.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Giovanna M. A. Rogati, Chiara Capecci, Enza Fazio, Scolastica Serroni, Fausto Puntoriero, Sebastiano Campagna, Leonardo Guidoni
Summary: The study investigated a decanuclear photo- and redox-active dendrimer based on Ru(II) polypyridine subunits using computer modelling. It was found that the stability of the dendrimer is governed by the steric constrains originated by the multimetallic assembly rather than the stability of the individual monomers. Additionally, molecular dynamics analysis showed a self-aggregation mechanism of Ru10. The results provide new insights for the design and development of light-harvesting multicomponent species for artificial photosynthesis.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
