Review
Chemistry, Inorganic & Nuclear
Giulia Di Rocco, Gianantonio Battistuzzi, Marco Borsari, Carlo Augusto Bortolotti, Antonio Ranieri, Marco Sola
Summary: Splitting the reduction potential of electron transport (ET) proteins and redox metalloenzymes into enthalpic and entropic contributions helps understand the molecular determinants of the metal center's propensity to accept or release electrons. Enthalpic terms related to ligation features and weak binding in the metal's coordination sphere play a significant role in this balance. Reduction-induced solvent-related events dominate measured entropy changes, but have less impact on reduction free energy due to compensatory enthalpic effects, known as enthalpy-entropy compensation (EEC).
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Microbiology
Sirui Han, Kailun Guo, Wei Wang, Yizhi J. Tao, Haichun Gao
Summary: In this study, HtpA was identified as a heme-trafficking protein in the bacterium Shewanella oneidensis. The absence of HtpA significantly reduced cytochrome c content and catalase activity. This research sheds light on the mechanism of heme transport across membranes in bacteria and extends the understanding of TANGO2 proteins.
Article
Biotechnology & Applied Microbiology
Wei Wang, Yawen Liang, Lulu Liu, Sirui Han, Shihua Wu, Haichun Gao
Summary: In S. oneidensis, Hfq plays a critical role in regulating the content of cytochromes c and pyomelanin production by differentially regulating heme biosynthesis and degradation, as well as HmgA activity through modulating intracellular iron levels.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Mehmet Yunus Genceroglu, Cansu Cavdar, Selen Manioglu, Halil Bayraktar
Summary: This study presents a genetically encoded fluorescence method for monitoring the conformational changes of Cytc upon binding to heme and CCHL. The results show that the noncovalent interaction of heme in the absence of CCHL induces a partially folded state of Cytc, while higher concentrations of heme and coexpression of CCHL lead to the recovery of Cytc native structure.
Review
Chemistry, Inorganic & Nuclear
Carlos A. Salgueiro, Leonor Morgado, Marta A. Silva, Marisa R. Ferreira, Tomas M. Fernandes, Pilar C. Portela
Summary: Iron is the most versatile of all biochemically active metals, with its properties encompassing electronic configuration, number of unpaired electrons, type of ligands and iron-complex stability. This versatility is reflected in the proteins it can be associated with, especially heme proteins, with a focus on c-type cytochromes. Geobacter bacteria encode an unusually high number of assorted c-type cytochromes, which showcase the diversity of cytochromes.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Nadezda A. Brazhe, Evelina I. Nikelshparg, Adil A. Baizhumanov, Vera G. Grivennikova, Anna A. Semenova, Sergey M. Novikov, Valentyn S. Volkov, Aleksey V. Arsenin, Dmitry I. Yakubovsky, Andrey B. Evlyukhin, Zhanna V. Bochkova, Eugene A. Goodilin, Georgy V. Maksimov, Olga Sosnovtseva, Andrey B. Rubin
Summary: A novel sensor using label-free surface-enhanced Raman spectroscopy (SERS) has been developed to identify conformational changes in cytochrome c heme and elucidate its role in functioning mitochondria. It has been shown that molecule bond vibrations assessed by SERS are a reliable indicator of heme conformation, which regulates the efficiency of the mitochondrial respiratory chain and adjusts mitochondrial respiration to the cell's consumption of ATP.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Pilar C. Portela, Marta A. Silva, Liliana R. Teixeira, Carlos A. Salgueiro
Summary: Geobacter bacteria are capable of electron transfer for potential bioremediation or energy harvesting. The cytochrome PpcA plays a crucial role in bridging electron transfer, with unique redox properties due to specific amino acids, allowing for modulation of redox potential and potential engineering for bioelectrochemical applications.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Sasiprapa Samsri, Soraya Pornsuwan
Summary: The study compared the cysteine-directed mutants of hCytc located in different parts of Omega-loops, revealing that these mutations led to different conformations and dynamic properties, influencing the peroxidase activity and potentially contributing to apoptosis.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Dipayan Bose, Shantanu Aggarwal, Debashree Das, Chandrabhas Narayana, Abhijit Chakrabarti
Summary: Hemoglobin oxidation leads to ROS generation and membrane damage, but the interaction with spectrin can increase its peroxidase activity and limit oxidative damage. Spectrin also modulates the peroxidase activity of different hemoglobin variants and other heme proteins.
Article
Plant Sciences
Tianzuo Wang, Jing Wang, Di Zhang, Li Chen, Min Liu, Xinxin Zhang, Wolfgang Schmidt, Wen-Hao Zhang
Summary: Fe deficiency is a limiting factor for plant growth, but the mechanisms regulating Fe acquisition and utilization are not fully known. This study reveals that CIPK12 regulates riboflavin biosynthesis and Fe-deficiency responses in plants, thereby affecting Fe accumulation and photosynthetic efficiency.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Crystallography
Rita Chertkova, Tatyana Bryantseva, Nadezhda A. Brazhe, Kseniya S. Kudryashova, Victor V. Revin, Alexei N. Nekrasov, Alexander Yusipovich, Alexey R. Brazhe, Andrew B. Rubin, Dmitry A. Dolgikh, Mikhail P. Kirpichnikov, Georgy Maksimov
Summary: The secondary structure of horse cytochrome c with mutations in the P(76)GTKMIFA(83) site of the Omega-loop, exhibiting reduced efficiency of electron transfer, was studied. CD spectroscopy and IR spectroscopy data showed changes in structural elements, with an increase in beta-structural elements and a decrease in non-structured elements. H-1-NMR spectra analysis revealed specific features in the secondary structure related to changes in the heme microenvironment. These changes likely contribute to the decreased efficiency of electron transfer in the studied cytochromes c.
Article
Chemistry, Physical
Laura Tadiello, Tommaso Gandini, Bernhard M. Stadler, Sergey Tin, Haijun Jiao, Johannes G. de Vries, Luca Pignataro, Cesare Gennari
Summary: The reductive opening of epoxides to synthesize alcohols is an attractive method, but faces limitations such as the use of expensive metal hydride reducing agents and poor regioselectivity. This study presents the use of a cheap and easy-to-handle iron complex as a precatalyst for this reaction, showcasing the possibility to control regioselectivity through a careful choice of Lewis acid. Further studies are needed to fully understand the reaction mechanism involving multiple pathways.
Article
Biochemistry & Molecular Biology
Srijeeb Karmakar, Arjun Sankhla, Vimal Katiyar
Summary: The holo form of Cytochrome-C remains structurally intact in the presence of heme, but prolonged thermal and pH stress can lead to dissociation of heme, resulting in the collapse of the protein structure into a macromolecular amyloid-network and FeQDs with 2-3 nm diameter. Further studies revealed that FeQDs can re-adsorb on the surface of the amyloid network, forming a FeQD-decorated amyloid matrix. Excitingly, the FeQDs exhibit gel-like properties and support cell growth without cytotoxicity, suggesting potential for diverse biological applications as advanced biomaterials.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Luke E. Formosa, Shadi Maghool, Alice J. Sharpe, Boris Reljic, Linden Muellner-Wong, David A. Stroud, Michael T. Ryan, Megan J. Maher
Summary: COA7 is a crucial assembly factor for the biogenesis of mitochondrial complex IV. It interacts with SCO1 and SCO2 to catalyze copper relay and reduction of disulfide bonds, which are important for complex IV assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Caiyong Chen, Iqbal Hamza
Summary: Heme is an iron-containing tetrapyrrole that plays a critical role in various biological processes, but its hydrophobic and toxic nature requires specific trafficking pathways for safe transport. The nematode Caenorhabditis elegans has been used as a model organism to study heme-trafficking proteins and pathways. This review provides an overview of the heme-trafficking proteins identified in C. elegans and their homologs in related organisms.
Article
Chemistry, Physical
Laura Zanetti-Polzi, Isabella Daidone, Andrea Amadei
Summary: In this paper, a theoretical model for fluid state thermodynamics based on modeling the fluctuation distributions is proposed. The model accurately describes the thermodynamics of fluid water, with insights into statistical/molecular organization and phase or pseudo-phase transitions. The model shows good agreement with experimental data under sub- and super-critical conditions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Giulia Di Rocco, Fabrizio Bernini, Gianantonio Battistuzzi, Antonio Ranieri, Carlo Augusto Bortolotti, Marco Borsari, Marco Sola
Summary: In this study, it was found that human neuroglobin (hNgb) undergoes H2O2-induced breakdown of the heme center at a slower rate than other globins. The rate is affected by the Cys46/Cys55 disulfide bond and the non-covalent interactions involving Tyr44, Lys67, the His64 heme iron axial ligand, and the heme propionate-7. The presence of a disulfide bridge, as well as certain mutations, can influence the rate and formation of beta-amyloid aggregates.
Article
Biochemistry & Molecular Biology
Giulia Di Rocco, Antonio Ranieri, Marco Borsari, Marco Sola, Carlo Augusto Bortolotti, Gianantonio Battistuzzi
Summary: The Met80Ala variant of yeast cytochrome c shows promising biocatalytic and biosensing properties due to its stable electrocatalytic properties in mixed solvents. Organic solvents have minimal effects on the redox and structural properties of the variant.
Article
Biochemistry & Molecular Biology
Andrea Amadei, Andrea Ciccioli, Antonello Filippi, Caterina Fraschetti, Massimiliano Aschi
Summary: A theoretical-computational procedure based on the quasi-Gaussian entropy theory and molecular dynamics simulations is proposed. It can construct an analytical model of the most relevant thermodynamic properties within a wide temperature range by automatically sampling the entire conformational repertoire of highly flexible systems. The method's reliability mainly depends on the quality of the force field used in the simulations and the ability to distinguish between semi-classical and quantum degrees of freedom in a physically coherent way.
Article
Chemistry, Multidisciplinary
Marta Monti, Maria Francisca Matus, Sami Malola, Alessandro Fortunelli, Massimiliano Aschi, Mauro Stener, Hannu Hakkinen
Summary: The water-soluble glutathione-protected [Au-25(GSH)(18)](-1) nanocluster was investigated using molecular dynamics simulations, essential dynamics analysis, and time-dependent density functional theory calculations. Conformational changes, weak interactions, and solvent effects, particularly hydrogen bonds, were found to significantly influence the optical response of the system. The analysis demonstrated the sensitive nature of the electronic circular dichroism to the presence of solvent and the active role of the solvent in forming a chiral solvation shell around the cluster. This work presents a successful strategy for studying chiral interfaces between metal nanoclusters and their environments, with potential applications in chiral electronic interactions with biomolecules.
Article
Chemistry, Multidisciplinary
Matteo Capone, Abhishek Sirohiwal, Massimiliano Aschi, Dimitrios A. Pantazis, Isabella Daidone
Summary: Photosystem-II (PSII) is a multi-subunit protein complex that performs oxygenic photosynthesis by harvesting sunlight. Studying the processes following light excitation has been challenging due to spectral congestion, ultrafast nature, and multi-component behavior. Using advanced computational multiscale approaches, researchers have identified two possible primary pathways to radical-pair formation, with significantly different kinetics. The dominant pathway is fast (short-range), but the existence of a slower (long-range) alternative pathway suggests the evolution of redundancy for other purposes related to the formation of oxidative species in PSII that drives water oxidation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
M. Monti, G. Brancolini, E. Coccia, D. Toffoli, A. Fortunelli, S. Corni, M. Stener, M. Aschi
Summary: The effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of chiral Au-38(SC2H4Ph)(24) clusters are investigated. ECD spectra are calculated using the first principle polTDDFT approach on a series of conformations extracted from MD simulations, and weighted to predict the final spectrum. The results show the importance of considering conformational effects in ECD modeling of chiral nanoclusters.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Massimiliano Aschi, Laura Palombi, Andrea Amadei
Summary: The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were successfully modeled using a theoretical-computational method combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations. The method accurately reproduced the experimental spectra and demonstrated its effectiveness in modeling spectral features in complex systems. The strategy involved performing a long timescale MD simulation, extracting relevant conformations, and calculating the ECD spectrum using the PMM approach.
Article
Biochemistry & Molecular Biology
Alessandro Nicola Nardi, Alessio Olivieri, Andrea Amadei, Riccardo Salvio, Marco D'Abramo
Summary: In this study, the kinetics of hydroxide-promoted hydrolysis of phosphoric diesters were modeled using a hybrid quantum/classical approach. The results suggest that the hydrolysis occurs through a concerted A(N)D(N) mechanism, with no formation of penta-coordinated intermediates. This modeling method has the potential to predict rate constants and reactivities/selectivities in complex environments.
Article
Chemistry, Multidisciplinary
Alessandro Paradisi, Marcello Berto, Matteo Di Giosia, Sara Mazzali, Marco Borsari, Tainah Dorina Marforio, Francesco Zerbetto, Matteo Calvaresi, Anna Orieshyna, Nadav Amdursky, Carlo Augusto Bortolotti, Fabio Biscarini
Summary: This study introduces a simple solution-based method for fabricating electrolyte-gated transistor (EGT) devices using stable dispersions of single-walled carbon nanotubes (SWCNTs)/bovine serum albumin (BSA) hybrids in water. The method allows the formation of a semiconducting random network of SWCNTs as the channel, enabling the fabrication of EGT devices with excellent electrical performance for biosensing applications. The method is demonstrated for the detection of cortisol in solution, showcasing its robustness and cost-effectiveness in overcoming limitations of standard SWCNTs biosensor fabrications.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Isabella Daidone, Riccardo Foffi, Andrea Amadei, Laura Zanetti-Polzi
Summary: In this study, we applied a theoretical model to investigate the thermodynamic properties of supercooled water. Our model, which incorporates clusters of molecules beyond the first hydration shell, accurately describes the two distinct liquid states and shows good agreement with the results of other two-state models.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Inorganic & Nuclear
Manuel Imperato, Alessio Nicolini, Marco Borsari, Matteo Briganti, Mario Chiesa, Yu-Kai Liao, Antonio Ranieri, Arsen Raza, Enrico Salvadori, Lorenzo Sorace, Andrea Cornia
Summary: We investigated the performance of heterobimetallic lantern complexes [PtVO(SOCR)4] as charge neutral electronic qubits based on vanadyl complexes. The results showed that these complexes exhibit good spin coherence properties, making them suitable for applications in materials science and quantum technologies.
INORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Materials Science, Multidisciplinary
Ambili Ramanthrikkovil Variyam, Yuval Agam, Alessandro Paradisi, Carlo Augusto Bortolotti, Nadav Amdursky
Summary: This article investigates the use of mixed ionic-electronic conductive biopolymers for electronic and bioelectronic applications. The authors demonstrate that by modifying specific amino acids of a protein-based biopolymer with naphthalenediimide (NDI), the electronic transport of the material can be improved without compromising its native ionic transport. The study also shows that by reducing the NDI moieties, a high conductivity value can be achieved. The easy post-polymerization functionalization chemistry of NDI makes this new strategy highly attractive for the development of sustainable mixed conductors using biopolymers.
JOURNAL OF MATERIALS CHEMISTRY C
(2022)
