Article
Environmental Sciences
Fu-Jie Zhu, Wan-Li Ma, Zi-Feng Zhang, Pu-Fei Yang, Peng-Tuan Hu, Li-Yan Liu, Wei-Wei Song
Summary: Gas/particle (G/P) partitioning is an important factor for the environmental fate of semi-volatile organic compounds (SVOCs). This study established empirical equations based on ambient temperature to predict the G/P partitioning quotient (Kp) of polycyclic aromatic hydrocarbons (PAHs) in a wide temperature range. The empirical equations showed good performance in predicting Kp based on ambient temperature. However, deviations from previous G/P partitioning models were observed, suggesting the need to consider additional influencing factors. Further research should be conducted to study the mechanism of PAHs G/P partitioning and improve the partitioning models.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Medicinal
Andrei L. Lomize, Kevin A. Schnitzer, Spencer C. Todd, Irina D. Pogozheva
Summary: The FMAP 2.0 method accurately predicts the positions, stabilities, and tilt angles of alpha-helices in different environments, demonstrating high accuracy and reproducibility in experimental data. This is important for understanding the biological activities of membrane-binding peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Physics, Multidisciplinary
Z. Y. Zhang, H. B. Yang, M. H. Huang, Z. G. Gan, C. X. Yuan, C. Qi, A. N. Andreyev, M. L. Liu, L. Ma, M. M. Zhang, Y. L. Tian, Y. S. Wang, J. G. Wang, C. L. Yang, G. S. Li, Y. H. Qiang, W. Q. Yang, R. F. Chen, H. B. Zhang, Z. W. Lu, X. X. Xu, L. M. Duan, H. R. Yang, W. X. Huang, Z. Liu, X. H. Zhou, Y. H. Zhang, H. S. Xu, N. Wang, H. B. Zhou, X. J. Wen, S. Huang, W. Hua, L. Zhu, X. Wang, Y. C. Mao, X. T. He, S. Y. Wang, W. Z. Xu, H. W. Li, Z. Z. Ren, S. G. Zhou
Summary: By combining experimental data, improved alpha-decay reduced widths for even-even Po-Pu nuclei near the magic neutron number N = 126 were deduced. It was found that the reduced widths of (214,216)U were significantly enhanced by a factor of two in certain conditions, indicating abnormal enhancement in specific nuclei under study.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Jorge Fernandez-Vazquez, Juan David Cabrer-Panes, Anna Aberg, Antonio Juarez, Cristina Madrid, Tania Gaviria-Cantin, Llorenc Fernandez-Coll, Andres Felipe Vargas-Sinisterra, Carlos Jonay Jimenez, Carlos Balsalobre
Summary: ppGpp is an intracellular sensor that coordinates gene expression in bacteria to adapt and survive under different environmental conditions, including urinary tract infections. It plays a crucial role in regulating the expression of alpha-hemolysin, a toxin that induces cytotoxicity in bladder epithelial cells during infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Marcel Aguilella-Arzo, Vicente M. Aguilella
Summary: The study found that the interaction between neutral polyethylene glycol (PEG) molecules of different molecular weights and the charged residues of the alpha-hemolysin channel secreted by Staphylococcus aureus depends on the charge state of the channel, requiring corrections to PEG-sizing techniques.
Article
Biochemistry & Molecular Biology
Suman Mishra, Anupam Roy, Somnath Dutta
Summary: This study used cryo-electron microscopy to investigate y-HL and found clustering and square lattice packing of octameric HlgAB pores on the membrane bilayer, as well as an octahedral superassembly of octameric pore complexes. The atomic model demonstrated the key residues involved in hydrophobic zipping between the rim domains of adjacent octameric complexes, providing additional structural stability in PFTs post oligomerization. Extra densities were observed at the octahedral and octameric interfaces, providing insights into the plausible lipid-binding residues involved for HlgA and HlgB components. Furthermore, the cryo-EM map resolved the previously elusive N-terminal region of HlgA, and an overall mechanism of pore formation for bicomponent 3-PFTs is proposed.
Article
Biochemistry & Molecular Biology
Jianfeng Sun, Dmitrij Frishman
Summary: The study introduces a novel deep-learning approach for predicting interaction sites in transmembrane proteins, which outperforms existing methods. Results also show that approximately 10-25% of amino acid sites are predicted to be involved in interactions in the main functional families of human transmembrane proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Caiying Zhang, Yuelong Li, Abdus Samad, Peiyi Zheng, Zheng Ji, Feng Chen, Huidong Zhang, Tengchuan Jin
Summary: phiYY P4 protein, a molecular motor with NTPase activity in the Cystoviridae family, plays a crucial role in viral particle assembly. Studies have shown that phiYY P4 differs in sequence, structure, and biochemical properties from P4 proteins of other Pseudomonas phages, highlighting its unique characteristics.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Immunology
Zhaochen Liu, Jingju Wang, Suxin Li, Luhao Li, Lin Li, Dingyang Li, Huahu Guo, Dute Gao, Shengyan Liu, Chengshuo Ruan, Xiaowei Dang
Summary: In this study, a prognostic model related to ferroptosis and EMT was developed, which could help predict overall survival in HCC patients. This model may provide a new idea for predicting the response to targeted therapies and immunotherapies in HCC patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Alicia M. Churchill-Angus, Thomas H. B. Schofield, Thomas R. Marlow, Svetlana E. Sedelnikova, Jason S. Wilson, John B. Rafferty, Patrick J. Baker
Summary: This study characterizes a tripartite toxin from Serratia marcescens and proposes a mechanism of pore assembly. The structure of soluble SmhA, as well as soluble and pore forms of SmhB, are presented. The study illustrates how the A, B, and C protomers would assemble on the membrane to produce a complete tripartite alpha-PFT pore.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Koji Ooka, Munehito Arai
Summary: Recent advancements in using deep neural networks for accurate protein structure prediction have made significant progress in solving the structure prediction aspect of the protein folding problem. However, predicting the detailed mechanisms of protein folding into specific native structures remains challenging, especially for multidomain proteins that make up the majority of proteomes. In this study, a simple structure-based statistical mechanical model was developed to incorporate nonlocal interactions that drive the folding of multidomain proteins. The model successfully predicted protein folding processes consistent with experimental results, overcoming limitations in protein size and shape. Additionally, slight modifications allowed for the prediction of disulfide-oxidative and disulfide-intact protein folding, providing insight into folding mechanisms beyond experimental reproduction. Therefore, these physics-based models enable accurate prediction of protein folding mechanisms with low computational complexity and pave the way for solving the folding process aspect of the protein folding problem.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Isabel M. Klein, Hanzhe Liu, Danika Nimlos, Alex Krotz, Scott Kevin Cushing
Summary: This article introduces a novel ab initio Bethe-Salpeter equation method for studying photoexcited-state effects in various material systems. The method demonstrates precise calculations of XUV absorption spectra and provides physical intuition on the origin of transient XUV spectra.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biochemical Research Methods
Luciano A. Abriata, Matteo Dal Peraro
Summary: Coupling residue coevolution estimations with machine learning methods is transforming protein structure prediction, particularly for proteins without clear homologous templates like in the recent CASP competition. However, making these advances accessible to non-experts and ensuring correct interpretation of predicted models still requires further development of web resources and tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Energy & Fuels
Haixu Yang, Jichao Hong, Fengwei Liang, Xiaoming Xu
Summary: This paper proposes a novel state of health prediction strategy based on ohmic internal resistance and long short-term memory networks, which can effectively evaluate the health condition of the battery system in electric vehicles.
JOURNAL OF ENERGY STORAGE
(2023)
Article
Thermodynamics
Jianping Wen, Xing Chen, Xianghe Li, Yikun Li
Summary: In this paper, a battery SOH prediction model based on incremental capacity analysis and BP neural network is proposed to predict battery SOH at different ambient temperatures. By analyzing the correlation between the characteristics of IC curve and SOH, the mapping relationship between temperature and IC curve characteristics is established, and the SOH prediction model at different temperatures is obtained. The accuracy of the model is verified by comparing the model test results and experimental results.
Article
Genetics & Heredity
Stefania Mantovani, Sergio Daga, Chiara Fallerini, Margherita Baldassarri, Elisa Benetti, Nicola Picchiotti, Francesca Fava, Anna Galli, Silvia Zibellini, Mirella Bruttini, Maria Palmieri, Susanna Croci, Sara Amitrano, Diana Alaverdian, Katia Capitani, Simone Furini, Francesca Mari, Ilaria Meloni, Elisa Frullanti, Mario U. Mondelli, Alessandra Renieri
Summary: TLR7 variants in male patients lead to impaired immune response to viruses like SARS-CoV-2, resulting in severe COVID-19. These variants cause significant damage to the TLR7 signaling pathway and hinder the type I and II interferon responses.
GENES AND IMMUNITY
(2022)
Article
Genetics & Heredity
Chiara Fallerini, Nicola Picchiotti, Margherita Baldassarri, Kristina Zguro, Sergio Daga, Francesca Fava, Elisa Benetti, Sara Amitrano, Mirella Bruttini, Maria Palmieril, Susanna Croci, Mirjam Lista, Giada Beligni, Floriana Valentino, Ilaria Meloni, Marco Tanfoni, Francesca Minnai, Francesca Colombo, Enrico Cabri, Maddalena Fratelli, Chiara Gabbi, Stefania Mantovani, Elisa Frullanti, Marco Gori, Francis P. Crawley, Guillaume Butler-Laporte, Brent Richards, Hugo Zeberg, Miklos Lipcsey, Michael Hultstrom, Kerstin U. Ludwig, Eva C. Schulte, Erola Pairo-Castineira, John Kenneth Baillie, Axel Schmidt, Robert Frithiof, Francesca Mari, Alessandra Renieri, Simone Furini
Summary: The study developed a machine-learning model using common and rare exonic variants to predict COVID-19 severity. By selecting key Boolean features and combining them into an Integrated PolyGenic Score, the model offers insights into the genetic contribution to disease severity. A quarter of the selected genes are sex-specific, and pathway analysis highlighted the multi-organ nature of COVID-19 severity. This model could potentially aid in diagnostics, therapeutics, and disease management at the bedside.
Review
Biochemistry & Molecular Biology
Kristina Zguro, Chiara Fallerini, Francesca Fava, Simone Furini, Alessandra Renieri
Summary: The COVID-19 pandemic has had a significant impact on global public health, societies, and economies. Understanding the disease better is crucial, and international collaborations have identified genetic markers that explain the varied clinical outcomes and can guide the development of diagnostics and therapeutics.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Chemistry, Medicinal
Carmen Domene, Leonardo Darre, Victoria Oakes, Saul Gonzalez-Resines
Summary: This study investigated the pathway of capsaicin entering TRP ion channels and identified two possible binding modes. The findings contribute to a better understanding of TRPV channels and provide guidance for the design of selective inhibitors, potentially leading to novel pharmacological applications targeting the TRPV1 channel.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Pharmacology & Pharmacy
Jose M. Espejo-Roman, Belen Rubio-Ruiz, Victoria Cano-Cortes, Olga Cruz-Lopez, Saul Gonzalez-Resines, Carmen Domene, Ana Conejo-Garcia, Rosario M. Sanchez-Martin
Summary: This study presents an innovative antitumor treatment strategy based on a nanodevice for selective release of an inhibitor of the HA-CD44 interaction. The conjugation of the CD44 inhibitor to the nanodevice reduces the required dosage and achieves a significant therapeutic effect.
Letter
Genetics & Heredity
Lucia Pia Bruno, Gabriella Doddato, Margherita Baldassarri, Caterina Lo Rizzo, Sara Resciniti, Mirella Bruttini, Lista Mirjam, Kristina Zguro, Simone Furini, Maria Antonietta Mencarelli, Alessandra Renieri, Francesca Ariani
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Correction
Biochemistry & Molecular Biology
Sergio Daga, Francesco Donati, Katia Capitani, Susanna Croci, Rossella Tita, Annarita Giliberti, Floriana Valentino, Elisa Benetti, Chiara Fallerini, Francesca Niccheri, Margherita Baldassarri, Maria Antonietta Mencarelli, Elisa Frullanti, Simone Furini, Silvestro Giovanni Conticello, Alessandra Renieri, Anna Maria Pinto
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Correction
Biochemistry & Molecular Biology
Susanna Croci, Miriam Lucia Carriero, Katia Capitani, Sergio Daga, Francesco Donati, Elisa Frullanti, Vittoria Lamacchia, Rossella Tita, Annarita Giliberti, Floriana Valentino, Elisa Benetti, Annalisa Ciabattini, Simone Furini, Caterina Lo Rizzo, Anna Maria Pinto, Silvestro Giovanni Conticello, Alessandra Renieri, Ilaria Meloni
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Chemistry, Medicinal
Francesco Pettini, Carmen Domene, Simone Furini
Summary: Fast C-type inactivation confers distinctive functional properties to the hERG potassium channel, but its mechanism and association with cardiac arrythmias are of paramount importance. Two models have been proposed for C-type inactivation in K+ channels, and this study used molecular dynamics simulations to investigate the mechanism in hERG. The findings suggest that C-type inactivation in hERG involves a widening of the extracellular entrance of the channel rather than a closure of the selectivity filter.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Correction
Oncology
Chiara Fallerini, Sergio Daga, Elisa Benetti, Nicola Picchiotti, Kristina Zguro, Francesca Catapano, Virginia Baroni, Simone Lanini, Alessandro Bucalossi, Giuseppe Marotta, Francesca Colombo, Margherita Baldassarri, Francesca Fava, Giada Beligni, Laura Di Sarno, Diana Alaverdian, Maria Palmieri, Susanna Croci, Andrea M. M. Isidori, Simone Furini, Elisa Frullanti, Alessandra GEN-COVID Multictr Study, Alessandra Renieri, Francesca Mari
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Biology
Eider Nunez, Frederick Jones, Arantza Muguruza-Montero, Janire Urrutia, Alejandra Aguado, Covadonga Malo, Ganeko Bernardo-Seisdedos, Carmen Domene, Oscar Millet, Nikita Gamper, Alvaro Villarroel, Henry M. Colecraft
Summary: Neuronal K(V)7 channels are highly sensitive to reactive oxygen species, and the S2S3 linker of the voltage sensor plays a crucial role in redox modulation of the channels. Recent structural studies have revealed interactions between this linker and the Ca2+-binding loop of calmodulin, specifically the EF3 hand, which is essential for the signaling. Disrupting Ca2+ binding to EF3 abolishes the oxidation-induced enhancement of K(V)7.4 currents. Furthermore, the loading of EF3 with Ca2+ is critical for the reorientation of the AB fork, which translates the Ca2+ signals.
Article
Psychiatry
Flavia Privitera, Maria A. Trusso, Floriana Valentino, Gabriella Doddato, Chiara Fallerini, Giulia Brunelli, Romina D'Aurizio, Simone Furini, Arianna Goracci, Andrea Fagiolini, Francesca Mari, Alessandra Renieri, Francesca Ariani
Summary: This study focuses on a large family with 12 members affected by bipolar disorder. Through whole-exome sequencing, certain genes, including CLN6 and ZNF92, were identified as having variations associated with the disorder. The findings suggest that heterozygous carriers of CLN6 may develop bipolar disorder later in life if combined with additional variants in ZNF92.
BRAZILIAN JOURNAL OF PSYCHIATRY
(2023)
Article
Chemistry, Medicinal
Francesco Pettini, Carmen Domene, Simone Furini
Summary: The study of the inactivation mechanism of hERG is crucial due to its association with cardiac arrhythmias. Two models, namely, the closure of the selectivity filter and the widening of the extracellular portion of the selectivity filter, have been proposed to describe C-type inactivation in potassium channels. Molecular dynamics simulations revealed that the extracellular entrance of hERG widens during inactivation, supporting the hypothesis of widening of the extracellular entrance rather than closure of the selectivity filter.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)