Article
Chemistry, Physical
Changwon Yang, Soonmin Jang, Youngshang Pak
Summary: Utilizing fully atomistic replica exchange molecular dynamics simulations, this study reveals the distinct thermodynamic roles of protein and water molecules in protein stability and their different responses to temperature variations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Polymer Science
Masayuki Hibino, Shin-ichi Takata, Kosuke Hiroi, Hiroyuki Aoki, Takaya Terashima
Summary: Amphiphilic random copolymers with PEG and alkyl groups form size-controlled micelles in water. The exchange kinetics and mechanism of the copolymer chains between micelles were investigated using TR-SANS. The exchange involved two mechanisms: a dominant unimer release and insertion pathway under diluted conditions, and an increasing contribution of micelle collision pathway with higher polymer concentration and temperature. The activation energy for the exchange process was dependent on the hydrophobic alkyl groups.
Article
Biology
Eva Bulyaki, Judit Kun, Tamas Molnar, Alexandra Papp, Andras Micsonai, Henrietta Vadaszi, Borbala Marialigeti, Attila Istvan Kovacs, Gabriella Gellen, Keiichi Yamaguchi, Yuxi Lin, Masatomo So, Mihaly Jozsi, Gitta Schlosser, Young-Ho Lee, Karoly Liliom, Yuji Goto, Jozsef Kardos
Summary: The exceptional amyloidogenicity of the pathogenic D76N beta 2m variant is realized by the deleterious synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules (e.g., lipids) and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular components, including extracellular matrix proteins, relative to WT beta 2m.
Article
Biochemistry & Molecular Biology
Jingwen Li, Jingfei Chen, Yefei Wang, Lishan Yao
Summary: The hydrogen bond cooperativity in the beta-sheet of GB3 protein is investigated using a NMR hydrogen/deuterium exchange method. It is found that weakening one hydrogen bond perturbs other neighboring hydrogen bonds, with three being cooperative and one being anticooperative. This hydrogen bond cooperativity plays a significant role in the stability and conformational coupling of the beta-sheet.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Nobuyuki Matubayasi
Summary: This article discusses the influence of solvation on protein structure and equilibrium of aggregate formation, presenting a theoretical framework and computational scheme to analyze solvation effects. The connection of solvation free energy to protein structure and aggregation tendency is quantitatively described through correlation analysis and molecular dynamics simulations.
CHEMICAL COMMUNICATIONS
(2021)
Article
Engineering, Chemical
Simon B. B. Solberg, Pauline Zimmermann, Oivind Wilhelmsen, Robert Bock, Odne S. Burheim
Summary: Using non-equilibrium thermodynamics, we analysed concentration cells and determined the transference coefficients of ion-exchange membranes in aqueous KCl solutions. The results showed that the membranes are selective to the target ion and each ion carries 3-4 water molecules through the membrane. We also found a large contribution to the measured concentration cell voltage from concentration gradients across the porous plug of the reference electrode.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Hematology
Qiuyue Ma, Roland Immler, Monika Pruenster, Markus Sellmayr, Chenyu Li, Albrecht von Brunn, Brigitte von Brunn, Rosina Ehmann, Roman Woelfel, Matteo Napoli, Qiubo Li, Paola Romagnani, Ralph Thomas Boettcher, Markus Sperandio, Hans-Joachim Anders, Stefanie Steiger
Summary: This study investigates the impact of uric acid on neutrophils and finds that hyperuricemia impairs neutrophil function. Partial reduction of uric acid levels using uricase can partially restore the neutrophil defects. The study reveals that uric acid affects neutrophil migration by regulating intracellular pH and cytoskeletal dynamics. These findings have important implications for understanding immunodeficiency in kidney disease and sterile inflammation.
Article
Chemistry, Physical
M. Bestetti
Summary: This paper first explains the definition of heat in thermodynamics, and then addresses the problem of temperature and heat exchange in bodies at thermal equilibrium, providing a new perspective based on the principle of mobile equilibrium.
RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Yuichi Yoshimura, Masatomo So, Yohei Miyanoiri
Summary: The N-15-H-1 heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy is affected by line-broadening effects such as chemical exchange of labile protons with solvent and exchange broadening for residues undergoing conformational dynamics. The amide resonance of beta(2)-microglobulin residue 588 is not observed in the HSQC spectrum, and line broadening of 588 resonance beyond detection in the HSQC spectrum is attributed to solvent exchange occurring on the order of similar to 10^3 s(-1).
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Kuo-Tung Tang, Ting-Yuan Wu, Hsin-Hua Chen, Chi-Chien Lin, Yuan-Hao Howard Hsu
Summary: Beta-2-glycoprotein I is the main antigen for antiphospholipid antibodies, with domain I being key to its interaction. When binding to DOPS, conformational changes in beta(2)GPI were localized to sequence 21-27, while interaction with CL induced changes across multiple domains. The high negative charge of CL membrane triggered a major conformational transition in beta(2)GPI.
Article
Chemistry, Multidisciplinary
Neng Li, Zhoulan Zeng, Youwei Zhang, Xingzhu Chen, Zhouzhou Kong, Arramel, Yong Li, Peng Zhang, Ba-Son Nguyen
Summary: This study theoretically investigated the HER catalytic mechanism of oxygen-terminated D-MXenes and highlighted the superior performance of Mo-based D-MXenes compared to Cr-based D-MXenes. The results suggest that constructing a sandwich-like configuration can improve the HER performance of M-MXenes, paving the way for designing efficient MXene-based HER electrocatalysts.
Article
Chemistry, Multidisciplinary
Dalia Naser, Michael Tarasca, Bruna Siebeneichler, Anna Schaefer, Harmeen K. Deol, Tyler G. B. Soule, Johnathan Almey, Susan Kelso, Gyana G. Mishra, Hilary Simon, Elizabeth M. Meiering
Summary: Protein aggregation plays a central role in aging, disease and biotechnology. This study used NMR quenched amide hydrogen/deuterium exchange, FTIR, and Congo red binding to analyze cellular inclusion bodies of immature human superoxide dismutase mutants. The results revealed multiple aggregation-prone regions in SOD1 and provided insights into the pathways of aggregation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Applied
Mengqi Peng, Hengzhao Li, Zixuan Qin, Junyu Li, Yanhao Sun, Xiaoxu Zhang, Ling Jiang, Hainam Do, Jie An
Summary: It was found that highly regioselective H/D exchange could be achieved on the alpha-position of the pentafluorophenyl (Pfp) ester using Et3N as the catalyst and D2O as the deuterium source. This method provides mild reaction conditions and high reactivity, allowing the synthesis of important bioactive alpha-deuterio carboxylic acid derivatives.
ADVANCED SYNTHESIS & CATALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Federico Bonaldo, Fulvio Mattivi, Daniele Catorci, Panagiotis Arapitsas, Graziano Guella
Summary: This passage discusses the behavior of different classes of flavonoids during hydrogen/deuterium exchange processes. Detailed kinetic measurements were reported using H-1-NMR spectra at different temperatures, leading to the proposal of a unifying reaction mechanism. Molecular modeling and QM calculations were also conducted to provide further insights into the proposed mechanism.
Article
Energy & Fuels
Simon B. B. Solberg, Pauline Zimmermann, Oivind Wilhelmsen, Jacob J. Lamb, Robert Bock, Odne S. Burheim
Summary: The reverse electrodialysis heat engine (REDHE) is a technology that can produce hydrogen using waste heat, driven by a salinity gradient. The concept of evaporation requires less waste heat and produces more hydrogen compared to the precipitation concept.
Article
Chemistry, Physical
Federico Fogolari, Gennaro Esposito, Bruce Tidor
Summary: The entropy associated with rotations, translations, and their coupled motions plays a vital role in physicochemical processes. The kth nearest neighbor method is effective for estimating entropy in high-dimensional spaces, even in cases involving correlated translational-rotational motion of multiple molecules. Experimental results show that accurate entropy estimates for two correlated translational-rotational motions can be achieved using this method.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Oncology
Diana Canetti, Paola Nocerino, Nigel B. Rendell, Nicola Botcher, Janet A. Gilbertson, Angel Blanco, Dorota Rowczenio, Alessandra Morelli, P. Patrizia Mangione, Alessandra Corazza, Guglielmo Verona, Sofia Giorgetti, Loredana Marchese, Per Westermark, Philip N. Hawkins, Julian D. Gillmore, Vittorio Bellotti, Graham W. Taylor
Summary: Apolipoprotein A-IV amyloidosis is a rare disease that may be associated with signal sequence residues. These residues can induce amyloid formation in vitro and may influence protein deposition and other pathological processes in vivo.
JOURNAL OF PATHOLOGY
(2021)
Article
Chemistry, Physical
Cristina Cantarutti, Yamanappa Hunashal, Carmelo La Rosa, Marcello Condorelli, Sofia Giorgetti, Vittorio Bellotti, Federico Fogolari, Gennaro Esposito
Summary: It has been discovered that changing the ionic strength of the medium can adjust the form and strength of the interaction between nanoparticles and proteins, thus impacting the mechanism of nanomaterials on proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Giulia Faravelli, Valentina Mondani, P. Patrizia Mangione, Sara Raimondi, Loredana Marchese, Francesca Lavatelli, Monica Stoppini, Alessandra Corazza, Diana Canetti, Guglielmo Verona, Laura Obici, Graham W. Taylor, Julian D. Gillmore, Sofia Giorgetti, Vittorio Bellotti
Summary: The transition of proteins from globular to fibrillar state is a key event in the development of amyloid diseases. The complex process of protein metamorphism is an ideal metaphor for studying protein folding and investigating folding dynamics. However, there is still a major gap between in vivo and in vitro models of fibrillogenesis, and studying the transformation of globular proteins in systems of increasing complexity may help bridge this gap.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Matteo Moretti, Isabella Marzi, Cristina Cantarutti, Mirella Vivoli Vega, Walter Mandaliti, Maria Chiara Mimmi, Francesco Bemporad, Alessandra Corazza, Fabrizio Chiti
Summary: TAR DNA-binding protein 43 (TDP-43) has been associated with amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The N-terminal domain (NTD) of TDP-43 plays a crucial role in its function and the formation of intraneuronal inclusions. The study identified an alternative conformation of NTD in the presence of SB3-10, which led to a more α-helical structure. The results also showed that the aggregation of TDP-43 was slower when pre-incubated with SB3-10, indicating the disruption of oligomeric seeds by the alternative conformation conditions. These findings provide insights into the plasticity of TDP-43 NTD and suggest strategies for monomerising TDP-43 NTD for various applications.
Article
Biochemistry & Molecular Biology
Cristina Cantarutti, Maria Chiara Mimmi, Guglielmo Verona, Walter Mandaliti, Graham W. Taylor, P. Patrizia Mangione, Sofia Giorgetti, Vittorio Bellotti, Alessandra Corazza
Summary: It has been found through research that there are labile interactions between the plasma protein transthyretin (TTR) and free calcium ions (Ca2+), which make TTR more prone to aggregation and may be related to the development of systemic amyloidosis (ATTR).
Article
Computer Science, Interdisciplinary Applications
Miguel Angel Soler, Ozge Ozkilinc, Yamanappa Hunashal, Paolo Giannozzi, Gennaro Esposito, Federico Fogolari
Summary: Biomolecular electrostatics plays a crucial role in biological function and recognition. The Poisson-Boltzmann equation and the Generalized Born model are commonly used methods to study biomolecular electrostatics. This work presents a tutorial on the program Bluues, which can efficiently calculate various properties related to electrostatic effects and pH dependence.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Saida Saad Mohamed Mahmoud, Beatrice Portelli, Giovanni D'Agostino, Gianluca Pollastri, Giuseppe Serra, Federico Fogolari
Summary: This study aims to analyze the influence of surrounding residues on the single-sequence secondary structure prediction of a protein. Different prediction methods are compared, and the results show that mutual information and linear models quantify direct effects, while DeepLIFT applied on deep learning networks quantifies both direct and indirect effects. The best results are obtained using the BERT architecture.
CURRENT BIOINFORMATICS
(2023)
Review
Chemistry, Multidisciplinary
Federico Fogolari, Roberto Borelli, Agostino Dovier, Gennaro Esposito
Summary: The article introduces the application and advantages of the kth nearest neighbor method in entropy estimation, as well as the relevant variables, metrics, and applications associated with this method. By combining this method with mutual information, high-dimensional problems can be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Gabriele Coluccino, Valentina Pia Muraca, Alessandra Corazza, Giovanna Lippe
Summary: Mitochondrial dysfunction is crucial in many complex diseases. Understanding the role of the mitochondrial matrix protein CyPD in regulating cell death and its involvement in neurodegenerative disorders, particularly Alzheimer's Disease and Parkinson's Disease, can provide new therapeutic targets. CyPD is involved in regulating the permeability transition pore in the inner mitochondrial membrane, and its dysregulated opening can lead to cell death. Additionally, CyPD interacts with various biochemical pathways. Exploring the post-translational modifications of CyPD can enhance our understanding. Development of CyPD-specific inhibitors holds promise for the treatment of these complex diseases.
Meeting Abstract
Biochemistry & Molecular Biology
Alessandra Franzoni, Daniela Driul, Nadia Passon, Dora Fabbro, Federica Baldan, Paola Cogo, Federico Fogolari, Giuseppe Damante
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Chemistry, Applied
Alina Ramona Buzatu, Miguel Angel Soler, Sara Fortuna, Ozge Ozkilinc, Diana Maria Dreava, Ioan Bitcan, Valentin Badea, Paolo Giannozzi, Federico Fogolari, Lucia Gardossi, Francisc Peter, Anamaria Todea, Carmen Gabriela Boeriu
Summary: In this study, a novel approach using reactive natural deep eutectic solvents as reaction medium was developed for the enzymatic esterification of carbohydrate polyols with fatty acids. The study successfully synthesized high-purity polyol esters under optimized reaction conditions.
Article
Endocrinology & Metabolism
Alessandra Franzoni, Federica Baldan, Nadia Passon, Catia Mio, Daniela Driul, Paola Cogo, Federico Fogolari, Federica D'Aurizio, Giuseppe Damante
Summary: This study used the AlphaFold artificial intelligence algorithm to predict the pathogenicity of IGFALS gene mutations, initially classified as variants of uncertain significance (VUS). This has potential implications for interpreting VUS results in genetic testing.
Article
Chemistry, Multidisciplinary
Thirumurugan Prakasam, Yamanappa Hunashal, Cristina Cantarutti, Sofia Giorgetti, Giulia Faravelli, Valentina Mondani, Sudhir Kumar Sharma, Ramesh Jagannathan, Giovanni Palmisano, Vittorio Bellotti, Federico Fogolari, John-Carl Olsen, Ali Trabolsi, Gennaro Esposito
Summary: This study investigates the interactions of metal-organic assemblies with beta(2)-microglobulin variants and finds that metal coordination can inhibit fibrillation in vitro, while zinc-free assemblies may induce protein aggregation. Administration of the best protein-contacting species TK in a disease model organism confirms its bioactivity potential.
CELL REPORTS PHYSICAL SCIENCE
(2021)
Article
Engineering, Environmental
Daniele Veclani, Marilena Tolazzi, Federico Fogolari, Andrea Melchior
Summary: This study utilized molecular dynamics simulations to investigate the adsorption of the anti-inflammatory diclofenac (DCF) by carbon nanomaterials with various functional groups. The results showed different types of interactions between DCF and the materials, with surface desolvation playing a major role in determining the thermodynamic affinity order for DCF adsorption.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
