Article
Chemistry, Multidisciplinary
Zhen Yu, Dale F. Kreitler, Yin Ting T. Chiu, Ruiwen Xu, Austin T. Bruchs, Craig A. Bingman, Samuel H. Gellman
Summary: Peptide engineering has successfully delivered drugs for various human diseases. While side chain alteration is a common strategy, the modification of peptide backbone has received less attention. This study demonstrates that rational and coordinated side chain modification and backbone extension can engineer new and favorable contacts between target proteins and synthetic peptide ligands. These findings support the synergy between backbone and side chain modification in ligands of the parathyroid hormone receptor-1, motivating the adoption of coordinated modifications to enhance peptide ligand engagement with target proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Samantha A. Miles, Joshua Andrew Nillama, Luke Hunter
Summary: This review summarizes the applications of side chain-fluorinated amino acids in medicinal chemistry and protein science. The paper outlines strategies for incorporating fluorine atoms into amino acid side chains and elaborating these building blocks into more complex fluorinated peptides and proteins. It then describes the diverse benefits of fluorine in amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
Article
Chemistry, Physical
Myung Keun Cho, Song-Ho Chong, Seokmin Shin, Sihyun Ham
Summary: Quantifying the site-specific thermodynamic stability of proteins at the molecular level allows for identification of critical residues and understanding of cooperative interactions that stabilize the folded structure. Simultaneous formation of backbone hydrogen bonds and side-chain contacts cooperatively stabilize protein folding structure, providing insights into protein structure origins and engineering more stable proteins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Polymer Science
Shadi Kordbacheh, Andrea M. Kasko
Summary: This article reviews recent advances in selective modification reactions of peptides and proteins through less common approaches to improve their stability and enhance their biological function.
POLYMER INTERNATIONAL
(2021)
Article
Chemistry, Applied
Kun Yang, Limei Wang, Juanjuan Guo, Di Wu, Xian Wang, Mengting Wu, Xiaolong Feng, Jing Ma, Yunhua Zhang, Weiqing Sun
Summary: The study demonstrates that direct current magnetic field treatment significantly enhances the water-holding capacity of myofibrillar protein gels, possibly by altering protein structure and intermolecular re-crosslinking. The treated samples exhibit a relatively loose and uniform microstructure post-treatment, facilitating more water trapping.
Article
Chemistry, Multidisciplinary
Maxim B. Gindele, Krzysztof K. Malaszuk, Christine Peter, Denis Gebauer
Summary: We experimentally investigated the binding characteristics and parameters of calcium ions to different polycarboxylates, and found that higher order effects play a crucial role in polymers with high polymerization degrees. Additionally, the presence of primary binding sites and the overall structure of the polymer chain are important factors to consider when interpreting binding data. Therefore, solely studying monomers or oligomers may not be sufficient to explain ion binding to polymers.
Article
Engineering, Biomedical
Daniela Serien, Aiko Narazaki, Koji Sugioka
Summary: Femtosecond laser direct write (fs-LDW) is a promising technology for high-resolution, flexible, and versatile three-dimensional printing using protein solution as a precursor. The diverse proteins with different native functions enable various applications of this technology. However, the lack of understanding of the printing mechanism hampers the design and generation of 3D microstructures for biomedical applications. In this study, we used eight commercially available homopeptides as precursors and found that tyrosine, histidine, glutamic acid, and lysine contribute more to the fabrication process, indicating the involvement of ions in addition to the previously proposed radical mechanism. The findings suggest that the uneven electron density over larger amino acid molecules plays a significant role in aiding fs-LDW.
ACTA BIOMATERIALIA
(2023)
Review
Electrochemistry
Elena Suprun
Summary: This review focuses on the direct electrochemistry of proteins and nucleic acids on solid electrodes, emphasizing the importance of understanding their redox transformations from a 3D structure perspective. The potential of the 3D concept in biopolymer electrochemistry for registering molecular events like complex formation and post-translational modifications is highlighted. It also points out the lack of systematic studies in this field and the need for in-depth investigation of reaction mechanisms.
ELECTROCHEMISTRY COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Naveed Ahmad, Wenbin Qian, Peixu Sun, Xiaoxiao Wang, Kai Zhang, Xia Xu
Summary: This study investigates the effect of side chains on CO2 absorption in deep eutectic solvents based on amino acids and monoethanolamine. The results show that the functional group types and the number of alkyl groups in amino acids have an impact on the reaction rate of CO2 absorption and the solvent viscosity. The study reveals the reaction mechanism of CO2 capture using deep eutectic solvents.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Review
Biotechnology & Applied Microbiology
Yoichi Toyokawa, Jirasin Koonthongkaew, Hiroshi Takagi
Summary: BCAT catalyzes transamination between BCAAs and BCKAs in the cell. Eukaryotic cells have mitochondrial BCAT (BCATm) and cytosolic BCAT (BCATc) isozymes, which have similar enzymatic functions but differences in physiological functions and regulatory mechanisms. The variations of BCAT could have significant implications for research into the relationship between their primary structures and protein functions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Hasan Siami, Mohammad Razmkhah, Fatemeh Moosavi
Summary: This study investigated the impact of different side chain groups on the absorption of SO2 using 1-propyl-3-methylimidazolium cation with various amino acid anions. The results showed that enlarging the alkyl group from glycinate to leucinate slightly decreased gas absorption interaction energy, while changing the side chain group to methyl thiol (cysteinate) or methyl alcohol (serinate) drastically altered the gas interaction energy. The charge transfer and distance between the anion and absorbed SO2 gas were found to be the lowest in glycinate, making it the most effective absorbent in the study. The distribution of van der Waals (vdW) interaction differed between the glycinate system and the other systems, with the vdW distribution being concentrated and clear in glycinate. (c) 2023 Elsevier B.V. All rights reserved.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Leonor Cruzeiro, Andrew C. Gill, J. Chris Eilbeck
Summary: The study indicates that amino acids play a crucial role in protein folding, with the alpha-helix potentially being the initial structure of most proteins before folding begins.
Article
Chemistry, Applied
Song Gao, Zixin Fu, Longteng Zhang, Bo Li, Yuqing Tan, Hui Hong, Yongkang Luo
Summary: This study investigated the effects of protein oxidation on digestion behavior. It found that frozen bighead carp fillets had high oxidation levels and low protein digestibility, which were further increased by brining. The oxidation resulted in various modifications in the amino acids, decreased protein digestibility, and impacted intestinal transportation. These findings emphasize the importance of considering oxidation in food processing and preservation strategies.
Article
Multidisciplinary Sciences
Lara Console, Mariafrancesca Scalise, Simona Salerno, Raffaella Scanga, Deborah Giudice, Loredana De Bartolo, Annamaria Tonazzi, Cesare Indiveri
Summary: CD98 is a membrane protein with pleiotropic roles and its stability and localization are crucial for human therapy, as mutations severely impair its function and affect other associated proteins.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Gang Xu, Yilin Wang, Qinghua Wang, Jianpeng Ma
Summary: In this study, the performance of the OPUS-Mut side-chain modeling method and other methods were evaluated on three oligomer datasets. OPUS-Mut outperformed other methods in terms of all residues and interfacial residues. The study also demonstrated the effectiveness of their method in evaluating protein-protein docking pose.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Instruments & Instrumentation
Andrew J. C. Dennison, Francesca Natali, Emmanuel Farhi, Giuliana Manzin, Pierre Courtois, Judith Peters
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT
(2018)
Article
Chemistry, Physical
Saara Laulumaa, Michael Marek Koza, Tilo Seydel, Petri Kursula, Francesca Natali
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Review
Physics, Condensed Matter
Giorgio Schiro, Martin Weik
JOURNAL OF PHYSICS-CONDENSED MATTER
(2019)
Article
Multidisciplinary Sciences
F. Natali, C. Dolce, J. Peters, C. Stelletta, B. Deme, J. Ollivier, M. Boehm, G. Leduc, I. Piazza, A. Cupane, E. L. Barbier
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2019)
Article
Multidisciplinary Sciences
F. Natali, C. Dolce, J. Peters, C. Stelletta, B. Deme, J. Ollivier, G. Leduc, A. Cupane, E. L. Barbier
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
P. Vauclare, F. Natali, J. P. Kleman, G. Zaccai, B. Franzetti
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Physical
M. Zanatta, L. Tavagnacco, E. Buratti, E. Chiessi, F. Natali, M. Bertoldo, A. Orecchini, E. Zaccarelli
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Multidisciplinary Sciences
Alexandre Colas de la Noue, Francesca Natali, Fatima Fekraoui, Patrick Gervais, Nicolas Martinez, Jean-Marie Perrier-Cornet, Judith Peters
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Amedeo Amedei, Fatemeh Asadzadeh, Francesco Papi, Maria Giuliana Vannucchi, Veronica Ferrucci, Iris A. Bermejo, Marco Fragai, Carolina Vieira De Almeida, Linda Cerofolini, Stefano Giuntini, Mauro Bombaci, Elisa Pesce, Elena Niccolai, Francesca Natali, Eleonora Guarini, Frank Gabel, Chiara Traini, Stefano Catarinicchia, Federica Ricci, Lorenzo Orzalesi, Francesco Berti, Francisco Corzana, Massimo Zollo, Renata Grifantini, Cristina Nativi
Article
Physics, Multidisciplinary
Giorgio Schiro, Yann Fichou, Alex P. S. Brogan, Richard Sessions, Wiebke Lohstroh, Michaela Zamponi, Gerald J. Schneider, Francois-Xavier Gallat, Alessandro Paciaroni, Douglas J. Tobias, Adam Perriman, Martin Weik
Summary: The study revealed that solvent-free protein-polymer hybrids can replace hydration water, preserving protein structure and function, with dynamics similar to water's.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Davide Bochicchio, Laura Cantu, Maria Vittoria Cadario, Leonardo Palchetti, Francesca Natali, Luca Monticelli, Giulia Rossi, Elena Del Favero
Summary: Synthetic plastic oligomers can interact with living organisms in various ways, and their effects on cell structure and dynamics are still not well understood. Research has shown that doping doses of polystyrene oligomers can alter the thermal properties of lipid membranes and modify their mechanical properties. This calls for a systematic and interdisciplinary assessment of the interaction mechanisms between synthetic polymers and cell membranes.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Andreas Santamaria, Krishna C. Batchu, Olga Matsarskaia, Sylvain F. Prevost, Daniela Russo, Francesca Natali, Tilo Seydel, Ingo Hoffmann, Valerie Laux, Michael Haertlein, Tamim A. Darwish, Robert A. Russell, Giacomo Corucci, Giovanna Fragneto, Armando Maestro, Nathan R. Zaccai
Summary: This study investigates the role of SARS-CoV-2 Spike fusion peptides in cellular infection using neutron scattering and spectroscopy techniques. The findings reveal that calcium drives the fusion peptides to cross the host plasma membrane, while removal of calcium leads to peptide reorientation and significant changes in lipid properties. Combining with other regions in the fusion domain, the molecular events of cell entry by SARS-CoV-2 are proposed.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Pharmacology & Pharmacy
Angela Faccendini, Eleonora Bianchi, Marco Ruggeri, Barbara Vigani, Cesare Perotti, Francesco Claudio Pavesi, Laura Caliogna, Francesca Natali, Elena Del Favero, Laura Cantu', Franca Ferrari, Silvia Rossi, Giuseppina Sandri
Summary: The study developed a scaffold that mimicked tissue fibrous arrangement and ECM composition, loaded with human platelet lysate to enhance tissue regeneration post-surgery. The results suggest that HP and PL have a synergic effect, making HP-loaded PL-aligned tubular scaffolds an effective strategy to support new tissue formation in tendon-to-bone interface regeneration.
Article
Biology
Derren J. Heyes, Samantha J. O. Hardman, Martin N. Pedersen, Joyce Woodhouse, Eugenio De La Mora, Michael Wulff, Martin Weik, Marco Cammarata, Nigel S. Scrutton, Giorgio Schiro
COMMUNICATIONS BIOLOGY
(2019)
Article
Physics, Multidisciplinary
L. Tavagnacco, M. Zanatta, E. Buratti, B. Rosi, B. Frick, F. Natali, J. Ollivier, E. Chiessi, M. Bertoldo, E. Zaccarelli, A. Orecchini
Summary: By combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, a proteinlike dynamical transition in linear chains of poly(N-isopropylacrylamide) has been observed, with the onset of the transition identified at a temperature T-d of about 225 K. Quantitative agreement between measured and calculated polymer mean-squared displacements at all temperatures and time resolutions was found through a global fit procedure. The results confirm the generality of the dynamical transition in macromolecular systems in aqueous environments, independently of the internal polymer topology.
PHYSICAL REVIEW RESEARCH
(2021)