Article
Chemistry, Physical
Keisuke Hirata, Ken-ichi Kasai, Gilles Gregoire, Shun-ichi Ishiuchi, Masaaki Fujii
Summary: UV and IR spectra of protonated dopamine and its hydrated clusters were measured, showing different spectral features. Structure and excited state lifetime were determined through calculations, suggesting that water insertion inhibits excited state proton transfer.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Food Science & Technology
Juliana F. da Silva, Aline T. do B. Morais, Willy G. Santos, Lilia M. Ahrne, Daniel R. Cardoso
Summary: Beta-lactoglobulin (beta-Lg) is a whey protein known for its allergenicity and resistance to digestion. UV-C light-induced cleavage of disulfide bonds in beta-Lg changes its secondary structure, reducing its resistance to pepsin digestion. The reduction of disulfide bonds occurs through direct electron transfer and reaction with a solvated electron. UV-C-treated beta-Lg showed increased gastric digestion index and production of bioactive peptides.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Engineering, Mechanical
Ping Liu, Qing-Xiang Pei, Yong -Wei Zhang
Summary: In this study, molecular dynamics simulations are used to investigate the low-cycle fatigue life and failure mechanism of MoS2 with a crack. It is found that factors such as strain range, strain ratio, initial crack size, and temperature have a negative impact on the fatigue life of MoS2. The study also reveals the detailed fatigue failure process and shows the occurrence of bond rupture and remaking at the crack tips during cyclic loading.
EXTREME MECHANICS LETTERS
(2023)
Article
Chemistry, Physical
Leila Shahrokh, Reza Omidyan, Gholamhassan Azimi
Summary: The non-radiative relaxation mechanism of protonated adenine was investigated using quantum chemical computational methods and dynamics simulations. It was found that the out-of-plane deformation of the six-member ring plays a significant role in the deactivation of the excited state to the ground state, which is important for the photostability of protonated DNA/RNA bases.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Rong Xu, Edwina Jap, Ben Gubbins, Christoph E. Hagemeyer, John A. Karas
Summary: Insulin replacement therapy is crucial for diabetes management, but there is a need to improve glycaemic control and patients' quality of life. Researchers have developed a semi-synthetic approach using biosynthetic peptide precursors and chemically synthesised fragments to produce stable insulin analogues. This approach has the potential to support the development of hyper-stable proteomimetics.
JOURNAL OF PEPTIDE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Lei Zhu, Hongxin Zhao, Juanjuan Liu, Hao Cai, Bo Wu, Zhijun Liu, Shu Zhou, Qingsong Liu, Xiaokun Li, Bin Bao, Jian Liu, Han Dai, Junfeng Wang
Summary: FGF21 is a regulator of glucose and lipid metabolism, and the designed FGF21(SS) chimera shows improved thermostability and effectiveness against T2DM through structural analysis and design.
Article
Biology
N. Dehghanbanadaki, H. Mehralitabar, R. Sotoudeh, H. Naderi-Manesh
Summary: In this study, the researchers investigated the role of the thumb palmitoleyl group and conserved disulfides in regulating the interaction and structural dynamics between Wnt and FZ receptors. Their results showed that the palmitoleyl group is important for stabilizing the Wnt-FZ interaction, and the disulfides modulate this contribution. Specifically, they identified the significant role of disulfide 183-190 in establishing a long-range salt-bridge interaction and positioning the palmitoleyl group appropriately for Wnt-FZ complex formation.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Physical
Christoph Schran, Fabien Brieuc, Dominik Marx
Summary: The neural network potential previously applied to protonated water clusters up to the tetramer is successfully extended to the protonated water hexamer with high accuracy, demonstrating its transferability and usefulness in extrapolation regimes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Yanyan Chu, Huanhuan Zhang, Mengke Yang, Rilei Yu
Summary: Transient receptor potential vanilloid 1 (TRPV1), a non-selective cation channel, can be activated by oxidants through cysteine modification. This study revealed that the formation of a disulfide bond between C387 and C391 leads to conformational changes in the channel, with several residues playing essential roles in the channel opening. These findings provide new insights into the activation mechanism of TRPV1 and have implications for the treatment of human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Applied
Jamoliddin Razzokov, Sunnatullo Fazliev, Dinora Erkinova, Shavkat Mamatkulov, Zhitong Chen
Summary: This study investigated the effects of reactive oxygen and nitrogen species (RONS) on the human epidermal growth factor (hEGF) through molecular dynamics simulations. The results showed that nitrosylation induced conformational changes in hEGF and disruption of disulfide bonds, but the structural stability of hEGF remained mostly unaffected.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2022)
Article
Optics
Ori Licht, Maria Nihamkin, Mirit Anaby, Patrick Rousseau, Alexandre Giuliani, Aleksandar R. Milosavljevic, Raj Singh, Vy T. T. Nguyen, Laurent Nahon, Yoni Toker
Summary: In our recent study, we have demonstrated that photon absorption can lead to the formation of chemical bonds within a protonated serine dimer, known as intra-cluster bond formation. This process is not observed following thermal excitation via low energy collision-induced dissociation. We provide further evidence for non-statistical photon-induced dissociation of the protonated serine dimer. Additionally, we discuss the results of studies on the protonated serine octamer, which also show non-statistical fragmentation and the formation of two bonds between three neighboring monomers through photon-induced dissociation.
JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Richard J. Spears, Alina Chrzastek, Steven Y. Yap, Kersti Karu, Abil E. Aliev, James R. Baker, Vijay Chudasama
Summary: In this study, we report a significant discovery regarding the use of tris(dialkylamino)phosphine reagents in peptide and protein modification. We found that C-terminal thiophosphonium species can be selectively and rapidly generated from their disulfide counterparts, with unique stability. In contrast, internal thiophosphonium species degrade quickly. We demonstrated this chemoselectivity on a model peptide and an antibody fragment, and characterized the species in various small molecule/peptide studies.
CHEMICAL COMMUNICATIONS
(2022)
Article
Polymer Science
Xiangrui Zheng, Hua Yang, Yaguang Sun, Yongqin Zhang, Yafang Guo
Summary: The paper investigates the self-healing mechanism based on disulfide bond exchange reactions at the atomic scale through molecular dynamics simulations. It explores the effects of crosslink density and healing time on self-healing efficiency and mechanical properties. The results show that high crosslink density improves mechanical properties but reduces molecular chain mobility, while shorter stress relaxation time leads to higher healing efficiency.
Article
Food Science & Technology
Paul W. Johns
Summary: The method described in the study provides a simple and effective way to accurately and precisely determine sulfur amino acids in protein powders and nutritional products, without the need for specialized amino acid analysis instrumentation. It involves acid hydrolysis and direct LC/UV quantification, with assessments showing good performance in terms of linearity, precision, accuracy, selectivity, and quantitation limit.
FOOD ANALYTICAL METHODS
(2021)
Article
Biochemistry & Molecular Biology
Mariana H. Moreira, Fabio C. L. Almeida, Tatiana Domitrovic, Fernando L. Palhano
Summary: Defensins are small, amphipathic proteins with disulfide bonds, challenging tertiary protein structure predictors. Comparing defensins with non-defensins showed no differences in residue proportions and solvent exposure. Bonded small proteins had more exposed apolar residues than unbonded proteins, with Robetta predicting unbonded proteins more accurately. trRosetta, using AI, improved prediction for bonded proteins but not unbonded ones, highlighting the complexity of predicting protein tertiary structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Chemistry, Multidisciplinary
Satchin Soorkia, Christophe Jouvet, Gilles Gregoire
Article
Dermatology
Melanie Pedrazzani, Josselin Breugnot, Pauline Rouaud-Tinguely, Maxime Cazalas, Arthur Davis, Sylvie Bordes, Arnaud Dubois, Brigitte Closs
SKIN RESEARCH AND TECHNOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Maheshwar Gopu, Sachin Rathod, Uma Namangalam, Ravi Kumar Pujala, S. Sunil Kumar, Dileep Mampallil
Article
Chemistry, Physical
Salvi Mohandas, Raghunath O. Ramabhadran, S. Sunil Kumar
JOURNAL OF PHYSICAL CHEMISTRY A
(2020)
Article
Physics, Multidisciplinary
Gayathry Rajeevan, Salvi Mohandas, S. Sunil Kumar
Summary: This study focused on numerical simulations of ion dynamics of small biomolecular ions in a 16-pole ion trap and a 16-wire ion trap under the influence of elastic collisions with a buffer gas. The comparison of effective potentials in these trap configurations was provided, with particular emphasis on storage efficiency and ion temperature. It was found that while the wire trap has a limited optimum operating range for storage efficiency compared to the pole trap, it can serve as a practical alternative with proper choice of operating parameters and lateral optical access for spectroscopic studies.
Article
Biochemical Research Methods
Julie Chauvel-Picard, Vincent Berot, Linda Tognetti, Carmen Orte Cano, Margot Fontaine, Clement Lenoir, Javiera Perez-Anker, Susana Puig, Arnaud Dubois, Sandra Forestier, Jilliana Monnier, Randa Jdid, Gabriel Cazorla, Melanie Pedrazzani, Antoine Sanchez, Sebastien Fischman, Pietro Rubegni, Veronique del Marmol, Joseph Malvehy, Elisa Cinotti, Jean L. Perrot, Mariano Suppa
Summary: This study utilized LC-OCT technology for quantitative analysis of epidermal three-dimensional topography, revealing variations in epidermal metrics across different body sites, and observing real-time evidence of keratinocyte maturation process.
JOURNAL OF BIOPHOTONICS
(2022)
Review
Instruments & Instrumentation
Hemanth Dinesan, S. Sunil Kumar
Summary: This review focuses on the development of laser-induced fluorescence (LIF) spectroscopy for trapped gas-phase molecular ions. It summarizes the current state-of-the-art techniques used for intrinsic fluorescence measurement and discusses the challenges and potential solutions for gas-phase ion experiments. The review suggests that borrowing measurement schemes from condensed-phase experiments and improving the signal-to-noise ratio by utilizing high-finesse optical cavities and high numerical aperture collection optics could greatly enhance the detection of weak gas-phase fluorescence emission.
APPLIED SPECTROSCOPY
(2022)
Article
Dermatology
C. Orsini, E. Trovato, G. Cortonesi, M. Pedrazzani, M. Suppa, P. Rubegni, L. Tognetti, E. Cinotti
Summary: This study investigated the potential of LC-OCT for non-invasive monitoring of microscopic changes associated with psoriasis during treatment. The results showed that LC-OCT can effectively recognize and quantify microscopic criteria, and there is a high correlation between these criteria and the clinical severity of the disease. LC-OCT may represent a valid tool for precise monitoring of therapeutic response.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Physics, Multidisciplinary
Nandana Pattathadathil, S. Sunil Kumar
Summary: In this work, numerical simulations were conducted to analyze the extraction characteristics of biomolecular ions stored in 16-pole and 16-wire ion traps. The results show that the ions extracted from a wire trap with a simple upgrade exhibit time-of-flight distributions two orders of magnitude narrower than that typically results from conventional ion traps. Furthermore, the upgraded design allows the ions to be confined within a much narrower region, making it compatible with fluorescence spectroscopy measurements due to higher optical access of the wire trap configuration.
Article
Instruments & Instrumentation
M. Salvi, N. N. Uma, Hemanth Dinesan, Abheek Roy, S. Sunil Kumar
Summary: A linear 16-pole ion trap-based experimental setup has been designed to investigate the photophysics of biomolecules in the gas phase. The instrument's versatility and capability are showcased by controlling ion energy and mass selection.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Multidisciplinary Sciences
Franck Bonnier, Melanie Pedrazzani, Sebastien Fischman, Theo Viel, Agnes Lavoix, Didier Pegoud, Meryem Nili, Yolande Jimenez, Samuel Ralambondrainy, Jean-Hubert Cauchard, Rodolphe Korichi
Summary: Quantitative biomarkers of facial skin ageing were studied using in vivo 3D Line-field Confocal Optical Coherence Tomography (LC-OCT) imaging coupled with Artificial Intelligence (AI)-based quantification algorithms. Age-related variations were observed in the epidermal layer, including a flatter and more homogeneous epidermis, a less dense cellular network, and larger and more heterogeneous nuclei within each layer.
SCIENTIFIC REPORTS
(2023)
Article
Astronomy & Astrophysics
Stepan Roucka, Serhiy Rednyk, Thuy Dung Tran, Artem Kovalenko, Dmytro Mulin, Sunil S. Kumar, Petr Dohnal, Radek Plasil, Juraj Glosik
Summary: This study experimentally confirms that there are no significant energy barriers involved in the formation of nitrogen hydrides in the interstellar medium.
ASTROPHYSICAL JOURNAL
(2023)
Proceedings Paper
Engineering, Biomedical
F. Latriglia, J. Ogien, S. Fischman, M. Pedrazzani, A. Dubois
Summary: LC-OCT is a technology that allows diagnosis and monitoring of skin pathologies at a cellular level. Its 3D images provide visualization of skin layers and tissue, while the use of artificial intelligence enables accurate diagnosis and follow-up treatment.
TRANSLATIONAL BIOPHOTONICS: DIAGNOSTICS AND THERAPEUTICS III
(2023)
Article
Optics
D. Muell, F. Grussie, K. Blaum, S. George, J. Goeck, M. Grieser, R. von Hahn, Z. Harman, A. Kalosi, C. H. Keitel, C. Krantz, C. Lyu, O. Novotny, F. Nuesslein, D. Paul, V. C. Schmidt, S. Singh, S. Sunil Kumar, X. Urbain, A. Wolf, H. Kreckel
Summary: The long-lived metastable states of silicon anions were studied using the Cryogenic Storage Ring at the Max Planck Institute for Nuclear Physics. The experimental results were in agreement with theoretical predictions and showed improvement in previous efforts. Various laser systems and techniques were utilized to measure lifetimes of different anionic states and produce pure ground state beams.
Article
Chemistry, Physical
Jordan Dezalay, Michel Broquier, Satchin Soorkia, Keisuke Hirata, Shun-ichi Ishiuchi, Masaaki Fujii, Gilles Gregoire
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
