Article
Chemistry, Multidisciplinary
Jacqueline R. Santhouse, Jeremy M. G. Leung, Lillian T. Chong, W. Seth Horne
Summary: By studying the folding kinetics and mechanism of the BdpA sequence, researchers found that altering the backbone connectivity can affect protein folding. This suggests that protein mimetic chains have a significant degree of plasticity in transitioning between unfolded and folded states.
Article
Nutrition & Dietetics
Berenice Palacios-Gonzalez, Guadalupe Leon-Reyes, Berenice Rivera-Paredez, Isabel Ibarra-Gonzalez, Marcela Vela-Amieva, Yvonne N. Flores, Samuel Canizales-Quinteros, Jorge Salmeron, Rafael Velazquez-Cruz
Summary: This study aims to investigate the sex-specific serum modifications of amino acids and acylcarnitines (ACs) and their relationship with MetS in the Mexican population. The findings show that a serum amino acid signature (citrulline and glycine) and medium-chain ACs (AC14:1, AC10, and AC18:10H) are associated with MetS. Glycine and AC10 are specific metabolites for discrimination based on sex-dependent MetS. Additionally, glycine and short-chain ACs (AC2, AC3, and AC8:1) are associated with age-dependent MetS.
Article
Chemistry, Physical
Santanu Santra, Shakuntala Dhurua, Madhurima Jana
Summary: Amino acids with basic side chains are known to increase the stability of proteins in their native-folded state, however, the efficiency and molecular mechanism behind this process are still controversial. A study using molecular dynamics simulations found that arginine, histidine, and lysine solutions have varying effects on the hydration and conformational stability of the insulin monomer. Arginine was observed to influence insulin stability by enhancing the exclusion of water molecules from the protein surface, leading to more rigid conformations compared to histidine and lysine.
JOURNAL OF CHEMICAL PHYSICS
(2021)
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
Immunology
Qiang Lei, Bo Yuan, Kun Liu, Li Peng, Zhiwei Xia
Summary: In this study, eight high-risk lncRNAs related to amino acid metabolism were identified, and it was found that these lncRNAs can predict the prognosis and treatment response of glioma patients, emphasizing the importance of amino acid metabolism in glioma.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Akito Machida, Kumiko Kondo, Ken-ichi Wakabayashi, Kan Tanaka, Toru Hisabori
Summary: In this study, the importance of the amino acid at position 252 across cyanobacteria was elucidated by introducing amino acid substitutions in Synechocystis sp. PCC 6803. The results showed that the specific volume of this amino acid is crucial for maintaining cell growth and is related to enzyme complex formation.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Agricultural Engineering
R. Bevilacqua, A. Regueira, M. Mauricio-Iglesias, J. M. Lema, M. Carballa
Summary: This study found that pH adjustment can influence the production of volatile fatty acids during mixed-culture fermentation of proteins. The conversion of proteins into VFAs is affected by pH, energetic yields, and the molecular configuration of amino acids.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Yang Liu, Andrew J. Wilson, Jiatong Han, Alisa Hui, Lucy O'Sullivan, Tao Huan, Cara H. Haney
Summary: Understanding how microbiota evade and suppress host immunity is critical to our knowledge of how beneficial microbes persist in association with a host. This work shows that microbial amino acid metabolism is not only critical for growth in the plant rhizosphere microbiome, but also for regulation of plant rhizosphere pH, and, consequentially, regulation of plant immunity.
Article
Chemistry, Physical
Yuanyuan Zhang, You Li, Zhaoming Ran, Na Wang, Aicha Mekkaoui, Ce Wang, Li Zhao, Baocai Xu
Summary: Amino acid surfactants have been increasingly studied due to their diverse molecular structures and properties. This study systematically investigated the interfacial behaviors of amino acid surfactants with different N-methyl and polar, nonpolar, and aromatic α-substituents using interfacial dilational rheological experiments. The results provide a research basis for the development and application of N-acyl amino acid surfactants.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Engineering, Biomedical
Meike N. Leiske, Bruno G. De Geest, Richard Hoogenboom
Summary: Zwitterionic polymers interact with cells and exhibit cancer cell specificity. The polymer backbone chemistry plays a significant role in the cellular specificity of amino-acid-derived polyzwitterions. Differences in cellular association and specificity were observed among the different polymer backbones, highlighting the importance of the polymer backbone design for cell-specific polymers.
BIOACTIVE MATERIALS
(2023)
Article
Polymer Science
Remi Casier, Jean Duhamel
Summary: The combination of a fluorescence blob model and molecular mechanics optimizations was used to determine the contribution of pyrene label in polypeptides and predict the protein folding times. This approach showed promising results with a correlation coefficient of 0.73 between calculated and experimentally determined folding times.
Article
Biochemistry & Molecular Biology
Yang Yang, Zhang Chong, Mauno Vihinen
Summary: Most proteins fold into unique three-dimensional structures and their folding rates can be influenced by variations in proteins. We developed a machine-learning-based method, PON-Fold, to predict the folding rate effects of amino acid substitutions in two-state folding proteins. PON-Fold outperformed existing tools in blind tests, showing higher specificity, sensitivity, and correlation coefficient. The tool was also tested for protein domain substitutions and showed varying predictions depending on protein conformations and structures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Green & Sustainable Science & Technology
Edmar Costa Alves, Israel Henrique dos Santos Alves, Bruna Borges Soares, Aurelio Ferreira Borges, Arshad Jalal, Arun Dilipkumar Jani, Cassio Hamilton Abreu-Junior, Gian Franco Capra, Thiago Assis Rodrigues Nogueira
Summary: This study fills important gaps in the geographic scope of poultry farming using Life Cycle Assessment analysis. The results show that greenhouse gas emissions during the feed production phase are the main environmental impact. The study also proposes three scenarios, demonstrating that using poultry viscera meal can lead to better environmental outcomes.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Chemistry, Multidisciplinary
Woojin Choi, Taesuk Jun, Milae Lee, Kyungtae Park, Moonhyun Choi, Sungwon Jung, Jae-Kook Cha, Jae-Sung Kwon, Youngho Jin, Sangmin Lee, Du Yeol Ryu, Jinkee Hong
Summary: Water-responsive crystallization is a typical behavior of biopolymers, which has implications for the development of intelligent human-robot interfaces. However, it also hinders the consistent adhesion of tissue adhesive. This study developed an amino acid-based technology to regulate the crystallization of silk fibroin, achieving targeted control over the crystallization process.
Article
Biodiversity Conservation
Zheng Jiang, Yuling Fu, Lingyan Zhou, Yanghui He, Guiyao Zhou, Peter Dietrich, Jilan Long, Xinxin Wang, Shuxian Jia, Yuhuang Ji, Zhen Jia, Bingqian Song, Ruiqiang Liu, Xuhui Zhou
Summary: Root exudates play a crucial role in plant-microbial interactions and are highly sensitive to climate change. This study examined how extreme drought affects root exudates and their components, as well as species-specific differences in response. Results showed that extreme drought significantly reduced root exudation rates of total carbon, sugar, and amino acid, but increased exudation rate of organic acid. This response was associated with changes in tree growth rates, root morphological traits, and mycorrhizal infection rates. These findings emphasize the importance of considering plant growth strategy in predicting climate change impacts on rhizosphere carbon dynamics.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Christian Opitz, Erik Ahrne, Kenneth N. Goldie, Alexander Schmidt, Stephan Grzesiek
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Layara Akemi Abiko, Anne Grahl, Stephan Grzesiek
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Immunology
Anne-Valerie Burgener, Glenn R. Bantug, Benedikt J. Meyer, Rebecca Higgins, Adhideb Ghosh, Olivier Bignucolo, Eric H. Ma, Jordan Loeliger, Gunhild Unterstab, Marco Geigges, Rebekah Steiner, Michel Enamorado, Robert Ivanek, Danielle Hunziker, Alexander Schmidt, Bojana Mueller-Durovic, Jasmin Grahlert, Raja Epple, Sarah Dimeloe, Jonas Loetscher, Ursula Sauder, Monika Ebnoether, Bettina Burger, Ingmar Heijnen, Sarai Martinez-Cano, Nathan Cantoni, Rolf Bruecker, Christian R. Kahlert, David Sancho, Russell G. Jones, Alexander Navarini, Mike Recher, Christoph Hess
Article
Biotechnology & Applied Microbiology
Christian Opitz, Grit Schade, Silvan Kaufmann, Marco Di Berardino, Marcel Ottiger, Stephan Grzesiek
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2019)
Article
Biochemical Research Methods
Bastian Franke, Tuomo Frigard, Stephan Grzesiek, Shin Isogai
JOURNAL OF CHROMATOGRAPHY A
(2020)
Article
Neurosciences
Omar Alijevic, Olivier Bignucolo, Echrak Hichri, Zhong Peng, Jan P. Kucera, Stephan Kellenberger
FRONTIERS IN CELLULAR NEUROSCIENCE
(2020)
Article
Multidisciplinary Sciences
Chee-Seng Hee, Judith Habazettl, Christoph Schmutz, Tilman Schirmer, Urs Jenal, Stephan Grzesiek
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Olivier Bignucolo, Simon Berneche
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Olivier Bignucolo, Sabrina Vullo, Nicolas Ambrosio, Ivan Gautschi, Stephan Kellenberger
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Layara Akemi Abiko, Marco Rogowski, Antoine Gautier, Gebhard Schertler, Stephan Grzesiek
Summary: The study presents strategies for E. coli expression of GPCRs and developed an optimized protocol with quantification of losses in receptor material during solubilization and purification steps, resulting in final yields of 0.2-0.3 mg per liter; High-quality NMR studies were successfully conducted using E. coli-expressed mutants, with similar results to mutants expressed in insect cells.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Biology
Sabrina Vullo, Nicolas Ambrosio, Jan P. Kucera, Olivier Bignucolo, Stephan Kellenberger
Summary: Acid-sensing ion channels (ASICs) play important roles in neuroscience, but their activation mechanism remains unclear. Research suggests that conformational changes in channel activation speed may be driven by local protonation events, indicating the existence of a pathway linking protonation sites to the channel pore.
Article
Chemistry, Physical
Olivier Bignucolo, Christophe Chipot, Stephan Kellenberger, Benoit Roux
Summary: A central problem in computational biophysics is the treatment of titratable residues in molecular dynamics simulations. Conventional methods assume a fixed ionization state for these residues, which is limited. Constant-pH simulation methods provide a more realistic approach by allowing the ionization state to vary statistically. These methods sample all accessible configurations and ionization states properly weighted according to their Boltzmann factor.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Feng-Jie Wu, Pascal S. Rieder, Layara Akemi Abiko, Philip Roessler, Alvar D. Gossert, Daniel Haeussinger, Stephan Grzesiek
Summary: The method presented in this study utilizes antibodies tagged with lanthanoid DOTA chelators to efficiently assign nuclei of biomacromolecules, providing insights into their chemical shift changes during functional dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Sophie Roy, Niklaus Johner, Viktor Trendafilov, Ivan Gautschi, Olivier Bignucolo, Ophelie Molton, Simon Berneche, Stephan Kellenberger
Summary: The extracellular Ca2+ concentration affects the function of ion channels in the nervous system, and we investigated how Ca2+ controls the activity of ASIC3. We discovered a new regulatory site in ASIC3 and demonstrated that ASIC3 activation involves the unbinding of Ca2+ from the channel pore.
Article
Allergy
Annaise J. Jauch, Olivier Bignucolo, Sayuri Seki, Marie Ghraichy, Ottavia M. Delmonte, Valentin von Niederhausern, Rebecca Higgins, Adhideb Ghosh, Masako Nishizawa, Mariko Tanaka, Adrian Baldrich, Julius Koppen, Julia R. Hirsiger, Robin Hupfer, Stephan Ehl, Anne Rensing-Ehl, Helmut Hopfer, Spasenija Savic Prince, Stephen R. Daley, Florian A. Marquardsen, Benedikt J. Meyer, Michael Tamm, Thomas D. Daikeler, Tamara Diesch, Thomas Kuehne, Arthur Helbling, Caroline Berkemeier, Ingmar Heijnen, Alexander A. Navarini, Johannes Truck, Jean-Pierre de Villartay, Annette Oxenius, Christoph T. Berger, Christoph Hess, Luigi D. Notarangelo, Hiroyuki Yamamoto, Mike Recher
Summary: This study reveals that monoallelic LIG4 mutations may lead to immune dysregulation in humans, characterized by autoimmune cytopenias, lymphoproliferation, decreased specific T cells, and DNA damage intolerance. This finding is important for understanding the pathogenesis of immune-related disorders.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)