Article
Materials Science, Ceramics
Adriana Serban, Florina Teodorescu, Ancuta M. Sofronia, Irina Atkinson, Cornelia A. Marinescu, Alina Botea-Petcu, Florentina Maxim, Speranta Tanasescu
Summary: Hydroxyapatite (HAP), a major inorganic component of human body's hard tissues, plays a critical role in its interaction with proteins. In this study, the interaction between different types of HAP materials and bovine serum albumin (BSA) was investigated. The results showed that the physicochemical properties of HAP materials significantly influenced the thermodynamic profile of the protein-HAP interactions.
CERAMICS INTERNATIONAL
(2023)
Article
Food Science & Technology
Rong Lu, Yanrui Ding
Summary: This study investigated the importance of water-protein interactions for protein structure and stability by analyzing the conformational changes of proteins at different temperatures. Results showed that stabilizing flexible regions is crucial for maintaining protein structure, and residues forming stable hydrogen bonds with water can also form stable interactions with other residues.
Article
Biochemistry & Molecular Biology
Bin Song, Xiuying Xu, Jingyao Hou, Meihong Liu, Ning Yi, Chengbin Zhao, Jingsheng Liu
Summary: The interaction between corn starch and black bean protein isolate (BBPI) during food processing was studied, and its effects on the physicochemical properties of the blends were investigated. The addition of BBPI reduced the rheological properties and increased light transmittance and gelatinization temperature of the corn starch/BBPI mixed system. Fourier transform infrared spectroscopy (FT-IR) revealed that BBPI decreased the number of hydrogen bonds within starch, and reduced the composite relative crystallinity. Moreover, protein addition influenced water migration during gelatinization, preventing water molecules from diffusing into starch particles.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Chemistry, Multidisciplinary
Seishi Shimizu, Nobuyuki Matubayasi
Summary: By using statistical thermodynamic fluctuation theory, the sorption mechanism can be elucidated directly from an experimental isotherm without the need of using an isotherm model. The key to understanding the sorption mechanism lies in how sorbate-sorbate interaction depends on activity, without assuming adsorption sites and planar layers.
Article
Chemistry, Physical
Andrea Auer, Bernhard Eder, Franz J. Giessibl
Summary: This paper presents a combined AFM/STM instrument realized with a qPlus sensor and a home-built potentiostat for electrochemical applications. It demonstrates the potential of the instrument by simultaneously imaging graphite with atomic resolution in acidic electrolytes and precisely measuring the interfacial solvent layering as a function of the applied potential.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Chen-Ming Lin, Zhengyang Jiang, Zhe Gao, Maritess Arancillo, Kevin Burgess
Summary: The study explored the potential disruption of the NEDD8·NAE interaction using various chemotype designs through EKO evaluation. A compound was identified from a targeted library for its ability to bind NAE, inhibit NEDDylation, and induce cytotoxicity in leukemia cells. It represents a first-in-class inhibitor of NEDDylation and demonstrates the utility of EKO in evaluating chemotypes as potential PPI inhibitors.
Article
Chemistry, Applied
Daniel Zmudzinski, Urszula Goik, Pawel Ptaszek, Anna Ptaszek, Jakub Barbasz, Joanna Banas, Dawid Lupa
Summary: This study conducted a comprehensive investigation on the protein concentrate aqueous solutions from Lens culinaris L. seeds, and found that the solvent parameters had a significant impact on the surface tension.
Article
Chemistry, Physical
Navathej Preetha Genesh, Daling Cui, Dominik Dettmann, Oliver MacLean, Tarnjit Kaur Johal, Andrey V. Lunchev, Andrew C. Grimsdale, Federico Rosei
Summary: The precise control of molecular self-assembly on surfaces provides opportunities for complex nanostructure creation. Selective patterning using molecular interactions at the solid-liquid interface was observed in the self-assembly of 1,3,5-tris(4-methoxyphenyl)benzene (TMPB) molecules on the Au(111) surface. Resulting from higher adsorption energy, TMPB molecules preferred to assemble in the face-centered cubic (FCC) regions of Au(111). The coverage of TMPB molecules increased with solution concentration, leading to a full monolayer, and induced the lifting of the herringbone reconstruction at higher concentrations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Engineering, Environmental
Xuan Yu, Joshua J. LeMonte, Junxia Li, Jason W. Stuckey, Donald L. Sparks, John G. Cargill, Christopher J. Russoniello, Holly A. Michael
Summary: Historical industrial activities have caused soil contamination at coastlines worldwide, which are susceptible to disruptions by climate change and rising sea levels. However, the effects of hydrologic dynamics on contaminant transportation in tidal environments have not been extensively studied. This research collected data from various sensors at a contaminated site near a freshwater tidal channel and found that seasonal groundwater interactions and sub-daily water level fluctuations in the channel contribute to varying redox conditions and contaminant concentrations. The findings highlight the importance of understanding the impacts of sea-level rise on the mobility of coastal solutes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Optics
Spencer T. Stober, Stuart M. Harwood, Dimitar Trenev, Panagiotis Kl Barkoutsos, Tanvi P. Gujarati, Sarah Mostame
Summary: Quantum chemistry applications rely on the VQE algorithm to compute thermodynamic properties. Designing efficient workflows that utilize both quantum and classical hardware is crucial. By carefully selecting workflow options, significant improvements in accuracy can be achieved.
Article
Food Science & Technology
Ohmura Masato, Matsumiya Kentaro, Maeda Tatsuro, Fujita Akio, Hayashi Yukako, Matsumura Yasuki
Summary: The study investigated the effects of manufacturing process and drying temperature on the properties of starch in pasta. Starch isolated from different sources had varied physicochemical properties, with starch from raw pasta forming a soft gel. Increasing drying temperature of pasta resulted in harder and more brittle gels, along with higher amounts of starch granule surface-bound protein. This indicates that the amount of starch granule surface-bound protein may be an indicator of starch-protein interaction affecting the physical properties of extracted starch gels.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Environmental Sciences
Jagannath Pal, Arnab Patla, Ranga Subramanian
Summary: Gas-phase properties of methanol-water and ethanol-water clusters were calculated using density functional theory, revealing that the free energy of specific clusters is negative only at certain temperature and pressure conditions. The Rayleigh scattering properties of these clusters were investigated and an increase in scattering intensity was observed at 400 nm compared to the static limit.
Article
Chemistry, Applied
Haobo Jin, Yi Sun, Jiajing Pan, Yue Fang, Yongguo Jin, Long Sheng
Summary: This study investigated the dynamic adsorption properties of ovalbumin and lysozyme at the air-water interface and the foam properties at neutral pH. A 5:5 ratio of ovalbumin to lysozyme was found to result in the most stable foam structure, with maximum turbidity. The appropriate protein ratio was crucial for the relaxation of the protein complex structure and the mechanical structure of the interfacial composite protein membrane.
FOOD HYDROCOLLOIDS
(2022)
Article
Chemistry, Physical
Qi Han, Yuyu Su, Kate M. Smith, Jack Binns, Calum J. Drummond, Connie Darmanin, Tamar L. Greaves
Summary: Ions play an important role in modulating protein properties, and ionic liquids (ILs) have the potential to control protein properties through specific ion binding. This study investigates the specific ion binding effect of ILs on the behavior of lysozyme protein, including phase behavior, activity, size, conformational change, aggregation, and intermolecular interactions. The results provide new insights into protein-IL binding interactions and the use of ILs to modulate protein properties.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Thao Vu, Elizabeth M. Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell P. Bowler, Farnoush Banaei-Kashani, Katerina J. Kechris
Summary: Biological networks provide a system-level understanding of underlying processes. In order to investigate the association between modules and variables of interest, a module summarization method that can explain the module's information and reduce dimensionality is needed. This article proposes NetSHy, a hybrid approach that incorporates topological properties to aid downstream analysis interpretation while reducing network dimensionality.
Article
Chemistry, Multidisciplinary
David J. Huggins, Bryn S. Hardwick, Pooja Sharma, Amy Emery, Luca Laraia, Fengzhi Zhang, Ana J. Narvaez, Meredith Roberts-Thomson, Alex T. Crooks, Robert G. Boyle, Richard Boyce, David W. Walker, Natalia Mateu, Grahame J. McKenzie, David R. Spring, Ashok R. Venkitaraman
Article
Biochemical Research Methods
David J. Huggins
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2020)
Article
Multidisciplinary Sciences
John H. Beale, May E. Marsh
Summary: A protocol is presented to create large volumes of micro-crystalline slurries for crystallography experiments, based on optimizing crystal morphology, transitioning to batch, and scaling strategies. Endothiapepsin is used as a demonstration protein for the protocol.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Medicinal
John Ginn, Xiuju Jiang, Shan Sun, Mayako Michino, David J. Huggins, Zodwa Mbambo, Robert Jansen, Kyu Y. Rhee, Nancy Arango, Christopher D. Lima, Nigel Liverton, Toshihiro Imaeda, Rei Okamoto, Takanobu Kuroita, Kazuyoshi Aso, Andrew Stamford, Michael Foley, Peter T. Meinke, Carl Nathan, Ruslana Bryk
Summary: The development and effectiveness of novel analogs targeting the mycobacterial lipoamide dehydrogenase in inhibiting the growth of Mycobacterium tuberculosis was discussed in the article. These analogs showed improved permeability, potency, and selectivity, as well as on-target activity within the mycobacteria by increasing intrabacterial pyruvate levels. Improved potency and selectivity were achieved through distinct binding modalities between the mycobacterial and human enzymes.
ACS INFECTIOUS DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Tobias Muehlethaler, Dario Gioia, Andrea E. Prota, May E. Sharpe, Andrea Cavalli, Michel O. Steinmetz
Summary: Using a combined computational and crystallographic approach, researchers identified 27 distinct binding sites in tubulin, including 11 previously unknown sites. They also observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. These results provide a structural basis for developing novel small molecules as tubulin modulators and lay down a framework that may aid in discovering new pockets in other pharmaceutically important targets.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Medicinal
Xiaomin Ni, Martin Schroeder, Vincent Olieric, May E. Sharpe, Victor Hernandez-Olmos, Ewgenij Proschak, Daniel Merk, Stefan Knapp, Apirat Chaikuad
Summary: The nsP3 macrodomain is crucial in regulating the host immune response during SARS-CoV-2 infection by recognizing and removing posttranslational ADP-ribosylation sites. Targeting this protein domain could provide a therapeutic strategy for combating virus pandemics. Crystal structures complexed with diverse nucleotides, small molecules, and nucleotide analogues, including active metabolites of remdesivir, provide valuable insights for inhibitor development.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Biochemical Research Methods
Isabelle Martiel, John H. Beale, Agnieszka Karpik, Chia-Ying Huang, Laura Vera, Natacha Olieric, Maximilian Wranik, Ching-Ju Tsai, Jonas Muhle, Oskar Aurelius, Juliane John, Martin Hogbom, Meitian Wang, May Marsh, Celestino Padeste
Summary: Serial data collection using thin supports made of polymer-based membranes has proven to be a useful method for challenging targets with small crystal sizes, weak diffraction, and stringent dose limits. These supports are suitable for a wide range of protein crystals suspended in liquid, including membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, resulting in optimally thin specimens with low background and minute amounts of mother liquor around the crystals, making it a flexible and adaptable solution for various cases. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Jakub W. Kaminski, Laura Vera, Dennis P. Stegmann, Jonatan Vering, Deniz Eris, Kate M. L. Smith, Chia Ying Huang, Nathalie Meier, Julia Steuber, Meitian Wang, Guenter Fritz, Justyna A. Wojdyla, May E. Sharpe
Summary: Fragment-based drug discovery has been proven to be an effective and efficient method for identifying new chemical scaffolds. X-ray crystallography can be used to validate and develop identified fragments, and recent technological advancements have enabled the development of dedicated platforms for FBDD using X-ray crystallography.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
David J. Huggins
Summary: This paper presents an approach to alchemical binding free energies using OpenMM and evaluates the prediction accuracy using benchmark test sets. The findings highlight the effectiveness of some AMBER forcefields, particularly AMBER ff15ipq.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Bill Pedrini, Aaron D. Finke, May Marsh, Pierangelo Luporini, Adriana Vallesi, Claudio Alimenti
Summary: The crystal structures of two pheromones Er-1 and Er-13 from the ciliate Euplotes raikovi support the cooperative model of pheromone/receptor binding, with molecules arranged into linear chains in an alternate opposite orientation. These structures provide new insights into the mechanisms underlying the different behavior of autocrine and heterologous pheromone/receptor complexes.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Chia Ying Huang, Sylvain Aumonier, Sylvain Engilberge, Deniz Eris, Kate Mary Louise Smith, Filip Leonarski, Justyna Aleksandra Wojdyla, John H. Beale, Dominik Buntschu, Anuschka Pauluhn, May Elizabeth Sharpe, Alexander Metz, Vincent Olieric, Meitian Wang
Summary: Continuous developments in cryogenic X-ray crystallography have provided us with most of our understanding of 3D protein structures. However, the use of cryogenic temperatures may result in fictitious structures, limiting our knowledge of protein dynamics. In this study, a room-temperature X-ray crystallographic method was developed to capture structural snapshots under physiological conditions, revealing surprising binding discrepancies and capturing multiple binding poses and their interactions with DMSO. This opens up new prospects for structure determination and interpretation at physiological temperatures.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Wei Chen, Di Cui, Steven V. Jerome, Mayako Michino, Eelke B. Lenselink, David J. Huggins, Alexandre Beautrait, Jeremie Vendome, Robert Abel, Richard A. Friesner, Lingle Wang
Summary: In the hit identification stage of drug discovery, absolute protein-ligand binding free-energy perturbation (ABFEP) is a theoretically rigorous and accurate method that can greatly improve hit rates in virtual screening. In this work, an implementation of ABFEP method in FEP+ was described and validated using different compounds and protein receptors. The calculated binding free energies showed good correlation with experimental results and demonstrated the usefulness of ABFEP in improving hit rates in virtual screening.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Instruments & Instrumentation
Kate Mary Louise Smith, Ezequiel Panepucci, Jakub Wojciech Kaminski, Sylvain Aumonier, Chia-Yiang Huang, Deniz Eris, Dominik Buntschu, Nathalie Meier, Wayne Glettig, Katherine Evelyn McAuley, Meitian Wang, May Elizabeth Sharpe, Justyna Aleksandra Wojdyla
Summary: Recent advances in automation have enabled the development of unattended data collection services in several synchrotron facilities globally. This paper focuses on the Swiss Light Source, where the implementation of new high-throughput sample changers and the commissioning of the Fast Fragment and Compound Screening pipeline provided an opportunity for automated data acquisition. The paper discusses the upgrades in the DA+ microservice software stack, the automatic loop-centering service, and the deployment of the Smart Digital User (SDU) software for unattended data collection. The SDU software plays a crucial role in communication between services, ensuring sample and device safety, sample centering, alignment with grid-based X-ray diffraction, and ultimately, data collection.
JOURNAL OF SYNCHROTRON RADIATION
(2023)
Article
Biochemistry & Molecular Biology
Duncan E. Scott, Nicola J. Francis-Newton, May E. Marsh, Anthony G. Coyne, Gerhard Fischer, Tommaso Moschetti, Andrew R. Bayly, Timothy D. Sharpe, Kalina T. Haas, Lorraine Barber, Chiara R. Valenzano, Rajavel Srinivasan, David J. Huggins, Miyoung Lee, Amy Emery, Bryn Hardwick, Matthias Ehebauer, Claudio Dagostin, Alessandro Esposito, Luca Pellegrini, Trevor Perrior, Grahame McKenzie, Tom L. Blundell, Marko Hyvonen, John Skidmore, Ashok R. Venkitaraman, Chris Abell
Summary: The study identifies CAM833 as an orthosteric inhibitor of RAD51:BRC, which affects DNA repair and potentiates cell death induced by DNA damage, working in coordination with PARP1 inhibitors to suppress growth in BRCA2-wildtype cells.
CELL CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Igor Maksimovic, Efrat Finkin-Groner, Yoshiyuki Fukase, Qingfei Zheng, Shan Sun, Mayako Michino, David J. Huggins, Robert W. Myers, Yael David
Summary: This study utilized the recent understanding of DJ-1 deglycation mechanism to develop a method for evaluating potential drug leads, establishing a new platform for targeting DJ-1.
RSC MEDICINAL CHEMISTRY
(2021)