Article
Pharmacology & Pharmacy
Michael H. Ronzetti, Bolormaa Baljinnyam, Zina Itkin, Sankalp Jain, Ganesha Rai, Alexey V. Zakharov, Utpal Pal, Anton Simeonov
Summary: Differential scanning fluorimetry is a rapid and economical biophysical technique used to monitor protein structure changes. By using a fluorescence dye sensitive to structural changes near histidine-tagged protein, a stable and sensitive DSF assay is established. The assay is optimized and miniaturized into a high-throughput biophysical platform, validated with BbHtrA as a proof of concept.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Medicinal
Soo Hyun Kim, Han Ju Yoo, Eun Ji Park, Dong Hee Na
Summary: Nano differential scanning fluorimetry (nanoDSF) is a powerful tool for thermal stability screening and optimal buffer selection in antibody formulations. In this study, the thermal stability of immunoglobulin G (IgG) was investigated in different buffers. The results showed that the sodium acetate buffer at pH 4.6 was suitable for IgG formulation, as it provided the best stability against aggregation. In contrast, the sodium citrate buffer had higher aggregation and viscosity than the sodium acetate buffer at the same pH. Protein-protein interaction studies suggested that the difference in aggregation between acetate and citrate buffers could be explained by attractive intermolecular interactions in citrate buffer and repulsive interactions in acetate buffer.
Article
Pharmacology & Pharmacy
Paula Leandro, Paulo R. Lino, Raquel Lopes, Joao Leandro, Mariana P. Amaro, Paulo Sousa, Joao B. Vicente, Antonio J. Almeida
Summary: The structural maintenance of therapeutic proteins during formulation and/or storage is crucial. Protein freeze-drying is a commonly used technique for preserving protein structure and function. In this study, differential scanning fluorimetry (DSF) and isothermal denaturation fluorimetry (ITDF) were used to screen for the most effective stabilizer for the model protein human phenylalanine hydroxylase (hPAH) among different freeze-drying additives. ITDF was found to be the most suitable screening method based on correlation studies with recovered enzyme amount and activity. The selected compounds prevented protein aggregation and preserved hPAH structural and functional properties throughout long-term storage.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2023)
Article
Biochemistry & Molecular Biology
Hubert Gorny, Angelique Mularoni, Jean-Guy Delcros, Celine Freton, Jordane Preto, Isabelle Krimm
Summary: The mitochondrial voltage-dependent anion channel 1 (VDAC1) has important roles in metabolism and apoptosis, making it a potential therapeutic target. However, the molecular mechanisms of VDAC1 functioning are still unclear. Small-molecule ligands that interact specifically with VDAC1 can be used to explore its structure-function relationships and potentially serve as foundations for future drug development. In this study, we used nano-differential scanning fluorimetry and microscale thermophoresis to perform ligand-binding assays on seventeen known VDAC1 ligands. By combining both technologies, we identified four molecules (cannabidiol, curcumin, DIDS, and VBIT4) as chemical starting points for the design of VDAC1 selective ligands.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Zhao Cui, Peng Chen, Caifeng Li, Shiwen Deng, Hongjun Yang
Summary: In this study, we developed a chip-DSF strategy that combines label-free differential scanning fluorimetry (DSF) with protein chips for rapid target verification, improving the accuracy and efficiency of protein chip target screening.
PHARMACOLOGICAL RESEARCH
(2022)
Article
Biology
Raniya Khadiullina, Regina Mirgayazova, Damir Davletshin, Elvina Khusainova, Vitaly Chasov, Emil Bulatov
Summary: The p53 protein plays a crucial role in maintaining genome integrity. Half of all human cancers have inactivating mutations in the TP53 gene. Certain missense mutations decrease the thermal stability of p53 protein, leading to its unfolding and aggregation under normal conditions. Understanding the impact of point mutations on mutant p53's stability and conformation is essential for developing small molecules that target specific p53 mutations. This study investigates the thermostability properties of several common mutant forms of p53 protein (p53(R273H), p53(R248Q), p53(R248W), and p53(Y220C)), which are potential therapeutic targets, and reveals their destabilization and decreased melting temperature.
Article
Biochemical Research Methods
Anna Serbina, Anthony C. Bishop
Summary: This study demonstrates the use of differential scanning fluorimetry as a rapid and quantitative method to measure the strength of SHP2 autoinhibition. This method does not require protein labeling or specialized instrumentation and is applicable for evaluating the autoinhibitory interactions in different SHP2 mutants.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Kari Kopra, Salla Valtonen, Randa Mahran, Jonas N. Kapp, Nazia Hassan, William Gillette, Bryce Dennis, Lianbo Li, Kenneth D. Westover, Andreas Plueckthun, Harri Harma
Summary: Thermal unfolding methods are commonly used to predict protein's thermal stability and to screen potential drugs. Differential scanning calorimetry is considered the gold standard, but other methods like differential scanning fluorimetry are also used. These methods have relatively low sensitivity. By comparing three thermal stability probes, researchers found that the Protein-Probe is more sensitive and can work at lower concentrations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ankur Saikia, Sebastian Springer
Summary: Recombinant major histocompatibility complex class I molecules are used in cancer immunotherapy, with studies utilizing nanoDSF to investigate peptide binding and the thermal denaturation of HLA-A*02:01.
MOLECULAR IMMUNOLOGY
(2021)
Article
Management
Fengfeng Huang, Pengfei Guo, Yulan Wang
Summary: This study analyzes a group testing strategy that aims to maximize the efficiency of the SARS-CoV-2 screening test while maintaining its effectiveness. The study finds that group testing may result in a higher probability of false negative results but a lower probability of false positive results compared to individual testing. To ensure test effectiveness, the group size and disease prevalence need to be controlled within certain thresholds.
OMEGA-INTERNATIONAL JOURNAL OF MANAGEMENT SCIENCE
(2022)
Article
Chemistry, Medicinal
Meifeng Nie, Yue Liu, Xiaofen Huang, Zhigang Zhang, Qinjian Zhao
Summary: Nano/microparticles are commonly used in vaccine adjuvants to improve antigen stability and enhance immune response. This study developed a high throughput microtiter plate-based differential scanning fluorimetry (DSF) method to assess protein thermal stability in the form of particulate adjuvants. Results showed enhanced sensitivity and correlation to traditional differential scanning calorimetry (DSC). The plate-based DSF method offers higher throughput and lower sample consumption compared to DSC, making it suitable for formulation development and early project stages.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2022)
Article
Biology
Annemarie Danielsson, Malgorzata M. Kogut, Martyna Maszota-Zieleniak, Pradeep Chopra, Geert-Jan Boons, Sergey A. Samsonov
Summary: This study proposes a molecular dynamics-based method to describe unbound Heparan Sulfate hexasaccharides and explain their binding affinity to protein receptors.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Pharmacology & Pharmacy
Sofia Lisina, Wali Inam, Mikko Huhtala, Fadak Howaili, Hongbo Zhang, Jessica M. Rosenholm
Summary: Poly (ethylene imine) (PEI) functionalized mesoporous silica nanoparticles (MSN) were used as a carrier for bovine serum albumin (BSA) with poly (sodium 4-styrenesulfonate) (NaPSS) and spermine-modified acetylated dextran (SpAcDEX) used as coating polymers. Nano differential scanning fluorimetry (NanoDSF) and circular dichroism (CD) spectroscopy were used to assess protein thermal stability and integrity during the formulation process.
Article
Biochemistry & Molecular Biology
Martynas Bagdonas, Kamile Cerepenkaite, Aurelija Mickeviciute, Ruta Kananaviciute, Birute Grybaite, Kazimieras Anusevicius, Audrone Ruksenaite, Tautvydas Kojis, Marius Gedgaudas, Vytautas Mickevicius, Daumantas Matulis, Asta Zubriene, Jurgita Matuliene
Summary: In this study, seven aromatic disulfide compounds were found to efficiently inhibit the activity of the SARS-CoV-2 protease PLpro, with two compounds showing higher potency against PLpro compared to the protease Mpro. These findings are important for the development of new drugs against COVID-19.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Optics
Hui Liao, Jiandong Xie, Liping Yan, Benyong Chen, Yingtian Lou, Huan Chen, Gangxiang Guo
Summary: A novel precision vibration measurement method using differential phase-modulated homodyne interferometry is presented in this article. It utilizes a distributed feedback (DFB) fiber laser and a fiber-coupled electro-optic phase modulator (EOM) to construct an orthogonal linearly polarized phase-modulated single frequency laser source. An auxiliary monitoring signal is employed to compensate for the optical path drift and common-mode noise of the fiber. Experimental results demonstrate the feasibility of the proposed method, with an average deviation of vibration amplitude of about 0.97 nm in the frequency range of 0.5 kHz to 10.0 kHz. The real-time signal processing is achieved based on a field programmable gate array (FPGA).
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Cell Biology
Xiaoqian Liu, Nadine Schneble-Loehnert, Martina Kristofova, Xiaobing Qing, Jan Labisch, Susanne Hofmann, Sandra Ehrenberg, Mara Sannai, Tjard Joerss, Alessandro Ori, Maren Godmann, Zhao-Qi Wang
Summary: The N-terminal BRCT domain of MCPH1 gene plays a crucial role in brain size determination and neurodevelopment. A mouse model lacking this domain exhibits reduced brain size and thinner cortex, indicating the essential function of the BRCT domain in controlling brain size and neural development. In addition, mutant mice lacking the N'-BRCT domain also show defects in DNA damage response and DNA repair, suggesting a broader physiological role of the domain in multiple cellular processes.
CELL DEATH & DISEASE
(2021)
Article
Cell Biology
Julia Dohla, Emilia Kuuluvainen, Nadja Gebert, Ana Amaral, Johanna Englund, Swetha Gopalakrishnan, Svetlana Konovalova, Anni Nieminen, Ella S. Salminen, Ruben Torregrosa Munumer, Kati Ahlqvist, Yang Yang, Hien Bui, Timo Otonkoski, Reijo Kakela, Ville Hietakangas, Henna Tyynismaa, Alessandro Ori, Pekka Katajisto
Summary: The study demonstrates that selectively and asymmetrically inherited mitochondria in mammary stem-like cells impose a metabolic bias on progeny, affecting the balance between self-renewal and differentiation. This metabolic feature, established by functionally distinct mitochondrial age-classes, acts as a fate determinant in asymmetric division of epithelial stem-like cells.Cells that inherit old mitochondria with oxidative energy metabolism promote differentiation, while cells inheriting newly synthesized mitochondria with low levels of Rieske iron-sulfur polypeptide 1 maintain stemness through the pentose phosphate pathway during early fate determination.
NATURE CELL BIOLOGY
(2022)
Article
Cell Biology
Martina Kristofova, Alessandro Ori, Zhao-Qi Wang
Summary: MCPH1, also known as BRIT1, is frequently mutated in human primary microcephaly type 1, leading to a smaller brain size at birth due to its role in regulating neuroprogenitor cell proliferation. Studies over the past 20 years have revealed MCPH1's multifaceted functions in various cellular processes, such as DNA damage repair, chromosome condensation regulation, and cell-cycle progression. Additionally, unexpected essential functions of MCPH1 in gonad development and tumorigenesis have been uncovered, although the underlying mechanisms remain unclear.
Article
Agriculture, Multidisciplinary
Christian Henning, Christine Stubner, Seyed Hamidreza Arabi, Jorg Reichenwallner, Dariush Hinderberger, Roman Fiedler, Matthias Girndt, Simone Di Sanzo, Alessandro Ori, Marcus A. Glomb
Summary: Glycation alters the properties of proteins and affects the transport capacity of fatty acids. This study investigates the modification of human serum albumin (HSA) by glyoxal, and the impact on fatty acid transport capacity. The findings provide insights into the molecular changes caused by glycation and its effects on protein function.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Verena Kluever, Belisa Russo, Sunit Mandad, Nisha Hemandhar Kumar, Mihai Alevra, Alessandro Ori, Silvio O. Rizzoli, Henning Urlaub, Anja Schneider, Eugenio F. Fornasiero
Summary: This study investigates the link between physiological aging and neurodegenerative disorders (NDDs) by studying protein turnover. The findings suggest that protein lifetimes are increased in aged brains and aging affects pathways associated with NDDs. A previously unknown alteration in proteostasis was also observed, indicating a metabolic adaptation that may precede neurodegeneration.
Article
Multidisciplinary Sciences
Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla Ramirez, Alessandro Ori, Matthias Gstaiger, Pascal Meier, Ruedi Aebersold
Summary: Protein-protein interactions (PPIs) are the main mode of proteome organization in cells. Traditional PPI networks lack contextual information. Generating context-dependent PPI networks is necessary for structural and systems-level modeling, but remains challenging. In this study, an experimental/computational strategy is described to achieve contextual modeling of PPIs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Changye Sun, Xiangqin Tian, Yangyang Jia, Mingming Yang, Yong Li, David G. Fernig
Summary: Fibroblasts can differentiate into myofibroblasts and express ECM proteins, and excessive expression of these proteins can lead to tissue fibrosis. FGF family proteins play a crucial role in fibroblast differentiation and fibrosis, and further research is needed to understand the underlying regulatory mechanisms.
Article
Chemistry, Analytical
Marissa L. Maciej-Hulme, Anaelle C. N. Leprince, Andre Lavin, Scott E. Guimond, Jeremy E. Turnbull, Julien Pelletier, Edwin A. Yates, Andrew K. Powell, Mark A. Skidmore
Summary: The fine structure of heparan sulfate plays a crucial role in cell signaling processes, infection, and other biochemical processes. An ultra-high sensitivity method utilizing reverse-phase HPLC and laser-induced fluorescence detection is described, which greatly improves the detection of HS disaccharides by six orders of magnitude. This method allows for the analysis of HS composition in minute tissue samples.
ANALYTICAL METHODS
(2023)
Article
Cell Biology
Patrick Schaedel, Anna Czapka, Nadja Gebert, Ilse Denise Jacobsen, Alessandro Ori, Oliver Werz
Summary: Using mass spectrometry-based proteomics and metabololipidomics, we revealed molecular determinants of age-related changes in the functional phenotypes of murine peritoneal macrophages (PM). Old mice exhibited aberrant PM phenotypes, impacting their capabilities to release immunomodulatory chemokines and cytokines. Aging compromised the polarization process of macrophages, resulting in abnormal and afunctional macrophage subtypes that cannot be readily assigned to a typical M1 or M2 phenotype, challenging the dogma of increased pro-inflammatory macrophage pre-activation due to aging.
Article
Cell Biology
Maryam Izadi, David Wolf, Eric Seemann, Alessandro Ori, Lukas Schwintzer, Frank Steiniger, Michael Manfred Kessels, Britta Qualmann
Summary: This study reveals the physical interactions and cooperative functions of members of two fundamentally different superfamilies of membrane shapers, uncovering a previously unknown pivotal principle in neuronal shape development. Membrane-shaping proteins play a crucial role in establishing cell morphology and function, but their reported properties seem inconsistent with physiological membrane topology requirements.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biology
Susan L. L. Lindsay, Rebecca Sherrard Smith, Edwin A. A. Yates, Colin Cartwright, Bryan E. E. Thacker, Jeremy E. E. Turnbull, Charles A. A. Glass, Susan C. C. Barnett
Summary: The complex tissue changes that occur after central nervous system (CNS) damage/injury require a multi-target treatment approach. Specialised sugar molecules called heparan sulphate (HS) play an important role in tissue repair. Heparin mimetics (mHeps) can mimic the function of HS and be used for CNS repair. However, mHeps are derived from pig intestines, increasing the risk of contamination and shortages. The use of recombinant HS mimetics (rHS) derived from cultured cells offers an alternative and potentially more readily available source for CNS repair therapies.
Article
Chemistry, Medicinal
Isabel Pagani, Linda Ottoboni, Paola Panina-Bordignon, Gianvito Martino, Guido Poli, Sarah Taylor, Jeremy E. Turnbull, Edwin Yates, Elisa Vicenzi
Summary: This study investigates the effects of chemically modified heparin derivatives with reduced anticoagulant activities on ZIKV infection, and finds that they can prevent cell death and inhibit ZIKV replication in infected neural progenitor cells. The combination of heparin with Sofosbuvir shows a synergistic effect.
Article
Biochemistry & Molecular Biology
Julia C. Heiby, Alessandro Ori
Summary: This review discusses the relationship between the remodeling of key organelles and metabolic alterations during the aging process, as well as the reciprocal interaction between organelle function and protein homeostasis. It also explores how cell-type-specific metabolic changes can influence whole-organism aging through inter-tissue communication.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2022)
Review
Multidisciplinary Sciences
M. A. Lima, T. R. Rudd, D. G. Fernig, E. A. Yates
Summary: Phosphate and sulfate groups play important roles in energy metabolism and precise binding/activation of protein partners. They have distinct properties and functions in biological systems, and are interconnected through complex signaling networks.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Chemistry, Multidisciplinary
James Andrew London, Sarah Louise Taylor, Igor Barsukov, Alan Cartmell, Edwin Alexander Yates
Summary: Complex glycans play essential roles in nature and exploring their potential chemical space is crucial. New polysaccharides (NPs) can be generated by synthesizing structures that do not occur naturally or by modifying existing polysaccharide structures. This method allows access to new functionalities and has diverse applications in biological, medical, biotechnological, and materials science fields.
