Article
Biochemistry & Molecular Biology
Petar Iliev, Danielle Hanke, Brent D. G. Page
Summary: In this study, the STAT protein thermal shift assay (PTSA) was used to test the binding of known STAT3 inhibitors to STAT3 and STAT1. The results revealed covalent protein modifications of STATs by STATTIC, BP-1-102, and Cpd188. Mass spectrometry experiments confirmed the nonspecific alkylation of these compounds on an unrelated protein, NUDT5.
Article
Chemistry, Multidisciplinary
Xiaowan Zheng, Siyuan Fang, Bicheng Guo, Bernard Sia, Lianxiang Yang
Summary: This research paper focuses on the development of a digital holography system that can simultaneously measure deformations at dual spatial resolutions. The system uses two optical channels with different fields of view to achieve this. By introducing spatial carrier fringes with different orientations and utilizing polarization techniques, the two interferograms can be separated and analyzed to calculate the deformations. The experimental results confirm the practicality of this method.
APPLIED SCIENCES-BASEL
(2023)
Article
Engineering, Multidisciplinary
Ju-Yi Lee, Ching-Tse Hsu, Shu-Han Chang, Wun-Yan Chen
Summary: This study presents a polarization interferometry-based technique for high-resolution and stable measurement of roll angular displacement. The technique uses a polarization camera to detect the phases of a light beam passed through a birefringent crystal and determines the angular displacement of the crystal based on variations in phase difference. The dual beam configuration of the proposed measurement scheme overcomes the effects of fluctuating incident angular displacement. Experimental results show that the system achieved a resolution of 0.58 arcsec within a 10-degree range and exhibited lower disturbance from incident angular displacement compared to previous techniques. The study also investigates nonlinear periodic system errors. The proposed technique offers higher resolution, wider range measurement capabilities, and robustness against external disturbance compared to existing methods.
Article
Biochemistry & Molecular Biology
Jaina A. Bhayani, Miguel A. Ballicora
Summary: The thermal shift assay is a powerful tool for detecting molecular interactions between proteins and ligands by tracking protein unfolding using temperature and an extrinsic fluorescent dye. A new analysis method based on equilibrium systems and the van't Hoff equation is proposed for determining Kd, showing promising results in testing with different proteins and enzymes. This method has the potential to offer broad applicability across protein classes and detect both active and allosteric site binding compounds.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Review
Pharmacology & Pharmacy
Marius Gedgaudas, Denis Baronas, Egidijus Kazlauskas, Vytautas Petrauskas, Daumantas Matulis
Summary: The thermal shift assay is a commonly used technique to study protein-ligand interactions. We have developed a user-friendly online analysis software that can provide comprehensive thermodynamic characterization of any protein-ligand interaction based on thermal shift data.
DRUG DISCOVERY TODAY
(2022)
Article
Chemistry, Multidisciplinary
Bo Cai, Casey J. Krusemark
Summary: A novel assay method combining DNA encoding with split-and-pool sample handling is developed to improve small-molecule binding assays to target proteins. The approach involves affinity labeling of DNA-linked ligands to a protein target, allowing for quantification of DNA barcodes to detect ligand binding. This method demonstrates potential utility in high-throughput small-molecule screening.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Long Li, Zhen Li, Ziying Wang, Shuyu Chen, Rongying Liu, Xuyang Xu, Zhi Zhang, Linfei Ye, Yu Ding, Quan Luo, Sheng Cao, Lei Zhang, Anne Imberty, Guosong Chen
Summary: By controlling the symmetry and number of supramolecular interactions on protein surfaces, nonspecific interactions between proteins can be induced to form various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulating the protein's native surfaces. These nanoscale assemblies can spontaneously evolve into more ordered architectures, crystals. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
Article
Biochemical Research Methods
Nan Zhang, Yueyang Liu, Xiaoyu Shi, Yuchen Zhang, Wenying Li, Yumeng Yang, Limin Chen, Yanxia Yin, Li Tong, Jingyu Yang, Jing Luo
Summary: This study determined the affinity between calcineurin and peptides using fluorescent labeling and two conserved motifs, showing that MST and FP assays are fast and accurate in determining protein-peptide interactions. Results laid the foundation for future screening of molecules affecting the binding between calcineurin and its substrates.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Bradley L. Hoare, David N. Tippett, Amandeep Kaur, Sean A. Cullum, Tamara Miljus, Eline J. Koers, Clare R. Harwood, Nicola Dijon, Nicholas D. Holliday, David A. Sykes, Dmitry B. Veprintsev
Summary: Measurements of membrane protein thermostability can reflect ligand binding, but current methods have limitations. This study presents a new method, ThermoBRET, for quantifying the relative thermostability of GPCRs, which does not require purified proteins or labelled ligands.
Article
Biochemistry & Molecular Biology
Thomas Lenz, Kai Stuehler
Summary: Chemical biology and the application of small molecules have been proven to be effective strategies for studying protein functions, and several tools have been developed to identify interactions between small molecules and target or non-target proteins. In this study, the use of cellular thermal shift assay (CETSA) and thermal proteome profiling (TPP) were explored to investigate the potential secondary effects of small molecule treatments, such as changes in post-translational modifications or protein-protein interactions (PPI).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Christian M. Beusch, Pierre Sabatier, Roman A. Zubarev
Summary: This study introduces a novel method for characterizing protein solubility alterations using ions, which can delineate targets of anticancer drugs and detect solubility changes in minute samples, thus expanding chemical proteomics applications to small and rare biological material.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Katarzyna Gajos, Alicja Orzech, Karolina Sanocka, Panagiota Petrou, Andrzej Budkowski
Summary: Immunosensors that combine planar transducers with microfluidics were analyzed for their surface binding capacity, immobilization stability, and binding stoichiometry. Two IgG immobilization schemes, physical adsorption and glutaraldehyde covalent coupling, were compared and monitored using white light reflectance spectroscopy sensors. The results showed that in-flow immobilization had higher surface binding capacity compared to static adsorption, and chemisorbed antibodies were more stable during blocking with bovine serum albumin. The data also revealed that IgG molecules were partially exchanged with BSA on APTES chips but not on APTES/GA chips.
Article
Chemistry, Multidisciplinary
Sergey Shityakov, Aleksandr S. Aglikov, Ekaterina V. Skorb, Michael Nosonovsky
Summary: This study investigates the correlation between the Voronoi entropy (VE) of ligand molecules and their affinity to receptors. The findings suggest a strong correlation between ligand complexity and affinity, indicating the importance of atomic spatial arrangement for molecular mobility and binding.
Article
Thermodynamics
Jimin Fang, Manzhuo Wang, Tingyu Liu, Jianbo Yue, Xiaoqiang Sun, Yuanda Wu, Daming Zhang
Summary: This work proposes and systematically investigates dual-polarization strong nonreciprocal thermal radiations with nanopore arrays. The proposed device, which adopts silicon as the substrate, is built by stacking metal layer, magneto-optical layer, and silicon-based nanopore arrays. The physical phenomenon of dual-polarization strong nonreciprocal radiation is explained using rigorous coupled-wave analysis theory and coupled-mode theory.
INTERNATIONAL JOURNAL OF THERMAL SCIENCES
(2024)
Article
Chemistry, Analytical
Xiaolei Zhang, Chengfei Ruan, Yan Wang, Keyun Wang, Xiaoyan Liu, Jiawen Lyu, Mingliang Ye
Summary: This article introduces a new protein target identification method, ipHSA, and compares it with other methods. It also proposes an integrated method, IPSSA, that improves the sensitivity of target identification.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Christopher Prior, Owen R. Davies, Daniel Bruce, Ehmke Pohl
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemical Research Methods
Renzo Angles, Mauricio Arenas-Salinas, Roberto Garcia, Jose Antonio Reyes-Suarez, Ehmke Pohl
BMC BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Charles W. E. Tomlinson, Katy A. S. Cornish, Andrew Whiting, Ehmke Pohl
Summary: This article presents crystal structures of cellular retinoic acid-binding proteins CRABPI and CRABPII in complex with fatty acids and synthetic retinoids, shedding light on how these compounds influence retinoid signaling pathways. These co-crystal structures demonstrate canonical binding behavior and suggest potential therapeutic implications in serious diseases, such as neurodegenerative disorders.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Virology
David Brandt, Marina Simunovic, Tobias Busche, Markus Haak, Peter Belmann, Sebastian Juenemann, Tizian Schulz, Levin Joe Klages, Svenja Vinke, Michael Beckstette, Ehmke Pohl, Christiane Scherer, Alexander Sczyrba, Joern Kalinowski
Summary: Genomic surveillance of the SARS-CoV-2 pandemic is crucial and achieved mainly through amplicon sequencing protocols. A significant deletion in the ORF8 gene has been discovered, indicating a mutation hotspot, with many deletions not identified in standard data analysis.
Article
Infectious Diseases
Douglas O. Escrivani, Rebecca L. Charlton, Marjolly B. Caruso, Gabriela A. Burle-Caldas, Maria Paula G. Borsodi, Russolina B. Zingali, Marcos Palmeira-Mello, Jessica B. de Jesus, Alessandra M. T. Souza, Barbara Abrahim-Vieira, Stefanie Freitag-Pohl, Ehmke Pohl, Paul W. Denny, Bartira Rossi-Bergmann, Patrick G. Steel
Summary: This study identified a novel broad-spectrum antileishmanial drug lead by targeting cytosolic tryparedoxin peroxidase with a chemical probe, leading to parasite death without host toxicity. The findings highlight the importance of cTXNPx as a potential drug target for antileishmanial chalcones, providing a promising avenue for future drug discovery programs.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Katy A. S. Cornish, Joanna Lange, Arnthor Aevarsson, Ehmke Pohl
Summary: The Candidate Phyla Radiation is a recently discovered expansion of the bacterial domain, consisting of uncharacterized phyla with genetic diversity. This study presents the structural and functional elucidation of a hypothetical protein, CPR-C4, from a thermophilic CPR organism. CPR-C4 was found to be a member of a highly conserved protein family within the Candidate Phyla Radiation and was predicted to function as a cysteine protease. Experimental assays confirmed this prediction and revealed unexpected similarities to human vasohibins at the structural and functional level, indicating an undetectable evolutionary relationship based on sequence alone.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Andrius Jasilionis, Magdalena Plotka, Lei Wang, Sebastian Dorawa, Joanna Lange, Hildegard Watzlawick, Tom van den Bergh, Bas Vroling, Josef Altenbuchner, Anna-Karina Kaczorowska, Ehmke Pohl, Tadeusz Kaczorowski, Eva Nordberg Karlsson, Stefanie Freitag-Pohl
Summary: Bacteriophages encode lytic enzymes that disrupt cell walls and have potential as novel antibacterials. This study presents the functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, an enzyme adapted to high temperatures. AmiP is shown to be highly efficient and has broad substrate specificity. It is the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme characterized so far.
Article
Biochemical Research Methods
Kate Sowerby, Stefanie Freitag-Pohl, Ana Milena Murillo, Ariel Mariano Silber, Ehmke Pohl
Summary: Chagas disease and leishmaniasis are significant health problems caused by parasites. The study focuses on the cysteine biosynthesis pathway, which is essential for parasite survival. Crystal structures of cysteine synthase enzymes from Trypanosoma cruzi, Leishmania infantum, and T. theileri were determined, revealing the active site and potential binding sites for inhibitor design. These findings can aid in the development of new drugs and protein-protein inhibitors.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Cell Biology
Miguel Jarrin, Alexia A. Kalligeraki, Alice Uwineza, Chris S. Cawood, Adrian P. Brown, Edward N. Ward, Khoa Le, Stefanie Freitag-Pohl, Ehmke Pohl, Bence Kiss, Antal Tapodi, Roy A. Quinlan
Summary: Research has shown that the C-terminal sequences of BFSP1 protein have independent membrane binding properties, binding to cell membranes through an adjacent amphipathic helix. This conclusion is of great significance for understanding the function of BFSP1 protein.
Article
Biochemistry & Molecular Biology
Zisis Koutsogiannis, John G. Mina, Christin A. Albus, Matthijs A. Kol, Joost C. M. Holthuis, Ehmke Pohl, Paul W. Denny
Summary: The study found that the ceramide synthases TgCerS1 and TgCerS2 in Toxoplasma gondii function differently, with TgCerS1 being catalytically active and TgCerS2 being inactive. While TgCerS1 is important but not indispensable for parasite growth, TgCerS2 plays a greater role in parasite fitness. This unique arrangement of ceramide synthase isoforms in Toxoplasma and other Apicomplexa highlights their unusual biology.
Article
Chemistry, Organic
Maria Schwarz, Rebecca F. M. Eno, Stefanie Freitag-Pohl, Christopher R. Coxon, Hannah E. Straker, David J. Wortley, David J. Hughes, Glynn Mitchell, Jenny Moore, Ian Cummins, Nawaporn Onkokesung, Melissa Brazier-Hicks, Robert Edwards, Ehmke Pohl, Patrick G. Steel
Summary: The study identified AmGSTF1 as a functional biomarker of MHR in black-grass and further explored its role in MHR using a combination of chemical and structural biology. It was found that the inhibitory activity of NBD-Cl is associated with the occlusion of the active site and inhibition of substrate binding, while flavonoids showed high affinity for AmGSTF1 and could reverse herbicide resistance in MHR black-grass.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Review
Microbiology
Arnthor Aevarsson, Anna-Karina Kaczorowska, Bjorn Thor Adalsteinsson, Josefin Ahlqvist, Salam Al-Karadaghi, Joseph Altenbuchner, Hasan Arsin, Ulfur August Atlasson, David Brandt, Magdalena Cichowicz-Cieslak, Katy A. S. Cornish, Jeremy Courtin, Slawomir Dabrowski, Hakon Dahle, Samia Djeffane, Sebastian Dorawa, Julia Dusaucy, Francois Enault, Anita-Elin Fedoy, Stefanie Freitag-Pohl, Olafur H. Fridjonsson, Clovis Galiez, Eirin Glomsaker, Mickael Guerin, Sigurd E. Gundeso, Elisabet E. Gudmundsdottir, Hordur Gudmundsson, Maria Hakansson, Christian Henke, Alexandra Helleux, Jorn Remi Henriksen, Sigridur Hjorleifdottir, Gudmundur O. Hreggvidsson, Andrius Jasilionis, Annika Jochheim, Ilmur Jonsdottir, Lilja Bjork Jonsdottir, Agata Jurczak-Kurek, Tadeusz Kaczorowski, Jorn Kalinowski, Lukasz P. Kozlowski, Mart Krupovic, Karolina Kwiatkowska-Semrau, Olav Lanes, Joanna Lange, Julien Lebrat, Javier Linares-Pasten, Ying Liu, Steffen A. Lorentsen, Tobias Lutterman, Thibaud Mas, William Merre, Milot Mirdita, Agnieszka Morzywolek, Eric Olo Ndela, Eva Nordberg Karlsson, Edda Olgudottir, Cathrine Pedersen, Francine Perler, Solveig K. Petursdottir, Magdalena Plotka, Ehmke Pohl, David Prangishvili, Jessica L. Ray, Birkir Reynisson, Tara Robertsdottir, Ruth-Anne Sandaa, Alexander Sczyrba, Sigurlaug Skirnisdottir, Johannes Soding, Terese Solstad, Ida H. Steen, Sigmar Karl Stefansson, Martin Steinegger, Katrine Stange Overa, Bernd Striberny, Anders Svensson, Monika Szadkowska, Emma J. Tarrant, Paul Terzian, Mathilde Tourigny, Tom van den Bergh, Justine Vanhalst, Jonathan Vincent, Bas Vroling, Bjorn Walse, Lei Wang, Hildegard Watzlawick, Martin Welin, Olesia Werbowy, Ewa Wons, Ruoshi Zhang
Summary: The Virus-X project aims to explore the genetic diversity of viruses in extreme natural environments and develop new gene products with high innovation value for various applications. The consortium, consisting of experts from multiple European countries, has successfully utilized high throughput bioinformatics technologies to analyze viral metagenomes and develop a biodiscovery pipeline. Through collaboration and advanced technologies, the project has made significant contributions to various fields such as biotechnology and pharmaceuticals.
FEMS MICROBIOLOGY LETTERS
(2021)
Editorial Material
Biochemical Research Methods
Ehmke Pohl
RETINOID SIGNALING PATHWAYS
(2020)
Article
Biochemical Research Methods
Muhammad Zohib, Diva Maheshwari, Ravi Kant Pal, Stefanie Freitag-Pohl, Bichitra Kumar Biswal, Ehmke Pohl, Ashish Arora
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2020)
Meeting Abstract
Biophysics
Christopher Prior, Ehmke Pohl, Owen Davies
BIOPHYSICAL JOURNAL
(2020)