Article
Multidisciplinary Sciences
Robert P. Sparks, William Lawless, Andres S. Arango, Emad Tajkhorshid, Rutilio A. Fratti
Summary: Determining the binding affinity of lipids to proteins is crucial for understanding protein-lipid interactions. Traditional methods like SPR and ITC have limitations, such as cost and time consumption. MST offers a fast and cost-effective alternative, using small amounts of sample to obtain binding curves.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Review
Biochemistry & Molecular Biology
Romain Magnez, Christian Bailly, Xavier Thuru
Summary: This review highlights the crucial roles of protein-protein interactions (PPIs) in life processes and their involvement in various human diseases. It introduces Microscale Thermophoresis (MST) as a rapid, robust, and efficient alternative method for detecting therapeutically pertinent proteins. The review summarizes selected case studies and discusses the benefits and limitations of MST in studying PPIs and identifying regulators.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Jeong Bin Yang, Kwang Sub Kim, Jiwon Heo, Jeong Min Chung, Hyun Suk Jung
Summary: This study investigates the interaction between actin and espin 1, revealing the actin binding and bundling mechanism of espin 1, as well as its elongation, stabilization, and tip-localization mechanisms with myosin III. These findings provide insights into the molecular structure of espin 1 and its relevance to hearing-related diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Chemistry, Analytical
Sami El Deeb, Ahmed Al-Harrasi, Ajmal Khan, Mohammed Al-Broumi, Ghanim Al-Thani, Mohammed Alomairi, Parthasarathy Elumalai, Rania Adel Sayed, Adel Ehab Ibrahim
Summary: This review explores the usefulness of microscale thermophoresis in studying molecular and biomolecular affinity interactions, and provides an overview of its current state and recent developments in the field. It also describes the principle of microscale thermophoresis and discusses its advantages, drawbacks, and application in different fields.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2022)
Article
Chemistry, Multidisciplinary
Wei Wang, Ni Zhang, Yahui Du, Juan Gao, Min Li, Liyuan Lin, Daniel M. Czajkowsky, Xiaowei Li, Chaoyong Yang, Zhifeng Shao
Summary: This study presents a novel strategy for three-dimensional imaging of indigenous gut microbiota, revealing the spatial distribution of microbiota in different gut sections and their relationship with the host epithelium. The unexpected presence of microbiota in small intestine crypts and significant bacterial overgrowth in an enteritis model were observed, highlighting the importance of understanding host-microbiota interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Lu Fan, Athanasia Warnecke, Julia Weder, Matthias Preller, Carsten Zeilinger
Summary: Microarray-based experiments showed that thyroid hormone T3 enhanced the binding of Cy5-labeled ATP on Hsp90. Molecular docking experiments identified a T3 binding site near the ATP binding site on Hsp90. A synthetic peptide derived from this binding site displayed T3 binding ability in experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Z-Y Liu, Q-G Zong, R. Rankin, H. Zhang, Y. F. Wang, X-Z Zhou, S-Y Fu, C. Yue, X-Y Zhu, C. J. Pollock, S. A. Fuselier, G. Le
Summary: Identifying the energy transfer from macroscales to microscales in collisionless plasmas is crucial for astrophysics and space physics. Two cross-scale energy-transfer events observed in Earth's magnetosphere demonstrate the efficiency and timescale of this process, where hot ions interact with ultra-low-frequency waves and electromagnetic-ion-cyclotron waves.
NATURE COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Mufarreh Asmari, Lenka Michalcova, Adel Ehab Ibrahim, Zdenek Glatz, Hermann Waetzig, Sami El Deeb
Summary: This review evaluates the applications of affinity capillary electrophoresis (ACE) and microscale thermophoresis (MST) techniques in studying molecular binding from 2016 to 2021. ACE has demonstrated high resolution efficiency for biomolecular characterization, with the potential for significant improvement compared to other analytical techniques. On the other hand, MST has shown higher sensitivity for smaller non-purified biosamples without compromising robustness and provides high throughput. The main motivation for this review is the ability of both techniques to carry out experiments without immobilizing one interacting partner, as well as the flexibility in buffering system usage. The review highlights the importance of these techniques in various areas of life sciences, and discusses recent advances in utilizing ACE and MST in other research interests.
Article
Chemistry, Multidisciplinary
Soumya Jyoti Singha Roy, Conor Loynd, Delilah Jewel, Sarah E. Canarelli, Elise D. Ficaretta, Quan A. Pham, Eranthie Weerapana, Abhishek Chatterjee
Summary: We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, for selective modification of 5-hydroxytryptophan residue (5HTP) on full-length proteins. This reaction enables rapid and site-specific protein bioconjugation using catalytic amounts of methylene blue and blue/red light-emitting diodes. The PhotoCLIC product has a unique structure likely formed through singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and is compatible with strain-promoted azide-alkyne click reaction, allowing for site-specific dual-labeling of a target protein.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Immunology
Omar Naneh, Mirijam Kozorog, Franci Merzel, Robert Gilbert, Gregor Anderluh
Summary: Perforin is a crucial pore-forming protein in the immune system that clears virus-infected or tumor cells by delivering apoptosis-inducing granzymes. Its activity is regulated by calcium ions, and our study showed that binding of at least three calcium ions is required for stable perforin binding to the lipid membrane. We also found that mouse perforin has a higher affinity for calcium ions compared to human perforin, due to a specific residue difference.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Sandra M. Kerbler, Roberto Natale, Alisdair R. Fernie, Youjun Zhang
Summary: AP-MS and PL-MS are two powerful techniques for studying protein-protein interactions, providing insights into the interactions between proteins in plant systems.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biophysics
Blanca Lopez-Mendez, Stephan Uebel, Li Peng Lundgren, Arthur Sedivy
Summary: NanoTemper Monolith instruments are widely used in academia and industry for measuring molecular interactions. The technology has been extensively reviewed, and some assumptions and limitations have been revised in the last decade. This letter presents the experience gathered in scientific service facilities and highlights possible pitfalls for scientists to promote knowledge and good practice in the scientific community.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Review
Biochemical Research Methods
Rebecca Elizabeth Kattan, Deena Ayesh, Wenqi Wang
Summary: During intracellular signal transduction, protein-protein interactions (PPIs) play a critical role in regulating protein localization and function. Mass spectrometry-based interactome analysis has become a popular method for studying PPI networks, but the analysis of large datasets can be challenging. In this review, we discuss the methods and resources commonly used for analyzing large interactome-related proteomic data and propose a guideline for identifying novel interacting proteins.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Xue Li, Lu Zhang, Suyang Wang, Xiangqin Liu, Ying Lin
Summary: A novel site-specific internal protein labeling method using two atypical split inteins was demonstrated, allowing for the incorporation of a fluorescent probe into recombinant proteins. The number of native extein amino acids was shown to affect trans-splicing activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Multidisciplinary
Samuel L. Scinto, Tyler R. Reagle, Joseph M. Fox
Summary: This study demonstrates a new method for site-selective functionalization of proteins using pyridyl-tetrazine tags, allowing for direct affinity purification on commonly used nickel-iminodiacetate (Ni-IDA) resins. The method is also applicable for protein purification from complex mixtures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Boshi Huang, Dongwei Kang, Ye Tian, Dirk Daelemans, Erik De Clercq, Christophe Pannecouque, Peng Zhan, Xinyong Liu
Summary: A series of piperidinyl-substituted [1,2,4]triazolo[1,5-a]pyrimidines were designed and synthesized based on the lead compound BH-7d, and their anti-HIV activities and cytotoxicities were evaluated. Some compounds showed moderate anti-HIV potency with reduced cytotoxicity. Molecular docking study revealed the binding conformation of the most active compound in the binding pocket of HIV-1 reverse transcriptase.
CHEMICAL BIOLOGY & DRUG DESIGN
(2021)
Article
Multidisciplinary Sciences
Lorena Sanchez-Felipe, Thomas Vercruysse, Sapna Sharma, Ji Ma, Viktor Lemmens, Dominique Van Looveren, Mahadesh Prasad Arkalagud Javarappa, Robbert Boudewijns, Bert Malengier-Devlies, Laurens Liesenborghs, Suzanne J. F. Kaptein, Carolien De Keyzer, Lindsey Bervoets, Sarah Debaveye, Madina Rasulova, Laura Seldeslachts, Li-Hsin Li, Sander Jansen, Michael Bright Yakass, Babs E. Verstrepen, Kinga P. Boszormenyi, Gwendoline Kiemenyi-Kayere, Nikki van Driel, Osbourne Quaye, Xin Zhang, Sebastiaan ter Horst, Niraj Mishra, Ward Deboutte, Jelle Matthijnssens, Lotte Coelmont, Corinne Vandermeulen, Elisabeth Heylen, Valentijn Vergote, Dominique Schols, Zhongde Wang, Willy Bogers, Thijs Kuiken, Ernst Verschoor, Christopher Cawthorne, Koen Van Laere, Ghislain Opdenakker, Greetje Vande Velde, Birgit Weynand, Dirk E. Teuwen, Patrick Matthys, Johan Neyts, Hendrik Jan Thibaut, Kai Dallmeier
Summary: The candidate vaccine YF-S0, utilizing the YF17D vaccine as a vector to express noncleavable prefusion form of the SARS-CoV-2 spike antigen, showed excellent safety, immunogenicity, and efficacy in animal models. It induced high levels of neutralizing antibodies, provided protective immunity against SARS-CoV-2, and prevented infection in hamsters and macaques. A single dose was able to confer protection from lung disease in most vaccinated hamsters within 10 days, highlighting the potential of YF-S0 as a potent SARS-CoV-2 vaccine candidate.
Article
Nanoscience & Nanotechnology
Julia Flesch, Maximilian Bettenhausen, Marcin Kazmierczak, Wolfgang M. Klesse, Oliver Skibitzki, Olympia E. Psathaki, Rainer Kurre, Giovanni Capellini, Subhajit Guha, Thomas Schroeder, Bernd Witzigmann, Changjiang You, Jacob Piehler
Summary: Label-free optical detection of biomolecules is currently limited by a lack of specificity rather than sensitivity. The engineered three-dimensional IR-resonant silicon micropillar arrays (Si-MPAs) for protein sensing utilize the characteristic refractive index dispersion in the mid-infrared (IR) regime. The spatially controlled surface functionalization enables efficient targeting of soluble and membrane proteins into sensing hotspots directly from cells cultured on Si-MPAs.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Raheem Fazal, Steven Boeynaems, Ann Swijsen, Mathias De Decker, Laura Fumagalli, Matthieu Moisse, Joni Vanneste, Wenting Guo, Ruben Boon, Thomas Vercruysse, Kristel Eggermont, Bart Swinnen, Jimmy Beckers, Donya Pakravan, Tijs Vandoorne, Pieter Vanden Berghe, Catherine Verfaillie, Ludo Van den Bosch, Philip Van Damme
Summary: The study investigated TDP-43 protein behavior in iPSC-derived motor neurons from ALS patients with TARDBP mutations, revealing various TDP-43 changes. Mutant TDP-43 was found to initiate disease phenotypes and have an altered interactome, leading to defects in mitochondrial transport. Pharmacological inhibition of HDAC6 restored TDP-43 pathologies and axonal mitochondrial motility, suggesting a potential therapeutic target for TDP-43-linked neurodegenerative disorders.
Article
Physics, Applied
Lara Jorde, Zehao Li, Adrian Poeppelwerth, Jacob Piehler, Changjiang You, Carola Meyer
Summary: By designing a surface architecture for reversible protein immobilization on CNTs, we have successfully fabricated reusable biosensors for multiple protein analysis. The specific capturing of His-tagged proteins was achieved by combining Py-PEG-tris-NTA and Ni(II) ions, with the protein binding capacity being restored by imidazole wash.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Biochemical Research Methods
Florian C. Grau, Andreas Burkovski, Yves A. Muller
Summary: P-II proteins are involved in regulating nitrogen/carbon balance in bacteria, archaea, plants, and algae through signal transduction modulated by effector molecules and post-translational modifications. The crystal structures of GlnK from Corynebacterium glutamicum, both adenylylated and unmodified, provide insights into the structural implications of covalent attachment of an AMP moiety to the T-loop. Adenylylation of GlnK does not alter the overall fold and does not interfere with the formation of functionally important T-loop conformations.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Microbiology
Johannes Schweininger, Myriam Scherer, Franziska Rothemund, Eva-Maria Schilling, Sonja Worz, Thomas Stamminger, Yves A. Muller
Summary: Cytomegaloviruses have evolved a species-specific IE1 protein tertiary structure to effectively bind and inactivate the important cellular restriction factor PML, forming a barrier to cross-species transmission. The highly conserved fold of IE1 maximizes the efficacy of PML targeting in a species-specific manner, illustrating the co-evolution of viruses and their hosts.
Article
Biochemistry & Molecular Biology
Christine Helsen, Tien Nguyen, Thomas Vercruysse, Staf Wouters, Dirk Daelemans, Arnout Voet, Frank Claessens
Summary: This study identifies a gain-of-function mutation in AR LBD, T850D, which enhances AR activity. The study also reveals the details of allosteric communications within the LBD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Correction
Multidisciplinary Sciences
Martin A. Redhead, C. David Owen, Lennart Brewitz, Amelia H. Collette, Petra Lukacik, Claire Strain-Damerell, Sean W. Robinson, Patrick M. Collins, Philipp Schafer, Mark Swindells, Chris J. Radoux, Iva Navratilova Hopkins, Daren Fearon, Alice Douangamath, Frank von Delft, Tika R. Malla, Laura Vangeel, Thomas Vercruysse, Jan Thibaut, Pieter Leyssen, Tu-Trinh Nguyen, Mitchell Hull, Anthony Tumber, David J. Hallett, Christopher J. Schofield, David I. Stuart, Andrew L. Hopkins, Martin A. Walsh
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Joni Vanneste, Thomas Vercruysse, Steven Boeynaems, Philip Van Damme, Dirk Daelemans, Ludo Van den Bosch
Summary: The study aimed to investigate the causal relationship between stress granule formation and nucleocytoplasmic transport deficits. The results demonstrate that while stress granules are formed in response to cellular stress, they are not a direct cause of stress-induced nucleocytoplasmic transport deficits.
Article
Virology
Bas Calcoen, Nico Callewaert, Aline Vandenbulcke, Winnie Kerstens, Maya Imbrechts, Thomas Vercruysse, Kai Dallmeier, Johan Van Weyenbergh, Piet Maes, Xavier Bossuyt, Dorinja Zapf, Kersten Dieckmann, Kim Callebaut, Hendrik Jan Thibaut, Karen Vanhoorelbeke, Simon F. De Meyer, Wim Maes, Nick Geukens
Summary: This study monitored the mid- and long-term adaptive immune response and breakthrough infections in healthcare workers who received the BNT162b2 vaccine. The results showed that the vaccine-induced humoral and cellular immune responses were not correlated in individuals without breakthrough infections. The decline in humoral immunity over time was more pronounced compared to cellular immunity. Additionally, a high incidence of symptomatic breakthrough infections caused by alpha and delta variants of concern was reported.
Article
Biochemistry & Molecular Biology
Sebastian Weigert, Pablo Perez-Garcia, Florian J. Gisdon, Andreas Gagsteiger, Kristine Schweinshaut, G. Matthias Ullmann, Jennifer Chow, Wolfgang R. Streit, Birte Hoecker
Summary: The handling of plastic waste and microplastic has become one of the greatest challenges of our time. Recent studies on plastic degrading enzymes have provided new prospects for biological decomposition and recycling. In this study, the candidate PET6 enzyme from Vibrio gazogenes was chosen for further investigation. The characterization of PET6 revealed its widespread occurrence in various Vibrio strains and its superior ability to degrade polyethylene terephthalate under high salt concentrations. Mutations from other PET degrading enzymes were introduced to PET6 to enhance its activity, demonstrating the evolutionary potential of the enzyme. The crystal structure and molecular dynamics simulations of PET6 provided insights into its adaptation to saline environments. The findings suggest that Vibrio and the PET6 enzyme are worthy subjects for studying PET degradation in marine environments.
Article
Multidisciplinary Sciences
Sapna Sharma, Thomas Vercruysse, Lorena Sanchez-Felipe, Winnie Kerstens, Madina Rasulova, Lindsey Bervoets, Carolien De Keyzer, Rana Abdelnabi, Caroline S. Foo, Viktor Lemmens, Dominique Van Looveren, Piet Maes, Guy Baele, Birgit Weynand, Philippe Lemey, Johan Neyts, Hendrik Jan Thibaut, Kai Dallmeier
Summary: This study demonstrates the need to update current first-generation COVID-19 vaccines to maintain efficacy against emerging variants of concern. It also assesses the protective effects and reduced transmission of a yellow fever 17D vectored vaccine candidate in a hamster model.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Junel Sotolongo Bellon, Oliver Birkholz, Christian P. Richter, Florian Eull, Hella Kenneweg, Stephan Wilmes, Ulrich Rothbauer, Changjiang You, Mark R. Walter, Rainer Kurre, Jacob Piehler
Summary: Localization and tracking of individual receptors by single-molecule imaging allows for the study of assembly and dynamics of signaling complexes in the plasma membrane. This article presents a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells using up to four colors. The use of engineered GFP variants and fluorescent dyes enables the quantitative resolution of the stoichiometry and dynamics of the IFNg receptor signaling complex in living cells.
CELL REPORTS METHODS
(2022)
Article
Immunology
Ji Ma, Robbert Boudewijns, Lorena Sanchez-Felipe, Niraj Mishra, Thomas Vercruysse, Dieudonne Buh Kum, Hendrik Jan Thibaut, Johan Neyts, Kai Dallmeier
Summary: Research evaluated the immunogenicity and protective efficacy of the live-attenuated yellow fever 17D (YF17D) vaccine in various mouse models, highlighting the model-dependent differences in vaccine-induced protective immunity.
EMERGING MICROBES & INFECTIONS
(2021)