Article
Multidisciplinary Sciences
Manish Gupta, Alexander J. Pak, Gregory A. Voth
Summary: Researchers use molecular dynamics simulations to reveal the molecular mechanism of HIV-1 capsid formation, including the role of IP6. This study shows that IP6 initially promotes curvature generation by trapping pentameric defects and shifts the assembly behavior towards kinetically favored outcomes. Additionally, IP6 can stabilize metastable capsid intermediates and induce structural pleomorphism in mature capsids.
Article
Biochemical Research Methods
Anna Yudenko, Anastasia Smolentseva, Ivan Maslov, Oleg Semenov, Ivan M. Goncharov, Vera V. Nazarenko, Nina L. Maliar, Valentin Borshchevskiy, Valentin Gordeliy, Alina Remeeva, Ivan Gushchin
Summary: Protein-fragment complementation assays are commonly used to study protein-protein interactions. The development of CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein, provides a split fluorescent reporter that can be used to investigate protein-protein interactions in anaerobic conditions without the need for exogenous fluorophores. This advancement in fluorescent protein technology may lead to further development of LOV and PAS domain-based fluorescent reporters and optogenetic tools.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Physics, Fluids & Plasmas
Giuliana Indelicato, Paolo Cermelli, Reidun Twarock
Summary: The structures of many large bacteriophages do not strictly adhere to the quasi-equivalence principle of viral architecture. The P23-77 capsids, classified as T = 28d, self-assemble from multiple copies of two types of coat protein subunits, resulting in hexameric capsomers that do not conform to the Caspar-Klug paradigm. The assembly mechanism that leads to such complex capsid organization remains an open problem.
Article
Biochemical Research Methods
Florent Velay, Melanie Soula, Marwa Mehrez, Clement Belbachir, Stefano D'Alessandro, Christophe Laloi, Patrice Crete, Ben Field
Summary: This study describes the development of a flexible modular cloning-based toolkit for bimolecular fluorescence complementation (BiFC) and proximity labelling in the chloroplast and other cellular compartments. The toolkit simplifies the construction of chloroplast fusion proteins, enables robust ratiometric quantification, and provides model positive and negative controls. The study highlights potential pitfalls in designing BiFC experiments, such as the choice of FP split, negative controls, cell type, and reference FP.
Article
Chemistry, Multidisciplinary
Suzanne B. P. E. Timmermans, Alireza Ramezani, Toni Montalvo, Mark Nguyen, Paul van der Schoot, Jan C. M. van Hest, Roya Zandi
Summary: This study reports on the spontaneous and reversible size conversion of empty capsids of CCMV, which is mediated by a hydrophobic elastin-like polypeptide and pH jump. The conversion process from T = 1 to T = 3 is 10 times slower than that from T = 3 to T = 1. The experimental findings are explained using a simple model based on classical nucleation theory.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Jingluan Han, Kun Ma, Huali Li, Jing Su, Lian Zhou, Jintao Tang, Shijuan Zhang, Yuke Hou, Letian Chen, Yao-Guang Liu, Qinlong Zhu
Summary: Fluorescent tagging protein localization (FTPL) and bimolecular fluorescence complementation (BiFC) are popular tools for studying protein localization and interactions in plant cells. This study developed an efficient, modular all-in-one fluorescent fusion protein (AioFFP) vector toolbox, which facilitates gene cloning and integration of target gene expression units, promoting functional genomics research in plants.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Ozge Ugurlu, Serap Evran
Summary: YopM, an essential effector protein of Yersinia, shows immunosuppressive effect through protein-protein interactions in host cells. This study investigated the protein-protein interactions of YopM with T3SS components LcrV and LcrG, and found that YopM interacts with LcrG. BiFC assay is proposed as a simple method to screen novel interaction partners of YopM.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Feng Liu, Huimin Hu, Mengying Deng, Zongqin Xiang, Yuting Guo, Xinmeng Guan, Dong Li, Qinxue Hu, Wenliang Lei, Hongjuan Peng, Jun Chu
Summary: This study reports a bright monomeric near-infrared fluorescent protein, mIFP663, with maximum excitation at 633 nm. It has high cellular brightness and can label critical cellular and viral proteins without affecting subcellular localization and virus replication. Additionally, mIFP663 can be used to improve bimolecular fluorescence complementation and bioluminescent resonance energy transfer systems for detecting protein-protein interactions in living cells.
Article
Microbiology
Eva Maria Borst, Sarah Harmening, Saskia Sanders, Enrico Caragliano, Karen Wagner, Tihana Lenac Rovis, Stipan Jonjic, Jens Bernhard Bosse, Martin Messerle
Summary: In human cytomegalovirus (HCMV), the small capsid protein (SCP) plays an essential role in ensuring stable levels of major capsid protein (MCP) and their mutual dependence guarantees appropriate levels of the other respective protein. The study provides insights into the mechanism of capsid assembly and identifies SCP as a potential target for antiviral inhibitors.
Article
Pharmacology & Pharmacy
Jingyuan Xi, Zhiqiang Gu, Chunyan Sun, Zimin Chen, Ting Zhang, Ran Chen, Tianyu Liu, Hao Liao, Jun Zou, Danli Yang, Qiang Xu, Jie Wang, Guochao Wei, Zhe Cheng, Fengmin Lu, Xiangmei Chen
Summary: QL-007, a small molecule compound, inhibits HBV replication by influencing the assembly of HBV core proteins, showing potential as an antiviral drug against HBV in preclinical studies and clinical trials.
ANTIVIRAL RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Yue Luo, Junjun Cheng, Zhanying Hu, Haiqun Ban, Shuo Wu, Nicky Hwang, John Kulp, Yuhuan Li, Yanming Du, Jinhong Chang, Usha Viswanathan, Ju-Tao Guo
Summary: The study identified critical Cp amino acid residues for capsid assembly, pgRNA encapsidation, and resistance to CpAMs through systematic mutagenesis analysis. Specific residues such as W102 and Y132 are crucial for capsid assembly, while other residues affect pgRNA encapsidation. Several mutant Cp support high levels of DNA replication but show strong resistance to CpAMs.
ANTIVIRAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Mark Sicking, Martin Jung, Sven Lang
Summary: Various landmark studies have illuminated the structures and functions of the Sec61/SecY complex across all biological domains, showcasing the conserved nature of this ancestral protein translocase. The eukaryotic Sec61 complex facilitates the transfer of precursor proteins into or across the endoplasmic reticulum membrane, accompanied by dynamically recruited auxiliary proteins. Utilizing TRAP and Sec62/Sec63 complexes as models, the study aimed to detect interactions of membrane proteins in living mammalian cells under physiological conditions, revealing multiple protein-protein interactions of diverse topological layouts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alexander Christiansen, Marie Weiel, Andreas Winkler, Alexander Schug, Jochen Reinstein
Summary: It is largely unknown how individual capsid proteins form stable oligomeric units (capsomers) and adapt structurally for further assembly. Using HDX mass spectrometry, researchers discovered differences in conformational flexibility between functional elements of the MCP trimer, with the N-terminal arm and clasp regions showing above average deuterium incorporation. Detachment of the N-terminal arm is crucial for capsomer dissociation and leads to irreversible structural rearrangements.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yuki Ohmuro-Matsuyama, Tetsuya Kitaguchi, Hiroshi Kimura, Hiroshi Ueda
Summary: A fluorogenic assay was developed to detect the acetylation of lysine 9 on histone H3, which is useful in evaluating the activity of HDAC inhibitors. The split YFP reporter system showed higher sensitivity to HDAC inhibitors than conventional cell viability tests, making it a valuable tool for assessment at both single-cell and cell population levels.
Article
Multidisciplinary Sciences
N'Toia C. Hawkins, James L. Kizziah, Jose R. Penades, Terje Dokland
Summary: Phage-inducible chromosomal islands (PICIs) are mobile genetic elements that hijack helper bacteriophages' replication and assembly machinery. Staphylococcus aureus pathogenicity islands (SaPIs), such as SaPIbov5, redirect the assembly pathway of their helper phages by introducing a capsid protein homolog, Ccm. Cryo-electron microscopy studies show that Ccm occupies the pentameric capsomers in SaPIbov5 procapsids, preventing the formation of the cylindrical midsection seen in typical phage procapsids.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Vivian Pogenberg, Josue Ballesteros-Alvarez, Romana Schober, Ingibjorg Sigvaldadottir, Agnieszka Obarska-Kosinska, Morlin Milewski, Rainer Schindl, Margret Helga Ogmundsdottir, Eirikur Steingrimsson, Matthias Wilmanns
NUCLEIC ACIDS RESEARCH
(2020)
Review
Biochemistry & Molecular Biology
Thomas D. Crosskey, Katherine S. H. Beckham, Matthias Wilmanns
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Mira Rosenthal, Eyal Metzl-Raz, Jerome Buergi, Eden Yifrach, Layla Drwesh, Amir Fadel, Yoav Peleg, Doron Rapaport, Matthias Wilmanns, Naama Barkai, Maya Schuldiner, Einat Zalckvar
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Yuliana A. Mokrushina, Andrey Golovin, Ivan Smirnov, Spyros D. Chatziefthimiou, Anastasia Stepanova, Tatyana Bobik, Arthur O. Zalevsky, Alexander S. Zlobin, Kirill A. Konovalov, Stanislav S. Terekhov, Alexey Stepanov, Sofiya O. Pipiya, Olga G. Shamborant, Ekaterina Round, Alexey A. Belogurov, Gleb Bourenkov, Alexander A. Makarov, Matthias Wilmanns, Jia Xie, G. Michael Blackburn, Alexander G. Gabibov, Richard A. Lerner
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Katherine S. H. Beckham, Sonja Staack, Matthias Wilmanns, Annabel H. A. Parret
Article
Multidisciplinary Sciences
Eike C. Schulz, Sara R. Henderson, Boris Illarionov, Thomas Crosskey, Stacey M. Southall, Boris Krichel, Charlotte Uetrecht, Markus Fischer, Matthias Wilmanns
SCIENTIFIC REPORTS
(2020)
Article
Hematology
Volker Huck, Po-Chia Chen, Emma-Ruoqi Xu, Alexander Tischer, Ulrike Klemm, Camilo Aponte-Santamaria, Christian Mess, Tobias Obser, Fabian Kutzki, Gesa Koenig, Cecile V. Denis, Frauke Graeter, Matthias Wilmanns, Matthew Auton, Stefan W. Schneider, Reinhard Schneppenheim, Janosch Hennig, Maria A. Brehm
Summary: This study uncovered a prothrombotic gain of function associated with a VWF variant located in the C4 domain, leading to an increase in platelet aggregate size and affecting the structural flexibility. The research highlights the uniqueness of this VWF variant and its significance for vascular health.
THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Chemistry, Multidisciplinary
Huijong Han, Ekaterina Round, Robin Schubert, Yasmin Gul, Jana Makroczyova, Domingo Meza, Philipp Heuser, Martin Aepfelbacher, Imrich Barak, Christian Betzel, Petra Fromme, Inari Kursula, Poul Nissen, Elena Tereschenko, Joachim Schulz, Charlotte Uetrecht, Jozef Ulicn, Matthias Wilmanns, Janos Hajdu, Victor S. Lamzin, Kristina Lorenzen
Summary: The success of X-ray free-electron lasers (XFELs) in scientific research relies on high-performing X-ray lasers and quality samples, especially as biological samples have limited stability and key biomolecular transformations occur rapidly. The XBI BioLab at the European XFEL is an integrated user facility supporting a wide range of biological experiments, with facilities for sample preparation, cell cultivation, purification, and characterization, as well as laboratories for various microscopy techniques.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Review
Cell Biology
Jerome Buergi, Lakhan Ekal, Matthias Wilmanns
Summary: Proteins with tetratricopeptide repeat (TPR) arrays exhibit unique conformational flexibility and the ability to bind to multiple protein ligands. Pex5 and TRIP8b use TPR structures to recognize specific protein cargos, with their less conserved N-terminal domain playing a crucial role in cargo loading and functional output.
Review
Urology & Nephrology
Nicola M. Tomas, Simon A. Mortensen, Matthias Wilmanns, Tobias B. Huber
Summary: In recent decades, structural biology methods like X-ray crystallography and cryo-electron microscopy have been increasingly utilized to study protein functions, molecular interactions, physiological processes, and disease mechanisms. This review discusses how these methods have contributed to a deeper understanding of life processes and how they can be applied to investigate kidney molecules' functions and pathogenic mechanisms of renal diseases.
KIDNEY INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Jan Philip Wurm, Sihyun Sung, Andrea Christa Kneuttinger, Enrico Hupfeld, Reinhard Sterner, Matthias Wilmanns, Remco Sprangers
Summary: Imidazole glycerol phosphate synthase (HisFH) is a heterodimeric bienzyme complex responsible for catalyzing the hydrolysis of glutamine and cyclase reaction. The catalytically active HisFH conformation is formed only when both substrates of HisH and HisF are bound, leading to allosteric activation. In solution, inactive and active conformations are dynamically balanced, with HisFH turnover rates correlating with the active conformation population.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Stephan Niebling, Osvaldo Burastero, Jerome Buergi, Christian Guenther, Lucas A. Defelipe, Simon Sander, Ellen Gattkowski, Raghavendra Anjanappa, Matthias Wilmanns, Sebastian Springer, Henning Tidow, Maria Garcia-Alai
Summary: The study evaluates binding affinity quantification based on thermal shifts, finding that results from isothermal analysis are more consistent with established biophysical techniques compared to apparent K(d)s obtained from melting temperatures. Additionally, a method to optionally fit the heat capacity change upon unfolding during isothermal analysis is described, along with the release of a web server for easy application of isothermal analysis to nDSF data.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Marion Lagune, Cecile Petit, Flor Vasquez Sotomayor, Matt D. Johansen, Kathrine S. H. Beckham, Christina Ritter, Fabienne Girard-Misguich, Matthias Wilmanns, Laurent Kremer, Florian P. Maurer, Jean-Louis Herrmann
Summary: Non-tuberculous mycobacteria (NTM) are a diverse group of microorganisms with over 200 individual species, mainly found in terrestrial and aquatic environments. In recent years, there has been increasing research on the association of NTM with infections in both immunocompetent and immunocompromised individuals. Significant developments have been made regarding the role of Type VII secretion systems (T7SS) in mycobacteria, with a focus on their impact on virulence and cell wall shaping.
Article
Multidisciplinary Sciences
Katherine S. H. Beckham, Christina Ritter, Grzegorz Chojnowski, Daniel S. Ziemianowicz, Edukondalu Mullapudi, Mandy Rettel, Mikhail M. Savitski, Simon A. Mortensen, Jan Kosinski, Matthias Wilmanns
Summary: The ESX-5 type VII secretion system is a membrane-spanning protein complex crucial to the virulence of mycobacterial pathogens. The high-resolution structure of the 2.1-megadalton ESX-5 core complex reveals a dynamic, secretion-competent conformation of the pore with flexibility for accommodating targeted protein secretion, suggesting that a highly dynamic state of the pore may be a fundamental principle of bacterial secretion machineries.
Article
Biochemistry & Molecular Biology
Jerome Buergi, Pascal Lill, Evdokia-Anastasia Giannopoulou, Cy M. Jeffries, Grzegorz Chojnowski, Stefan Raunser, Christos Gatsogiannis, Matthias Wilmanns
Summary: Oxalyl-CoA synthetase from Saccharomyces cerevisiae, a peroxisomal protein, assembles into concentration-dependent dimers, tetramers and hexamers by self-association. The hexameric assembly has an asymmetric horseshoe-like arrangement, different from other protein structures. A single mutation in the self-association interface abolishes higher-level oligomerization, resulting in a homogenous dimeric assembly. The data provide a basis to mechanistically study peroxisomal translocation of this target.
BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.
