Article
Biochemistry & Molecular Biology
William Benman, Erin E. Berlew, Hao Deng, Caitlyn Parker, Ivan A. Kuznetsov, Bomyi Lim, Arndt F. Siekmann, Brian Y. Chow, Lukasz J. Bugaj
Summary: The study introduces single-component optogenetic probes with activation dynamics dependent on both light and temperature. The BcLOV4 photoreceptor was utilized to stimulate signaling in mammalian cells, showing tunable membrane translocation dynamics in response to light and temperature. Quantitative modeling predicted the activation dynamics of BcLOV4 and demonstrated its versatility in generating widely applicable optogenetic tools.
NATURE CHEMICAL BIOLOGY
(2022)
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
Multidisciplinary Sciences
Tracy M. Josephs, Matthew J. Belousoff, Yi-Lynn Liang, Sarah J. Piper, Jianjun Cao, Daniel J. Garama, Katie Leach, Karen J. Gregory, Arthur Christopoulos, Debbie L. Hay, Radostin Danev, Denise Wootten, Patrick M. Sexton
Summary: This study provides insights into the mechanisms of class B1 GPCR activation by analyzing the structures and protein conformational dynamics of GPCRs.
Article
Biochemistry & Molecular Biology
Hui Lin, Peng Xiao, Rui-Qian Bu, Shengchao Guo, Zhao Yang, Daopeng Yuan, Zhong-Liang Zhu, Chuan-Xin Zhang, Qing-Tao He, Chao Zhang, Yu-Qi Ping, Ru-Jia Zhao, Chuan-Shun Ma, Chang-Hao Liu, Xiao-Ning Zhang, Dan Jiang, Shaohui Huang, Yue-Tong Xi, Dao-Lai Zhang, Chen-Yang Xue, Bai-Sheng Yang, Jian-Yuan Li, Hao-Cheng Lin, Xu-Hui Zeng, Han Zhao, Wen-Ming Xu, Fan Yi, Zhongmin Liu, Jin-Peng Sun, Xiao Yu
Summary: In this study, the cryo-EM structure of apo-ADGRG2 in complex with a G(s) trimer was solved, providing insights into the activation and ligand-binding of ADGRG2. The identification of steroid hormones, such as DHEA, as potential ligands of ADGRG2 was also reported.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ana Clara Barbosa Antonelli, Vinnycius Pereira Almeida, Fernanda Oliveira Feitosa de Castro, Jacyelle Medeiros Silva, Irmtraut Araci Hoffmann Pfrimer, Edecio Cunha-Neto, Andrea Queiroz Maranhao, Marcelo Macedo Brigido, Renato Oliveira Resende, Anamelia Lorenzetti Bocca, Simone Goncalves Fonseca
Summary: In this study, an in silico universal vaccine against Zika virus was developed, which is predicted to induce broad and high-coverage cellular and humoral immune responses.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Luciana Esposito, Nicole Balasco, Luigi Vitagliano
Summary: Oligomerization plays an important role in conferring certain properties to proteins. This study utilized the machine-learning algorithms implemented in AlphaFold to predict the structural states of functional oligomers in the KCTD protein family. The findings identified reliable three-dimensional models for several pentameric states that were previously uncharacterized from a structural point of view. The study provides a comprehensive view of KCTD protein oligomerization and offers insights into key biological processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Neda Ojaghlou, Justin Airas, Lauren M. McRae, Cooper A. Taylor, Bill R. Miller, Carol A. Parish
Summary: Recent experiments have shown that JIP1 activates JNK, which is involved in cell apoptosis and diseases like Alzheimer's disease, obesity, and cancer. The structure and dynamics of JIP1, particularly a functionally active 10mer fragment, were studied using MD simulations. A Markov state model identified four metastable states with dominant pathways of conformational interconversions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Zakariyya Ishtaiwi, Deeb Taher, Marcus Korb, Wissam Helal, Hassan K. Juwhari, Afnan Al-Hunaiti, Hazem Amarne, Khaleel Assaf, Lubna Alrawashdeh, Mohammad W. Amer, Yaser A. Yousef, Heinrich Lang
Summary: A series of N-(3-NO2-C6H4)-N'-(4-R-C6H4)oxamato zincate(II) complexes were synthesized to study the influence of different electron-withdrawing and electron-donating groups R on their electronic properties. The crystal structures of 3c and 3f were determined, confirming the tetrahedral environment around Zn(II) set by the oxamato ligands. UV-Vis spectra and TD-DFT calculations confirmed the presence of LLCT (π -> π*) bands in the complexes, indicating their potential as luminescent materials.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Review
Biochemistry & Molecular Biology
Bingying Liu, Daiwen Yang
Summary: Nanobodies, derived from heavy-chain antibodies of camelids, possess small size, high specificity, and high stability. Construction of synthetic nanobody libraries using DNA oligonucleotides offers a cost-effective alternative and has great potential in identifying antigen-specific nanobodies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Computer Science, Artificial Intelligence
Yinfeng Zhou, Jinjin Li, Hailong Yang, Qingyuan Xu, Taoli Yang, Danlu Feng
Summary: Knowledge structure is a crucial factor in assessing and guiding individual learning, and this paper presents an extended method to construct knowledge structures and recommend learning paths that overcomes the limitations of existing approaches.
INTERNATIONAL JOURNAL OF MACHINE LEARNING AND CYBERNETICS
(2023)
Article
Multidisciplinary Sciences
Ryo Mori, Samuel Ciocys, Kazuaki Takasan, Ping Ai, Kayla Currier, Takahiro Morimoto, Joel E. Moore, Alessandra Lanzara
Summary: By using time-, spin- and angle-resolved photoemission spectroscopy, we directly observe the formation of a long-lived exciton state in a transient excitonic topological surface state (TSS) in Bi2Te3. This state inherits the spin-polarization of the TSS and is spatially indirect along the z axis, as it couples photoinduced surface electrons and bulk holes in the same momentum range, which ultimately leads to an excitonic state of the TSS. These results establish Bi2Te3 as a possible candidate for the excitonic condensation of TSSs and open up a new paradigm for exploring other spatially indirect excitons and non-equilibrium many-body topological physics.
Article
Biochemistry & Molecular Biology
Amelia T. Yuan, Natalie C. Korkola, Martin J. Stillman
Summary: Metallothioneins (MTs) are essential mammalian metal chaperones. MT1 is expressed in the kidneys and MT3 in nervous tissue. Through various methods, this study provides evidence that apo-MT3 adopts a compact structure under physiological conditions and an extended structure under denaturing conditions. Furthermore, the study suggests that MT3 acts as a non-inducible regulator of the nervous system, while MT1 acts as an inducible scavenger in the kidneys.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Sergio M. Marques, Joan Planas-Iglesias, Jiri Damborsky
Summary: Enzymes are in high demand for various biotechnological applications, and computational methods are increasingly used to engineer enzymes for optimized properties. These web-based tools are user-friendly and reduce the experimental burden significantly.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
David H. Brookes, Amirali Aghazadeh, Jennifer Listgarten
Summary: Fitness functions map biological sequences to specific properties, but accurately estimating these functions with limited data is a challenge. This study develops a framework to investigate the sparsity of fitness functions sampled from the GNK model and validates its effectiveness.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Hubert Anysz, Magdalena Apollo, Beata Grzyl
Summary: High monetary value of construction projects leads to disputes between GCs and clients, machine learning tools are used to predict dispute outcomes and calculate decision risks.
Article
Biology
Florian Bleffert, Joachim Granzin, Muttalip Caliskan, Stephan N. Schott-Verdugo, Meike Siebers, Bjoern Thiele, Laurence Rahme, Sebastian Felgner, Peter Doermann, Holger Gohlke, Renu Batra-Safferling, Karl-Erich Jaeger, Filip Kovacic
Summary: Cells adapt their membrane composition to changing conditions by regulating GPL synthesis and degradation. This study identified a cytoplasmic membrane-bound phospholipase A(1) (PlaF) from Pseudomonas aeruginosa that might be involved in GPL remodeling. PlaF is an important virulence factor and its structure and activation mechanism were revealed, offering insights for the development of therapeutics targeting PlaF.
Article
Chemistry, Medicinal
Raphael J. Eberle, Ian Gering, Markus Tusche, Philipp N. Ostermann, Lisa Muller, Ortwin Adams, Heiner Schaal, Danilo S. Olivier, Marcos S. Amaral, Raghuvir K. Arni, Dieter Willbold, Monika A. Coronado
Summary: The C30 endopeptidase is crucial for the life cycle of SARS-CoV-2 and is a potential drug target. Crotamine, a peptide isolated from rattlesnake venom, has shown promising activities and derivatives such as L-peptides have exhibited inhibitory effects on 3CL protease. D-peptides have shown potential as a prototype for peptide-based drugs targeting viral protease 3CL(pro).
Article
Biochemistry & Molecular Biology
Niloufar Mosaddeghzadeh, Silke Pudewell, Farhad Bazgir, Neda S. Kazemein Jasemi, Oliver H. F. Krumbach, Lothar Gremer, Dieter Willbold, Radovan Dvorsky, Mohammad R. Ahmadian
Summary: This study provides evidence for the mechanistic framework model that IQGAP GRD might act as a 'scaffolding domain' by binding CDC42 irrespective of its nucleotide-bound forms. The study found that the binding affinity of GRD1 and GRD2 to CDC42 is lower compared to C794/C795, and mutation of the switch regions of CDC42 greatly affected the binding of C794/C795 but had little effect on GRD1 and no effect on GRD2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Marc Sevenich, Joop van den Heuvel, Ian Gering, Jeannine Mohrlueder, Dieter Willbold
Summary: The binding between the spike protein of SARS-CoV-2 and hACE2 is a two-step interaction, which enhances the stability of the complex. This interaction is not only present in the wild type strain but also in the B.1.1.7 variant, with an increased transition rate. These findings are important for understanding the infectivity and characterizing emerging variants of SARS-CoV-2 spike proteins.
JOURNAL OF VIROLOGY
(2022)
Article
Microbiology
Raphael J. Eberle, Danilo S. Olivier, Marcos S. Amaral, Carolina C. Pacca, Mauricio L. Nogueira, Raghuvir K. Arni, Dieter Willbold, Monika A. Coronado
Summary: This study demonstrates the inhibitory potential of the water-soluble vitamin riboflavin against NS2B/NS3(pro) of ZIKV and YFV and nsP2(pro) of CHIKV, and its ability to inhibit the viral entry of CHIKV. Molecular dynamics simulations validate the repurposing of riboflavin as a promising molecule in drug development against these viruses.
Article
Biochemistry & Molecular Biology
Thomas Pauly, Najoua Bolakhrif, Jesko Kaiser, Luitgard Nagel-Steger, Lothar Gremer, Holger Gohlke, Dieter Willbold
Summary: The polymorphism of Methionine/valine at position 129 in the human prion protein (huPrP) is closely associated with the pathogenic phenotype, disease progression, and onset age of neurodegenerative diseases. This study investigates the influence of the amino acid type at position 129 on the structural properties of huPrP using various biophysical techniques. The results reveal differences in aggregation propensity and oligomer content between the 129M and 129V variants, leading to divergent pathways for amyloid formation. The study also identifies intramolecular interactions responsible for the enhanced monomer stability of the 129M variant.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Oliver H. Weiergraeber, Dusan Petrovic, Andreas Kislat, Martin Pattky, Judith Fabig, Renu Batra-Safferling, Jan Schulte Am Esch, Karen Haenel, Carolin Huhn, Birgit Strodel, Bernhard Homey, Dieter Willbold
Summary: CCL16 is primarily synthesized by hepatocytes, circulates in the blood as a full-length protein, and the C-terminal extension may impair its biological activity modulation.
Article
Biochemistry & Molecular Biology
Raphael J. Eberle, Marc Sevenich, Ian Gering, Lara Scharbert, Birgit Strodel, Nils A. . Lakomek, Karoline Santur, Jeannine Mohrlueder, Monika A. . Coronado, Dieter Willbold
Summary: A novel and efficient next-generation sequencing (NGS) supported phage display selection strategy was used to identify a set of peptide ligands that inhibit the SARS-CoV-2 3CL protease. These ligands have the potential to be lead compounds for therapeutic development and address limitations associated with current L-peptide inhibitors.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tim Altendorf, Ian Gering, Beatrix Santiago-Schuebel, Selma Aghabashlou Saisan, Gueltekin Tamgueney, Markus Tusche, Dominik Honold, Sarah Schemmert, Wolfgang Hoyer, Jeannine Mohrlueder, Dieter Willbold
Summary: Alzheimer's disease and other tauopathies are caused by the misfolding and aggregation of the tau protein, leading to neurodegeneration. In this study, two all D-enantiomeric peptides were developed, which bind to monomeric tau protein and inhibit its aggregation into amyloid fibrils. These peptides show promise as potential therapeutic agents for Alzheimer's disease and other tauopathies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Lea Sundermeyer, Graziella Bosco, Srushti Gujar, Melanie Brocker, Meike Baumgart, Dieter Willbold, Oliver H. Weiergraeber, Marco Bellinzoni, Michael Bott
Summary: In this study, we investigated the roles of GlnH and GlnX in the GlnH-GlnX-PknG-OdhI-OdhA signal transduction cascade in C. glutamicum, and confirmed their involvement through genetic, biochemical, and structural modeling approaches.
MICROBIOLOGY SPECTRUM
(2022)
Article
Pharmacology & Pharmacy
Monika A. Coronado, Ian Gering, Marc Sevenich, Danilo S. Olivier, Mohammadamin Mastalipour, Marcos S. Amaral, Dieter Willbold, Raphael J. Eberle
Summary: Epigallocatechin molecules, found in green tea, have shown great potential in inhibiting flaviviruses such as Dengue, yellow fever, West Nile, and Zika. This discovery could lead to the development of more effective antiviral drugs.
Article
Medicine, General & Internal
Marlene Pils, Alexandra Dybala, Fabian Rehn, Lara Bloemeke, Tuyen Bujnicki, Victoria Kraemer-Schulien, Wolfgang Hoyer, Detlev Riesner, Dieter Willbold, Oliver Bannach
Summary: Protein misfolding and aggregation are key factors in neurodegenerative diseases. In this study, a synthetic β-amyloid oligomer sample was developed for quality control and standardization of diagnostic methods. The combination of atomic force microscopy and fluorescence analysis showed promising results for the detection of Aβ oligomers in bodily fluids.
Article
Biochemistry & Molecular Biology
Katharina Wintz, Julia Post, Karl-Josef Langen, Dieter Willbold, Antje Willuweit, Janine Kutzsche
Summary: Amyotrophic lateral sclerosis (ALS) is a deadly disease with no cure, causing complete muscle loss and respiratory arrest. Only three symptomatic drugs have been approved by the FDA so far. RD2RD2, a new drug candidate, has shown the ability to delay symptom onset in mouse models of ALS.
Article
Biotechnology & Applied Microbiology
Nora Lisa Bitzenhofer, Carolin Hoefel, Stephan Thies, Andrea Jeanette Weiler, Christian Eberlein, Hermann J. J. Heipieper, Renu Batra-Safferling, Pia Sundermeyer, Thomas Heidler, Carsten Sachse, Tobias Busche, Jorn Kalinowski, Thomke Belthle, Thomas Drepper, Karl-Erich Jaeger, Anita Loeschcke
Summary: This study found that the formation of outer membrane vesicles (OMV) in Pseudomonas putida KT2440 is correlated with the recombinant production of the natural compound tripyrrole prodigiosin. By manipulating the expression of genes associated with OMV formation, the yields of various compounds such as prodigiosin, violacein, phenazine-1-carboxylic acid, and zeaxanthin were significantly increased.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alexandra Albus, Yannick Kronimus, Monika Burg-Roderfeld, Hendrik van der Wurp, Dieter Willbold, Tamar Ziehm, Richard Dodel, Jean Alexander Ross
Summary: The accumulation and aggregation of alpha-synuclein are crucial mechanisms in the development of Parkinson's disease. This study investigated the levels and binding characteristics of naturally occurring autoantibodies against alpha-synuclein in patients with Parkinson's disease and healthy controls. The results showed no significant differences in the levels or affinities of these autoantibodies between the two groups, regardless of the presence of LRRK2 gene mutations.