Article
Biochemical Research Methods
Nathan Ponzar, Nicola Pozzi
Summary: Disulfide bonds are essential for protein folding and stability, and dysregulation of this process can lead to various disorders. Thiol-isomerases (TIs) are a family of enzymes that oversee this process in human cells. However, our understanding of how TIs select and interact with their substrates, as well as their response to changes in redox environment, remains limited.
Article
Chemistry, Medicinal
Laszlo Petri, Peter Abranyi-Balogh, Darius Vagrys, Timea Imre, Nikolett Varro, Istvan Mandity, Anita Racz, Lucia Wittner, Kinga Toth, Estilla Zsofia Toth, Tunde Juhasz, Ben Davis, Gyoergy Miklos Keseru
Summary: In this study, a covalent design strategy targeting intrinsically disordered proteins (IDPs) was developed based on the promising results of targeted covalent inhibitors (TCIs) on challenging targets. Using tau protein as a model system, suitable warheads were introduced to non-covalent scaffolds of potential tau aggregation inhibitors. The designed covalent tau binders effectively inhibited tau aggregation in aggregation models, providing promising candidates for the treatment of tauopathies.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Biophysics
Aritra Chowdhury, Daniel Nettels, Benjamin Schuler
Summary: Many proteins have structurally disordered regions or are entirely disordered under physiological conditions. Understanding the mechanisms of interactions for these intrinsically disordered proteins (IDPs) is important, and single-molecule fluorescence spectroscopy is a versatile tool to investigate their conformational heterogeneity and dynamics. Through this technique, we can observe the diverse structural and dynamic properties of bound IDPs and the kinetic mechanisms facilitated by disorder. This review also discusses emerging links to aggregation, liquid-liquid phase separation, and cellular processes.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Sreemantee Sen, Harish Kumar, Jayant B. Udgaonkar
Summary: Tau protein fragment tau-K18 undergoes a disorder to order transition in the presence of lipid micelles and vesicles, forming helical structures induced by a phospholipid mimetic. It has been shown that the mechanism of helical structure formation involves an intermediate state I, which can further progress to form a final helical state with a time constant of 50-200 microseconds. The helical conformation is found to be an aggregation-competent state that can lead to the formation of amyloid fibrils.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Nanoscience & Nanotechnology
T. Ehm, H. Shinar, S. Meir, A. Sekhon, V Sethi, I. L. Morgan, G. Rahamim, O. A. Saleh, R. Beck
Summary: This article reviews the abundance of intrinsically disordered proteins in the human proteome and their role in biological functions. Recent evidence strongly suggests that this structural plasticity contributes to multiple biological functions.
Review
Biochemistry & Molecular Biology
Samuel Naudi-Fabra, Martin Blackledge, Sigrid Milles
Summary: Single molecule fluorescence and nuclear magnetic resonance spectroscopy are powerful techniques for analyzing intrinsically disordered proteins. They provide complementary views to decipher the complex properties and interactions of IDPs, and have made significant contributions to our understanding of their molecular characteristics.
Review
Physics, Multidisciplinary
Pei Li, Ting Chen, Liang Chen, Yan-Wen Tan
Summary: Improved single-molecule methods have the potential to greatly enhance our understanding of the molecular mechanism underlying cellular signal transduction. By monitoring individual molecules, these methods can bypass averaging effects and provide unique information. They are frequently used for quantitatively investigating molecular translocation, protein-protein interactions, and conformational dynamics involved in signal transduction.
FRONTIERS IN PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Lukas S. Stelzl, Lisa M. Pietrek, Andrea Holla, Javier Oroz, Mateusz Sikora, Juergen Koefinger, Benjamin Schuler, Markus Zweckstetter, Gerhard Hummer
Summary: This study builds a structural ensemble of the tau K18 protein and reveals the factors controlling the balance between functional and disease-associated conformational states. It shows that pathogenic mutations shift the population from functional to aggregation-prone conformations. This research provides a detailed view of the equilibrium between functional and aggregation-prone states of the tau K18 protein.
Review
Chemistry, Multidisciplinary
Matti Mar, Kateryna Nitsenko, Petur O. Heidarsson
Summary: Eukaryotic transcription factors play a crucial role in integrating molecular feedback and regulating gene expression. They consist of structured DNA-binding domains and long intrinsically disordered regions (IDRs). The dynamic multifunctionality of IDRs is essential for their functions in genome regulation. This review analyzes the chemical features of TF IDRs and their involvement in protein interactions, DNA binding, chromatin opening, and phase separation. Suggestions are given for future research to integrate experiments and simulations in understanding TF functions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Iwo Konig, Andrea Soranno, Daniel Nettels, Benjamin Schuler
Summary: The concentrations of macromolecules within cells can affect the conformations and dynamics of proteins. By reducing cell volume through hyperosmotic stress, it was found that intrinsically disordered proteins exhibit compaction and slower dynamics in more crowded cells. This concentration and length-scale dependence of crowding can be explained by polymer theory and depletion interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Jhullian J. Alston, Andrea Soranno, Alex S. Holehouse
Summary: Over the past two decades, intrinsically disordered proteins and protein regions have been recognized as essential drivers of cellular function, with singlemolecule fluorescence spectroscopy and molecular simulations providing insight into their behavior. When combined, these techniques offer complementary information that can help uncover complex molecular details.
Review
Biochemistry & Molecular Biology
Anna Svirina, Neharika Chamachi, Michael Schlierf
Summary: Outer membrane proteins (OMPs) play important roles in maintaining the viability of Gram-negative bacteria through various functions. Previous studies have identified proteins and mechanisms involved in OMP biogenesis, but the mechanisms of action of these molecular machines without ATP as an energy source are still not fully understood. Single-molecule studies can provide additional insights into the mechanisms and kinetics of OMP biogenesis.
Article
Neurosciences
Michael S. LaCroix, Hilda Mirbaha, Ping Shang, Stephanie Zandee, Chan Foong, Alexandre Prat, Charles L. White, Olaf Stuve, Marc Diamond
Summary: This study found tau seeding in frozen brain tissue of multiple sclerosis patients, suggesting that progressive MS may be a secondary tauopathy. The study also observed seeding outside of MS plaques.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Taryn M. Kay, Cody P. Aplin, Rowan Simonet, Julie Beenken, Robert C. Miller, Christin Libal, Arnold J. Boersma, Erin D. Sheets, Ahmed A. Heikal
Summary: The study developed a simple approach using FCS to investigate FRET of genetically encoded crTC2.1, finding that the molecular brightness of the cleaved form is higher than the intact form at 405nm, but similar at 488nm. FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of time constants associated with autocorrelation curves, allowing for potential use in living cells with low expression levels of genetically encoded constructs to limit interference with cell machinery.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Samuel Naudi-Fabra, Maud Tengo, Malene Ringkjobing Jensen, Martin Blackledge, Sigrid Milles
Summary: Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and requires an integrated approach using multiple techniques to accurately describe the conformational ensembles of these proteins. This integrated approach has been successfully tested and validated, providing new insights into the conformational landscape of viral proteins and demonstrating its potential for integrative dynamic structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)