Article
Chemistry, Multidisciplinary
Jinyang Liu, Bingjie Zhao, Xuebo Zhang, Daoming Guan, Kuangshi Sun, Yunxiang Zhang, Qian Liu
Summary: In this study, we developed a novel thiolation strategy for squaraine dyes to improve their photostability and extend their application in single-molecule imaging. By introducing thiolation of the central cyclobutene of squaraine, we observed a significant increase in photobleaching lifetime, allowing for stable single-molecule tracking of membrane protein CD56 and monitoring mitochondria movements in live neurons. This research contributes to the advancement of single-molecule imaging probes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Michael J. T. Senior, Carina Monico, Eve E. Weatherill, Robert J. Gilbert, Alejandro P. Heuck, Mark Wallace
Summary: By utilizing single-molecule tracking and optical single channel recording, we investigated the assembly pathway and pore formation of cholesterol-dependent cytolysin Perfringolysin O. Our results demonstrate a stepwise irreversible assembly dominated by monomer addition, with infrequent assembly from larger partial complexes.
Article
Biochemical Research Methods
Lara Dresser, Patrick Hunter, Fatima Yendybayeva, Alex L. Hargreaves, Jamieson A. L. Howard, Gareth J. O. Evans, Mark C. Leake, Steven D. Quinn
Summary: Alzheimer's disease is characterized by misfolding and aggregation of Aβ, with small soluble Aβ oligomers now recognized as more toxic than larger fibrillar aggregates. Techniques to characterize oligomer stoichiometry and assembly are crucial for understanding neurodegeneration. By integrating biophysics techniques, new insights into oligomer formation at the single-molecule level can be gained, offering potential for investigating other protein aggregation systems.
Article
Chemistry, Physical
Benjamin Vermeer, Sonja Schmid
Summary: Biomolecular systems rely on dynamic processes at the nanoscale, and detecting biomolecular nanodynamics is crucial for understanding the driving forces that control them. The technique of single-molecule fluorescence resonance energy transfer (smFRET) is limited by irreversible photobleaching, but the introduction of DyeCycling has the potential to break this limit and provide more information per single molecule. It has the ability to revolutionize time-resolved smFRET and uncover a wealth of biomolecular dynamics.
Article
Biochemistry & Molecular Biology
Arpan Dey, Vicky Vishvakarma, Anirban Das, Mamata Kallianpur, Simli Dey, Roshni Joseph, Sudipta Maiti
Summary: The text describes a method for measuring the degree of surface exposure of protein molecules through photobleaching and fluorescence quenching techniques. By analyzing the increase in step length, the accessibility of fluorophores to solvents is determined, revealing different species with varying levels of exposure. This approach provides a simple way to probe the conformational states of membrane proteins at a single molecule level.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Analytical
Yu P. Zhang, Evgeniia Lobanova, Derya Emin, Sergey V. Lobanov, Antonina Kouli, Caroline H. Williams-Gray, David Klenerman
Summary: This study introduces a new method for the diagnosis of early Parkinson's disease. The results show that the proportion of soluble alpha-synuclein aggregates can distinguish between Parkinson's disease patients and control groups, with Parkinson's disease patients having a higher proportion of larger and rounder alpha-synuclein aggregates. By combining the number and morphology of the aggregates, a new biomarker with improved accuracy for early Parkinson's disease diagnosis was constructed.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Biao-Feng Zeng, Yu-Ling Zou, Gan Wang, Wenjing Hong, Zhong-Qun Tian, Yang Yang
Summary: Recent advances in single-molecule electronics have opened up new opportunities to investigate single-molecule chemistry. The focus has shifted towards quantitative analysis of the physical and chemical behavior of single molecules, including dynamic molecular configurations, redox states, single-molecule reactions, single-molecule sensing, and molecular adsorption behaviors.
Article
Biochemistry & Molecular Biology
Inwha Baek, Larry J. Friedman, Jeff Gelles, Stephen Buratowski
Summary: Research shows that in activator-dependent PIC assembly, RNA Pol II, TFIIF, and TFIIE can preassemble on enhancer-bound activators, and multiple RNA Pol II complexes can simultaneously bind to form a localized cluster, while TFIIH binding is unique and depends on the basal promoter.
Article
Chemistry, Physical
Dmitrii E. Makarov, Alexander Berezhkovskii, Gilad Haran, Eli Pollak
Summary: This study investigates the measurement issue of transition path times in single-molecule experiments and finds that the observed times are generally longer than the true times due to the effect of multiple crossings of the molecule trajectory on the boundary.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Multidisciplinary Sciences
Sonja Schmid, Cees Dekker
Summary: NEOtrap is a novel single-molecule technique that can be applied in various fields such as biosensing, enzymology, protein folding, and protein dynamics, demonstrating unique versatility and potential.
Article
Chemistry, Multidisciplinary
Qiong-Qiong Yao, Jitao Wen, Sarah Perrett, Si Wu
Summary: This study reveals the mechanisms by which lipid membranes influence the amyloid formation of Tau protein. It shows that lipid membranes can induce conformational changes in Tau and either accelerate or inhibit its fibrillation process depending on the concentration of the lipid membrane.
Article
Chemistry, Physical
Mirjam Kummerlin, Abhishek Mazumder, Achillefs N. Kapanidis
Summary: We present a general strategy to overcome photobleaching in single-molecule fluorescence measurements by replenishing fluorescent probes using transient binding of complementary DNA strands. This allows for near-continuous observation of single-molecule fluorescence for over an hour, much longer than typical photobleaching times. Our approach is adaptable to FRET and can be used to study the conformational dynamics of dynamic structures.
Article
Chemistry, Multidisciplinary
Yaxian Liu, Xiaoyi Wang, Giulia Campolo, Xiangyu Teng, Liming Ying, Joshua B. Edel, Aleksandar P. Ivanov
Summary: This study develops a strategy that combines nanopore-based sensing with molecular carriers to detect α-Synuclein oligomers directly in clinical samples, providing a new approach for the diagnosis and mechanism study of Parkinson's disease.
Article
Chemistry, Analytical
Diana Soukarie, Philippe Rousseau, Maya Salhi, Alexia de Caro, Jean-Marc Escudier, Catherine Tardin, Vincent Ecochard, Laurence Salome
Summary: This study successfully developed an aptasensor based on high-throughput single-molecule techniques, which enables rapid, simple, and sensitive detection of single target molecules. The presence and concentration of the target molecules can be monitored in real time by combining videomicroscopy and image analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Stefan Niekamp, Nico Stuurman, Nan Zhang, Ronald D. Vale
Summary: The study reveals that during motility, the motor protein dynein exhibits variability in the movement between its domains, with the AAA ring and MTBDs not always stepping simultaneously and taking differently sized steps. This variability results in a large number of unexpected conformational states of dynein during motility. The flexibility between major dynein domains is found to be critical for dynein motility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Arshdeep Sidhu, Ine Segers-Nolten, Vincent Raussens, Mireille M. A. E. Claessens, Vinod Subramaniam
ACS CHEMICAL NEUROSCIENCE
(2017)
Article
Chemistry, Physical
Kristian L. Goeken, Richard B. M. Schasfoort, Vinod Subramaniam, Ron Gill
Article
Chemistry, Multidisciplinary
D. Wasserberg, J. Cabanas-Danes, V. Subramaniam, J. Huskens, P. Jonkheijm
CHEMICAL COMMUNICATIONS
(2018)
Article
Chemistry, Physical
Mohammad A. A. Fakhree, Ine Segers Nolten, Christian Blum, Mireille M. A. E. Claessens
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2018)
Article
Physics, Multidisciplinary
Slav A. Semerdzhiev, Saskia Lindhoud, Anja Stefanovic, Vinod Subramaniam, Paul van der Schoot, Mireille M. A. E. Claessens
PHYSICAL REVIEW LETTERS
(2018)
Article
Multidisciplinary Sciences
G. C. Hassink, C. C. Raiss, I. M. J. Segers-Nolten, R. J. A. van Wezel, V. Subramaniam, J. le Feber, M. M. A. E. Claessens
Article
Biochemistry & Molecular Biology
Mohammad A. A. Fakhree, Sjoerd A. J. Engelbertink, Kirsten A. van Leijenhorst-Groener, Christian Blum, Mireille M. A. E. Claessens
Article
Biophysics
Gerardo Abbandonato, Barbara Storti, Ilaria Tonazzini, Martin Stoeckl, Vinod Subramaniam, Costanza Montis, Riccardo Nifosi, Marco Cecchini, Giovanni Signore, Ranieri Bizzarri
BIOPHYSICAL JOURNAL
(2019)
Article
Optics
N. Mateos, R. Molenaar, M. M. A. E. Claessens, C. Blum
Review
Biochemistry & Molecular Biology
Mohammad A. A. Fakhree, Christian Blum, Mireille M. A. E. Claessens
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2019)
Article
Chemistry, Physical
Jord C. Prangsma, Robert Molenaar, Laura van Weeren, Daphne S. Bindels, Lindsay Haarbosch, Jente Stouthamer, Theodorus W. J. Gadella, Vinod Subramaniam, Willem L. Vos, Christian Blum
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
Theresa S. Braun, Juliane Stehle, Sylwia Kacprzak, Patrick Carl, Peter Hoefer, Vinod Subramaniam, Malte Drescher
Summary: Protein-membrane interactions are crucial for cellular processes, and the study of these interactions presents a challenge in modern biophysical chemistry. By employing rapid-scan electron paramagnetic resonance spectroscopy, the interaction between αS and negatively charged vesicles in vitro was studied, with reflections observed in cells as well.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Neurosciences
Aditya Iyer, Arshdeep Sidhu, Vinod Subramaniam
Summary: N-alpha-acetylation is a common post-translational modification in eukaryotic proteins, which has significant effects on protein regulation and function. However, the precise mechanisms and implications of N-alpha-acetylation of alpha-synuclein (alpha S) are not fully understood. This review provides an overview of current knowledge and discusses the impact of N-alpha-acetylation on the conformational, oligomeric, and fibrillar states of alpha S, as well as its relevance to Lewy body formation and synucleinopathies.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Arshdeep Sidhu, Jonathan Vaneyck, Christian Blum, Ine Segers-Nolten, Vinod Subramaniam
AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
(2018)
