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Article ; Online: Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET.

Schuler, Benjamin

2018 Volume 149, Issue 1, Page(s) 10901

Abstract: The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have ... ...

Abstract	The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Förster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of polymer physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the dynamics of disordered proteins.
MeSH term(s)	Fluorescence Resonance Energy Transfer/methods ; Intrinsically Disordered Proteins/chemistry ; Molecular Dynamics Simulation ; Protein Folding ; Protein Unfolding ; Spectrometry, Fluorescence/methods
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2018-07-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.5037683
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Article ; Online: Single-Molecule FRET at 10 MHz Count Rates.

Grabenhorst, Lennart / Sturzenegger, Flurin / Hasler, Moa / Schuler, Benjamin / Tinnefeld, Philip

Journal of the American Chemical Society

2024 Volume 146, Issue 5, Page(s) 3539–3544

Abstract: A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that ... ...

Abstract	A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.
MeSH term(s)	Fluorescence Resonance Energy Transfer/methods ; Nanotechnology ; DNA/chemistry ; Nucleic Acid Hybridization ; Fluorescent Dyes/chemistry
Chemical Substances	DNA (9007-49-2) ; Fluorescent Dyes
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c13757
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Article ; Online: Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy.

Chowdhury, Aritra / Nettels, Daniel / Schuler, Benjamin

Annual review of biophysics

2023 Volume 52, Page(s) 433–462

Abstract: Many proteins contain large structurally disordered regions or are entirely disordered under physiological conditions. The functions of these intrinsically disordered proteins (IDPs) often involve interactions with other biomolecules. An important ... ...

Abstract	Many proteins contain large structurally disordered regions or are entirely disordered under physiological conditions. The functions of these intrinsically disordered proteins (IDPs) often involve interactions with other biomolecules. An important emerging effort has thus been to identify the molecular mechanisms of IDP interactions and how they differ from the textbook notions of biomolecular binding for folded proteins. In this review, we summarize how the versatile tool kit of single-molecule fluorescence spectroscopy can aid the investigation of these conformationally heterogeneous and highly dynamic molecular systems. We discuss the experimental observables that can be employed and how they enable IDP complexes to be probed on timescales from nanoseconds to hours. Key insights include the diverse structural and dynamic properties of bound IDPs and the kinetic mechanisms facilitated by disorder, such as fly-casting; disorder-mediated encounter complexes; and competitive substitution via ternary complexes, which enables rapid dissociation even for high-affinity complexes. We also discuss emerging links to aggregation, liquid-liquid phase separation, and cellular processes, as well as current technical advances to further expand the scope of single-molecule spectroscopy.
MeSH term(s)	Intrinsically Disordered Proteins/chemistry ; Protein Conformation ; Single Molecule Imaging ; Kinetics
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2023-02-07
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2434725-5
ISSN	1936-1238 ; 1936-122X
ISSN (online)	1936-1238
ISSN	1936-122X
DOI	10.1146/annurev-biophys-101122-071930
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Book ; Thesis: Faltungsmutanten des P22-Tailspikeproteins

Schuler, Benjamin

Stabilität der beta-Helix-Domäne

1998

Author's details	Benjamin Schuler
Language	German
Size	Getr. Zählung : Ill., graph. Darst.
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Regensburg, Univ., Diss., 1998
HBZ-ID	HT010627709
Database	Catalogue ZB MED Medicine, Health

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Article: Association of Use of a Mobile Tackling Dummy During College Football Practice With Reduced Sport-Related Concussion: Results of a Pilot Investigation.

Aita, Stephen L / Muchintala, Rohan / Suresh, Advith / Patel, Suraj / Schuler, Benjamin / Lichtenstein, Jonathan D

Orthopaedic journal of sports medicine

2024 Volume 12, Issue 2, Page(s) 23259671241228316

Abstract: Background: Considering the multifaceted consequences of improperly managed sport-related concussions (SRCs) in American football, identifying efficacious prevention measures for enhancing player safety is crucial.: Purpose: To investigate the ... ...

Abstract	Background: Considering the multifaceted consequences of improperly managed sport-related concussions (SRCs) in American football, identifying efficacious prevention measures for enhancing player safety is crucial. Purpose: To investigate the association of primary prevention measures (no-tackle practices and using a mobile tackling dummy in practice) with the frequency of SRCs within college football programs in the United States. Study design: Descriptive epidemiology study. Methods: In this pilot study, we analyzed the frequency of new SRCs recorded during various settings (total, in preseason, in season, in practice, and game) across 14 seasons (2007-2019 and 2021) for Dartmouth College and across 7 seasons (2013-2019) for the 7 other teams in the Ivy League men's athletic football conference. Trends between seasons and the number of SRCs sustained were examined using correlations and basic descriptive statistics. We also examined SRC frequency in relation to primary prevention measures (no-tackle practices, use of mobile tackling dummies during practice) in the Dartmouth College football program, and we compared SRCs with regard to the no-tackle practice policy in the other Ivy League teams. Results: There was a statistically significant reduction in the number of SRCs over the seasons studied, with the strongest finding observed for Dartmouth College in-game SRCs ( Conclusion: Our data indicate that the use of the mobile tackling dummy in practice was related to the reduced number of SRCs sustained at multiple settings during the football season. To a lesser extent, the no-tackle practice policy was also associated with a reduced number of SRCs.
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2706251-X
ISSN	2325-9671
ISSN	2325-9671
DOI	10.1177/23259671241228316
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Article ; Online: Editorial overview: Molecular interactions that drive folding and binding: new challenges and opportunities.

Gosavi, Shachi / Schuler, Benjamin

Current opinion in structural biology

2020 Volume 60, Page(s) iii–iv

MeSH term(s)	Protein Binding ; Protein Folding ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2020-03-30
Publishing country	England
Document type	Editorial ; Introductory Journal Article
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2020.03.001
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Article ; Online: Effects of Daily Posttraumatic Stress Disorder Symptoms on Heart Rate Variability.

Slavish, Danica C / Ruggero, Camilo J / Schuler, Keke / Schwartz, Joseph E / Luft, Benjamin / Kotov, Roman

Psychosomatic medicine

2023 Volume 86, Issue 1, Page(s) 30–36

Abstract: Objective: Posttraumatic stress disorder (PTSD) is common, debilitating, and associated with an increased risk of health problems, including cardiovascular disease. PTSD is related to poor autonomic function indicated by reduced heart rate variability ( ... ...

Abstract	Objective: Posttraumatic stress disorder (PTSD) is common, debilitating, and associated with an increased risk of health problems, including cardiovascular disease. PTSD is related to poor autonomic function indicated by reduced heart rate variability (HRV). However, very little work has tested the timescale or direction of these effects, given that most evidence comes from cross-sectional studies. Documentation of when effects occur and in what direction can shed light on mechanisms of cardiovascular disease risk and inform treatment. The present study of 169 World Trade Center responders, oversampled for PTSD, tested how daily PTSD symptoms were associated with autonomic function as reflected through HRV. Methods: Participants ( N = 169) completed surveys of PTSD symptoms three times a day at 5-hour intervals for 4 days while also wearing ambulatory monitors to record electrocardiograms to derive HRV (i.e., mean absolute value of successive differences between beat-to-beat intervals). Results: HRV did not predict PTSD symptoms. However, PTSD symptoms during a 5-hour interval predicted reduced HRV at the next 5-hour interval ( β = -0.09, 95% confidence interval = -0.16 to -0.02, p = .008). Results held adjusting for baseline age, current heart problems, and current PTSD diagnosis. Conclusions: Findings underscore growing awareness that PTSD symptoms are not static. Even their short-term fluctuations may affect cardiovascular functioning, which could have more severe impacts if disruption accumulates over time. Research is needed to determine if momentary interventions can halt increases in PTSD symptoms or mitigate their impact on cardiovascular health.
MeSH term(s)	Humans ; Stress Disorders, Post-Traumatic ; Heart Rate/physiology ; Cardiovascular Diseases ; Cross-Sectional Studies ; Autonomic Nervous System
Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	3469-1
ISSN	1534-7796 ; 0033-3174
ISSN (online)	1534-7796
ISSN	0033-3174
DOI	10.1097/PSY.0000000000001265
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Article ; Online: Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy.

Zosel, Franziska / Holla, Andrea / Schuler, Benjamin

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2376, Page(s) 207–233

Abstract: Single-molecule fluorescence spectroscopy has become an important technique for studying the conformational dynamics and folding of proteins. A key step for performing such experiments is the availability of high-quality samples. This chapter describes a ...

Abstract	Single-molecule fluorescence spectroscopy has become an important technique for studying the conformational dynamics and folding of proteins. A key step for performing such experiments is the availability of high-quality samples. This chapter describes a simple and widely applicable strategy for preparing proteins that are site-specifically labeled with a donor and an acceptor dye for single-molecule Förster resonance energy transfer (FRET) experiments. The method is based on introducing two cysteine residues that are labeled with maleimide-functionalized fluorophores, combined with high-resolution chromatography. We discuss how to optimize site-specific labeling even in the absence of orthogonal coupling chemistry and present purification strategies that are suitable for samples ranging from intrinsically disordered proteins to large folded proteins. We also discuss common problems in protein labeling, how to avoid them, and how to stringently control sample quality.
MeSH term(s)	Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; Intrinsically Disordered Proteins ; Single Molecule Imaging ; Spectrometry, Fluorescence
Chemical Substances	Fluorescent Dyes ; Intrinsically Disordered Proteins
Language	English
Publishing date	2021-11-29
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1716-8_12
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Article ; Online: Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein.

König, Iwo / Soranno, Andrea / Nettels, Daniel / Schuler, Benjamin

Angewandte Chemie (International ed. in English)

2021 Volume 60, Issue 19, Page(s) 10724–10729

Abstract: The conformations and dynamics of proteins can be influenced by crowding from the large concentrations of macromolecules within cells. Intrinsically disordered proteins (IDPs) exhibit chain compaction in crowded solutions in vitro, but no such effects ... ...

Abstract	The conformations and dynamics of proteins can be influenced by crowding from the large concentrations of macromolecules within cells. Intrinsically disordered proteins (IDPs) exhibit chain compaction in crowded solutions in vitro, but no such effects were observed in cultured mammalian cells. Here, to increase intracellular crowding, we reduced the cell volume by hyperosmotic stress and used an IDP as a crowding sensor for in-cell single-molecule spectroscopy. In these more crowded cells, the IDP exhibits compaction, slower chain dynamics, and much slower translational diffusion, indicating a pronounced concentration and length-scale dependence of crowding. In vitro, these effects cannot be reproduced with small but only with large polymeric crowders. The observations can be explained with polymer theory and depletion interactions and indicate that IDPs can diffuse much more efficiently through a crowded cytosol than a globular protein of similar dimensions.
MeSH term(s)	Eukaryotic Cells/chemistry ; HeLa Cells ; Humans ; Intrinsically Disordered Proteins/chemistry ; Molecular Dynamics Simulation ; Protein Conformation
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2021-03-30
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202016804
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Book ; Online: Towards Machine Learning-Enabled Context Adaption for Reliable Aerial Mesh Routing

Schüler, Cedrik / Sliwa, Benjamin / Wietfeld, Christian

2021

Abstract: In this paper, we present Context-Adaptive PARRoT (CA-PARRoT) as an extension of our previous work Predictive Ad-hoc Routing fueled by Reinforcement learning and Trajectory knowledge (PARRoT). Short-term effects, as occurring in urban surroundings, have ... ...

Abstract	In this paper, we present Context-Adaptive PARRoT (CA-PARRoT) as an extension of our previous work Predictive Ad-hoc Routing fueled by Reinforcement learning and Trajectory knowledge (PARRoT). Short-term effects, as occurring in urban surroundings, have shown to have a negative impact on the Reinforcement Learning (RL)-based routing process. Therefore, we add a timer-based compensation mechanism to the update process and introduce a hybrid Machine Learning (ML) approach to classify Radio Environment Prototypes (REPs) with a dedicated ML component and enable the protocol for autonomous context adaption. The performance of the novel protocol is evaluated in comprehensive network simulations considering different REPs and is compared to well-known established routing protocols for Mobile Ad-hoc Networks (MANETs). The results show, that CA-PARRoT is capable to compensate the challenges confronted with in different REPs and to improve its Key Performance Indicators (KPIs) up to 23% compared to PARRoT, and outperform established routing protocols by up to 50 %.
Keywords	Computer Science - Networking and Internet Architecture
Subject code	629
Publishing date	2021-07-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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