scholarly journals POTATO: An automated pipeline for batch analysis of optical tweezers data

2021 ◽  
Author(s):  
Stefan Buck ◽  
Lukas Pekarek ◽  
Neva Caliskan
Keyword(s):  
Data Analysis ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Analysis Tool ◽  
Recent Developments ◽  
Protein Nucleic Acid ◽  
Programming Knowledge ◽  
Nucleic Acid Interactions ◽  
User Friendly

Optical tweezers is a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (Practical Optical Tweezers Analysis TOol). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to worm-like chain and freely-jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface (https://github.com/REMI-HIRI/POTATO), which allows researchers without programming knowledge to perform sophisticated data analysis.

Molecular Motors: Force and Movement Generated by Single Myosin II Molecules

Physiology ◽  
2002 ◽  
Vol 17 (5) ◽  
pp. 213-218 ◽  
Author(s):  
Caspar Rüegg ◽  
Claudia Veigel ◽  
Justin E. Molloy ◽  
Stephan Schmitz ◽  
John C. Sparrow ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Myosin Ii ◽  
Force Production ◽  
Myosin Isoforms ◽  
Single Molecule Level ◽  
Recent Developments ◽  
Muscle Myosin

Muscle myosin II is an ATP-driven, actin-based molecular motor. Recent developments in optical tweezers technology have made it possible to study movement and force production on the single-molecule level and to find out how different myosin isoforms may have adapted to their specific physiological roles.

scholarly journals Stochastically pumped adaptation and directional motion of molecular machines

2018 ◽  
Vol 115 (38) ◽  
pp. 9405-9413 ◽  
Author(s):  
R. Dean Astumian
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
High Efficiency ◽  
Probability Distributions ◽  
Molecular Machines ◽  
High Energy ◽  
Stochastic Thermodynamics ◽  
Recent Developments ◽  
Directional Motion ◽  
External Fluctuations

Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium.

scholarly journals Recent advances in user-friendly computational tools to engineer protein function

2020 ◽  
Author(s):  
Carlos Eduardo Sequeiros-Borja ◽  
Bartłomiej Surpeta ◽  
Jan Brezovsky
Keyword(s):  
Protein Engineering ◽  
Protein Design ◽  
Protein Function ◽  
Transport Processes ◽  
Allosteric Communication ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
User Friendly ◽  
Ligand Transport ◽  
Further Development

Abstract Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

scholarly journals Single-Stranded DNA Curtains for Real-Time Single-Molecule Visualization of Protein–Nucleic Acid Interactions

2012 ◽  
Vol 84 (18) ◽  
pp. 7607-7612 ◽  
Author(s):  
Bryan Gibb ◽  
Tim D. Silverstein ◽  
Ilya J. Finkelstein ◽  
Eric C. Greene
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Single Molecule ◽  
Single Stranded Dna ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

scholarly journals B-COURSE: A WEB-BASED TOOL FOR BAYESIAN AND CAUSAL DATA ANALYSIS

2002 ◽  
Vol 11 (03) ◽  
pp. 369-387 ◽  
Author(s):  
PETRI MYLLYMÄKI ◽  
TOMI SILANDER ◽  
HENRY TIRRI ◽  
PEKKA URONEN
Keyword(s):  
Data Analysis ◽  
Bayesian Network ◽  
Network Models ◽  
Causal Modeling ◽  
Analysis Tool ◽  
Support Material ◽  
Online Data ◽  
Web Based ◽  
User Friendly ◽  
Bayesian Network Models

B-Course is a free web-based online data analysis tool, which allows the users to analyze their data for multivariate probabilistic dependencies. These dependencies are represented as Bayesian network models. In addition to this, B-Course also offers facilities for inferring certain type of causal dependencies from the data. The software uses a novel "tutorial stylerdquo; user-friendly interface which intertwines the steps in the data analysis with support material that gives an informal introduction to the Bayesian approach adopted. Although the analysis methods, modeling assumptions and restrictions are totally transparent to the user, this transparency is not achieved at the expense of analysis power: with the restrictions stated in the support material, B-Course is a powerful analysis tool exploiting several theoretically elaborate results developed recently in the fields of Bayesian and causal modeling. B-Course can be used with most web-browsers (even Lynx), and the facilities include features such as automatic missing data handling and discretization, a flexible graphical interface for probabilistic inference on the constructed Bayesian network models (for Java enabled browsers), automatic prettyHyphen;printed layout for the networks, exportation of the models, and analysis of the importance of the derived dependencies. In this paper we discuss both the theoretical design principles underlying the B-Course tool, and the pragmatic methods adopted in the implementation of the software.

NuProPlot: nucleic acid and protein interaction analysis and plotting program

2015 ◽  
Vol 71 (3) ◽  
pp. 667-674 ◽  
Author(s):  
Lagnajeet Pradhan ◽  
Hyun-Joo Nam
Keyword(s):  
Nucleic Acid ◽  
Interaction Analysis ◽  
Three Dimensional ◽  
Data Bank ◽  
Van Der Waals Interactions ◽  
Acid Complex ◽  
Protein Nucleic Acid ◽  
The Individual ◽  
Nucleic Acid Interactions ◽  
User Friendly

Growing numbers of protein and nucleic acid complex structures are being determined and deposited in the Protein Data Bank and the Nucleic Acid Database. With the increasing complexity of these structures, it is challenging to analyse and visualize the three-dimensional interactions. The currently available programs for such analysis and visualization are limited in their applications. They can only analyse a subset of protein–nucleic acid complexes and require multiple iterations before obtaining plots that are suitable for presentation. An interactive web-based program,NuProPlot(http://www.nuproplot.com), has been developed which can automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein–DNA and protein–RNA interactions can be visualized in simple two-dimensional schematics. Interactive schematic drawing options allow selection of the plotted area and repositioning of the individual interactions for better legibility.NuProPlotis a fully automated and user-friendly program providing various custom options.NuProPlotrepresents a greatly improved option for analysis and presentation of protein–nucleic acid interactions.

TDAview: an online visualization tool for topological data analysis

2020 ◽  
Vol 36 (18) ◽  
pp. 4805-4809
Author(s):  
Kieran Walsh ◽  
Mircea A Voineagu ◽  
Fatemeh Vafaee ◽  
Irina Voineagu
Keyword(s):  
Data Analysis ◽  
Open Source Software ◽  
Topological Data Analysis ◽  
Graph Visualization ◽  
Online Tool ◽  
Wide Range ◽  
Data Points ◽  
Programming Knowledge ◽  
User Friendly ◽  
Topological Data

Abstract Summary TDAview is an online tool for topological data analysis (TDA) and visualization. It implements the Mapper algorithm for TDA and provides extensive graph visualization options. TDAview is a user-friendly tool that allows biologists and clinicians without programming knowledge to harness the power of TDA. TDAview supports an analysis and visualization mode in which a Mapper graph is constructed based on user-specified parameters, followed by graph visualization. It can also be used in a visualization only mode in which TDAview is used for visualizing the data properties of a Mapper graph generated using other open-source software. The graph visualization options allow data exploration by graphical display of metadata variable values for nodes and edges, as well as the generation of publishable figures. TDAview can handle large datasets, with tens of thousands of data points, and thus has a wide range of applications for high-dimensional data, including the construction of topology-based gene co-expression networks. Availability and implementation TDAview is a free online tool available at https://voineagulab.github.io/TDAview/. The source code, usage documentation and example data are available at TDAview GitHub repository: https://github.com/Voineagulab/TDAview.

scholarly journals Towards physiological complexity with in vitro single-molecule biophysics

2013 ◽  
Vol 368 (1611) ◽  
pp. 20120271 ◽  
Author(s):  
Daniel Duzdevich ◽  
Eric C. Greene
Keyword(s):  
Single Molecule ◽  
Future Research ◽  
Biological Macromolecules ◽  
Protein Diffusion ◽  
Explicit Statement ◽  
Physiological Relevance ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
New Generation

Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein–nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance.

scholarly journals Argonaute bypasses cellular obstacles without hindrance during target search

2019 ◽  
Author(s):  
Tao Ju Cui ◽  
Misha Klein ◽  
Jorrit W. Hegge ◽  
Stanley D. Chandradoss ◽  
John van der Oost ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
High Efficiency ◽  
Lateral Diffusion ◽  
Secondary Structures ◽  
Single Molecule Fret ◽  
Tight Contact ◽  
Dna Backbone ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Argonaute (Ago) proteins are key players in gene regulation in eukaryotes and host defense in prokaryotes. For specific interference, Ago relies on base pairing between small nucleic acid guides and complementary target sequences. To efficiently scan nucleic acid chains for potential targets, Ago must bypass both secondary structures in mRNA and single stranded DNA as well as protein barriers. Through single-molecule FRET, we reveal that lateral diffusion is mediated mainly through protein-nucleic acid interactions, rather than interactions between the guide and targeted strand. This allows Ago to scan for targets with high efficiency but without maintaining tight contact with the DNA backbone. Real-time observations show that Ago “glides” short distances over secondary structures while using intersegmental jumps to reduce scanning redundancy and bypass protein barriers. Our single-molecule method in combination with kinetic analysis may serve as a novel platform to study the effect of sequence on search kinetics for other nucleic acid-guided proteins.

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