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Biomolecules
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Single-Molecule Protein Dynamics
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Single-Molecule Protein Dynamics

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Cellular Biochemistry".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 14136

Special Issue Editors

Dr. Si Wu

E-Mail Website
Guest Editor
Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
Interests: chaperones; amyloid; protein folding; single-molecule detection; single-molecule biophysics; fluorescence imaging
Prof. Dr. Sarah Perrett

E-Mail Website
Guest Editor
Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
Interests: protein folding, post-translational modification and quality control; functional amyloids; amyloid-based nanomaterials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins play a critical role in maintaining every aspect of cell survival and metabolism. The inherent dynamics of proteins in their native functional state, as well as when folding/unfolding and forming interactions, results in an ensemble of protein molecules with distinct conformational states. The dynamic conformational populations and transitions between conformational states, which have been found to be closely related to protein function and regulation, are often challenging to explore by bulk techniques. Single-molecule techniques, including both fluorescence-based and force-based approaches, have been developed as powerful tools to investigate the conformational dyamics of proteins and provide mechanistic insights into the working mechanisms of biomolecules at single-molecule resolution.

This Special Issue on “Single-Molecule Protein Dynamics” calls for manuscripts applying or developing single-molecule approaches to investigate the dynamics of the structure, folding, and interactions of proteins, furthering a deeper understanding of how proteins function in biological processes.

Dr. Si Wu
Prof. Dr. Sarah Perrett

Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein conformational dynamics
  • protein structure
  • protein function
  • protein folding
  • protein–protein interactions
  • protein–nucleic acid interactions
  • single-molecule techniques
  • single-molecule fluorescence
  • single-molecule imaging
  • single-molecule force spectroscopy

Published Papers (5 papers)

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Research

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15 pages, 3056 KiB  
Article
Molecular Recognition of Proteins through Quantitative Force Maps at Single Molecule Level
by Carlos Marcuello, Rocío de Miguel and Anabel Lostao
Biomolecules 2022, 12(4), 594; https://doi.org/10.3390/biom12040594 - 18 Apr 2022
Cited by 23 | Viewed by 2793
Abstract
Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific [...] Read more.
Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies. Full article
(This article belongs to the Special Issue Single-Molecule Protein Dynamics)
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15 pages, 2483 KiB  
Article
Impact of Molecule Concentration, Diffusion Rates and Surface Passivation on Single-Molecule Fluorescence Studies in Solution
by Olessya Yukhnovets, Henning Höfig, Nuno Bustorff, Alexandros Katranidis and Jörg Fitter
Biomolecules 2022, 12(3), 468; https://doi.org/10.3390/biom12030468 - 18 Mar 2022
Cited by 2 | Viewed by 2248
Abstract
For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance [...] Read more.
For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance energy transfer (smFRET) or two-color coincidence detection (TCCD), the molecule concentration must be set explicitly to targeted values and furthermore needs to be stable over a period of several hours. As a consequence, specific demands must be imposed on the surface passivation of the cover slides during the measurements. The aim of having only one molecule in the detection volume at the time is not only affected by the absolute molecule concentration, but also by the rate of diffusion. Therefore, we discuss approaches to control and to measure absolute molecule concentrations. Furthermore, we introduce an approach to calculate the probability of chance coincidence events and demonstrate that measurements with challenging smFRET samples require a strict limit of maximal sample concentrations in order to produce meaningful results. Full article
(This article belongs to the Special Issue Single-Molecule Protein Dynamics)
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13 pages, 3084 KiB  
Article
AimR Adopts Preexisting Dimer Conformations for Specific Target Recognition in Lysis-Lysogeny Decisions of Bacillus Phage phi3T
by Kai Pei, Jie Zhang, Tingting Zou and Zhu Liu
Biomolecules 2021, 11(9), 1321; https://doi.org/10.3390/biom11091321 - 07 Sep 2021
Cited by 7 | Viewed by 2161
Abstract
A bacteriophage switches between lytic and lysogenic life cycles. The AimR-AimP-AimX communication system is responsible for phage lysis-lysogeny decisions during the infection of Bacillus subtilis. AimX is a regulator biasing phage lysis, AimR is a transcription factor activating AimX expression, and AimP [...] Read more.
A bacteriophage switches between lytic and lysogenic life cycles. The AimR-AimP-AimX communication system is responsible for phage lysis-lysogeny decisions during the infection of Bacillus subtilis. AimX is a regulator biasing phage lysis, AimR is a transcription factor activating AimX expression, and AimP is an arbitrium peptide that determines phage lysogeny by deactivating AimR. A strain-specific mechanism for the lysis-lysogeny decisions is proposed in SPbeta and phi3T phages. That is, the arbitrium peptide of the SPbeta phage stabilizes the SPbeta AimR (spAimR) dimer, whereas the phi3T-derived peptide disassembles the phi3T AimR (phAimR) dimer into a monomer. Here, we find that phAimR does not undergo dimer-to-monomer conversion upon arbitrium peptide binding. Gel-filtration, static light scattering (SLS) and analytical ultracentrifugation (AUC) results show that phAimR is dimeric regardless of the presence of arbitrium peptide. Small-angle X-ray scattering (SAXS) reveals that the arbitrium peptide binding makes an extended dimeric conformation. Single-molecule fluorescence resonance energy transfer (smFRET) analysis reveals that the phAimR dimer fluctuates among two distinct conformational states, and each preexisting state is selectively recognized by the arbitrium peptide or the target DNA, respectively. Collectively, our biophysical characterization of the phAimR dynamics underlying specific target recognition provides new mechanistic insights into understanding lysis-lysogeny decisions in Bacillus phage phi3T. Full article
(This article belongs to the Special Issue Single-Molecule Protein Dynamics)
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Review

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15 pages, 1418 KiB  
Review
Observing Protein One-Dimensional Sliding: Methodology and Biological Significance
by Xiao-Wen Yang and Jiaquan Liu
Biomolecules 2021, 11(11), 1618; https://doi.org/10.3390/biom11111618 - 02 Nov 2021
Cited by 3 | Viewed by 2125
Abstract
One-dimensional (1D) sliding of DNA-binding proteins has been observed by numerous kinetic studies. It appears that many of these sliding events play important roles in a wide range of biological processes. However, one challenge is to determine the physiological relevance of these motions [...] Read more.
One-dimensional (1D) sliding of DNA-binding proteins has been observed by numerous kinetic studies. It appears that many of these sliding events play important roles in a wide range of biological processes. However, one challenge is to determine the physiological relevance of these motions in the context of the protein’s biological function. Here, we discuss methods of measuring protein 1D sliding by highlighting the single-molecule approaches that are capable of visualizing particle movement in real time. We also present recent findings that show how protein sliding contributes to function. Full article
(This article belongs to the Special Issue Single-Molecule Protein Dynamics)
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21 pages, 2309 KiB  
Review
Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy
by Yuanlei Cheng, Yashuo Zhang and Huijuan You
Biomolecules 2021, 11(11), 1579; https://doi.org/10.3390/biom11111579 - 25 Oct 2021
Cited by 16 | Viewed by 3402
Abstract
G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety [...] Read more.
G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins. Full article
(This article belongs to the Special Issue Single-Molecule Protein Dynamics)
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