Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Single Molecule Tracking and Dynamics
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Single Molecule Tracking and Dynamics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 6354

Special Issue Editor

Dr. Ben Ovryn

E-Mail Website
Guest Editor
Department of Physics, New York Institute of Technology, Old Westbury, NY, USA
Interests: biophysics; microscopy; single molecule imaging

Special Issue Information

Dear Colleagues,

Please join me as we explore the latest developments in "Single Molecule Tracking and Dynamics". With this Special Issue, I encourage you to present the findings from your experimental, theoretical or computational research. Review articles that highlight recent developments and applications are also welcome. Although the foundations for many of the methods that enable single particle tracking and single molecule imaging are now well established, this area of research is remarkably vibrant. Advances in research on photoactivated proteins and permeable dyes have enabled applications to progress from imaging cell membranes to imaging intracellularly with single molecule sensitivity and specificity. Concomitant with these developments, optical instrumentation and methods that were once restricted to an individual's laboratory are now widely commercially available. This terrific progress has been highlighted by a series of recent Nobel Prizes, including the 2022 prize for developments and applications in click chemistry and bio-orthogonal chemistry. Furthermore, the advent of ubiquitous pattern recognition approaches has simplified the analysis of tracking results. These methods have reduced the number of experimental errors and significantly increased the confidence in analytical interpretation of acquired data. Since their inception, single molecule tracking approaches have enabled the verification of proposed models. Nevertheless, contemporary applications continue to push the boundaries and establish new frontiers.

Dr. Ben Ovryn
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

15 pages, 7429 KiB  
Article
PvdL Orchestrates the Assembly of the Nonribosomal Peptide Synthetases Involved in Pyoverdine Biosynthesis in Pseudomonas aeruginosa
by Hanna Manko, Tania Steffan, Véronique Gasser, Yves Mély, Isabelle Schalk and Julien Godet
Int. J. Mol. Sci. 2024, 25(11), 6013; https://doi.org/10.3390/ijms25116013 - 30 May 2024
Cited by 2 | Viewed by 1000
Abstract
The pyoverdine siderophore is produced by Pseudomonas aeruginosa to access iron. Its synthesis involves the complex coordination of four nonribosomal peptide synthetases (NRPSs), which are responsible for assembling the pyoverdine peptide backbone. The precise cellular organization of these NRPSs and their mechanisms of [...] Read more.
The pyoverdine siderophore is produced by Pseudomonas aeruginosa to access iron. Its synthesis involves the complex coordination of four nonribosomal peptide synthetases (NRPSs), which are responsible for assembling the pyoverdine peptide backbone. The precise cellular organization of these NRPSs and their mechanisms of interaction remain unclear. Here, we used a combination of several single-molecule microscopy techniques to elucidate the spatial arrangement of NRPSs within pyoverdine-producing cells. Our findings reveal that PvdL differs from the three other NRPSs in terms of localization and mobility patterns. PvdL is predominantly located in the inner membrane, while the others also explore the cytoplasmic compartment. Leveraging the power of multicolor single-molecule localization, we further reveal co-localization between PvdL and the other NRPSs, suggesting a pivotal role for PvdL in orchestrating the intricate biosynthetic pathway. Our observations strongly indicates that PvdL serves as a central orchestrator in the assembly of NRPSs involved in pyoverdine biosynthesis, assuming a critical regulatory function. Full article
(This article belongs to the Special Issue Single Molecule Tracking and Dynamics)
►▼ Show Figures

Figure 1

16 pages, 2376 KiB  
Article
Single-Molecule Imaging Reveals Differential AT1R Stoichiometry Change in Biased Signaling
by Gege Qin, Jiachao Xu, Yuxin Liang and Xiaohong Fang
Int. J. Mol. Sci. 2024, 25(1), 374; https://doi.org/10.3390/ijms25010374 - 27 Dec 2023
Cited by 3 | Viewed by 2400
Abstract
G protein-coupled receptors (GPCRs) represent promising therapeutic targets due to their involvement in numerous physiological processes mediated by downstream G protein- and β-arrestin-mediated signal transduction cascades. Although the precise control of GPCR signaling pathways is therapeutically valuable, the molecular details for governing biased [...] Read more.
G protein-coupled receptors (GPCRs) represent promising therapeutic targets due to their involvement in numerous physiological processes mediated by downstream G protein- and β-arrestin-mediated signal transduction cascades. Although the precise control of GPCR signaling pathways is therapeutically valuable, the molecular details for governing biased GPCR signaling remain elusive. The Angiotensin II type 1 receptor (AT1R), a prototypical class A GPCR with profound implications for cardiovascular functions, has become a focal point for biased ligand-based clinical interventions. Herein, we used single-molecule live-cell imaging techniques to evaluate the changes in stoichiometry and dynamics of AT1R with distinct biased ligand stimulations in real time. It was revealed that AT1R existed predominantly in monomers and dimers and underwent oligomerization upon ligand stimulation. Notably, β-arrestin-biased ligands induced the formation of higher-order aggregates, resulting in a slower diffusion profile for AT1R compared to G protein-biased ligands. Furthermore, we demonstrated that the augmented aggregation of AT1R, triggered by activation from each biased ligand, was completely abrogated in β-arrestin knockout cells. These findings furnish novel insights into the intricate relationship between GPCR aggregation states and biased signaling, underscoring the pivotal role of molecular behaviors in guiding the development of selective therapeutic agents. Full article
(This article belongs to the Special Issue Single Molecule Tracking and Dynamics)
►▼ Show Figures

Figure 1

Review

Jump to: Research

27 pages, 3403 KiB  
Review
Trajectory Analysis in Single-Particle Tracking: From Mean Squared Displacement to Machine Learning Approaches
by Chiara Schirripa Spagnolo and Stefano Luin
Int. J. Mol. Sci. 2024, 25(16), 8660; https://doi.org/10.3390/ijms25168660 - 8 Aug 2024
Viewed by 2505
Abstract
Single-particle tracking is a powerful technique to investigate the motion of molecules or particles. Here, we review the methods for analyzing the reconstructed trajectories, a fundamental step for deciphering the underlying mechanisms driving the motion. First, we review the traditional analysis based on [...] Read more.
Single-particle tracking is a powerful technique to investigate the motion of molecules or particles. Here, we review the methods for analyzing the reconstructed trajectories, a fundamental step for deciphering the underlying mechanisms driving the motion. First, we review the traditional analysis based on the mean squared displacement (MSD), highlighting the sometimes-neglected factors potentially affecting the accuracy of the results. We then report methods that exploit the distribution of parameters other than displacements, e.g., angles, velocities, and times and probabilities of reaching a target, discussing how they are more sensitive in characterizing heterogeneities and transient behaviors masked in the MSD analysis. Hidden Markov Models are also used for this purpose, and these allow for the identification of different states, their populations and the switching kinetics. Finally, we discuss a rapidly expanding field—trajectory analysis based on machine learning. Various approaches, from random forest to deep learning, are used to classify trajectory motions, which can be identified by motion models or by model-free sets of trajectory features, either previously defined or automatically identified by the algorithms. We also review free software available for some of the analysis methods. We emphasize that approaches based on a combination of the different methods, including classical statistics and machine learning, may be the way to obtain the most informative and accurate results. Full article
(This article belongs to the Special Issue Single Molecule Tracking and Dynamics)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop