Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Glutamine Tautomerization Drives RhoGAP-Aided GTP Hydrolysis in Small Rho GTPases.

Journal of the American Chemical Society·2026
Same author

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.

Journal of chemical information and modeling·2024
Same author

Artificial, biomimetic and hybrid enzymes: general discussion.

Faraday discussions·2024
Same author

Enzyme evolution, engineering and design: mechanism and dynamics: general discussion.

Faraday discussions·2024
Same author

PBP-A, a cyanobacterial DD-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli.

Scientific reports·2024
Same author

Computational Tools to Assist in Analyzing Effects of the <i>SERPINA1</i> Gene Variation on Alpha-1 Antitrypsin (AAT).

Genes·2024

Related Experiment Video

Updated: Aug 22, 2025

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images
12:45

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Published on: August 31, 2022

3.0K

Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.

Karolina Mitusińska1, Maria Bzówka1, Tomasz Magdziarz1

  • 1Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland.

Journal of Chemical Information and Modeling
|November 14, 2022
PubMed
Summary

Comparing tunnel identification methods reveals that while small-molecule tracking offers detailed insights, it is computationally intensive. Careful analysis is crucial for understanding tunnel functionality, especially for low-diameter tunnels.

More Related Videos

Using plusTipTracker Software to Measure Microtubule Dynamics in Xenopus laevis Growth Cones
07:32

Using plusTipTracker Software to Measure Microtubule Dynamics in Xenopus laevis Growth Cones

Published on: September 7, 2014

10.5K
Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

8.3K

Related Experiment Videos

Last Updated: Aug 22, 2025

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images
12:45

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Published on: August 31, 2022

3.0K
Using plusTipTracker Software to Measure Microtubule Dynamics in Xenopus laevis Growth Cones
07:32

Using plusTipTracker Software to Measure Microtubule Dynamics in Xenopus laevis Growth Cones

Published on: September 7, 2014

10.5K
Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

8.3K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Accurate identification and characterization of internal tunnels in biological macromolecules are crucial for understanding molecular mechanisms, such as substrate transport and allosteric signaling.
  • Existing methods for tunnel identification, including geometry-based and small-molecule tracking approaches, have distinct advantages and limitations.

Purpose of the Study:

  • To compare the benefits and pitfalls of geometry-based versus small-molecule tracking methods for tunnel identification.
  • To evaluate the utility of computationally demanding methods for analyzing tunnel properties.
  • To assess the challenges in describing and functionally assessing low-diameter tunnels.

Main Methods:

  • Comparison of geometry-based tunnel identification algorithms.
  • Application of small-molecule tracking simulations.
  • Analysis of results from both crystal structures and molecular dynamics (MD) simulations.

Main Results:

  • Geometry-based methods provide a foundational description of tunnels.
  • Small-molecule tracking offers a more detailed, dynamic view of tunnel pathways and occupancy.
  • Assessing tunnel functionality solely on geometric parameters is often insufficient, particularly for low-diameter tunnels.
  • Small-molecule tracking can be computationally expensive but yields comprehensive system descriptions.

Conclusions:

  • Both geometry-based and small-molecule tracking methods are valuable for tunnel identification, each with specific strengths.
  • The choice of method depends on the desired level of detail and available computational resources.
  • A thorough analysis of results is essential for accurate interpretation of tunnel properties and functionality.