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

Conserved Binding Sites01:49

Conserved Binding Sites

4.6K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.6K
Synaptic Signaling01:12

Synaptic Signaling

76.6K
Neurons communicate at synapses, or junctions, to excite or inhibit the activity of other neurons or target cells, such as muscles. Synapses may be chemical or electrical.
76.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.0K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.0K
Integration of Synaptic Events01:28

Integration of Synaptic Events

2.4K
Synaptic integration mainly includes the summation of graded potentials. Graded potentials, regardless of their type, cause subtle alterations in membrane voltage, resulting in either depolarization or hyperpolarization. These incremental changes, when combined or summed, can propel the neuron toward its threshold. Consider, for example, a membrane experiencing a +15 mV shift, causing it to depolarize from -70 mV to -55 mV. In this scenario, graded potentials govern the membrane's ability to...
2.4K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.0K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.0K
Protein Networks02:26

Protein Networks

4.1K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K

You might also read

Related Articles

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

Sort by
Same author

Amyloid β-Cholesterol Interplay: Removal of Cholesterol From the Membranes to Catalyze Aggregation and Amyloid Pathology.

Journal of neurochemistry·2026
Same author

Catalytic Effect of Amyloid-β on Native Tau Aggregation at Physiologically Relevant Concentrations.

International journal of molecular sciences·2025
Same author

Spray Drying: A Promising Technique for Inhalable Vaccine Development.

Current pharmaceutical biotechnology·2025
Same author

Uncovering Amyloid-β Interactions: Gray versus White Matter.

ACS chemical neuroscience·2025
Same author

Nanoscale Characterization of Interaction of Nucleosomes with H1 Linker Histone.

International journal of molecular sciences·2025
Same author

Damage of the Phospholipid Bilayer by Aβ42 at Physiologically Relevant Peptide Concentrations.

ACS chemical neuroscience·2024

Related Experiment Video

Updated: Oct 7, 2025

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements
08:50

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements

Published on: May 12, 2023

2.4K

Site-Search Process for Synaptic Protein-DNA Complexes.

Sridhar Vemulapalli1, Mohtadin Hashemi1, Yuri L Lyubchenko1

  • 1Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.

International Journal of Molecular Sciences
|January 11, 2022
PubMed
Summary

Specialized proteins assemble DNA complexes for genetic processes. This study visualizes SfiI enzyme

Keywords:
SFiIhigh-speed AFMsite-bound segment transfersite-searchsynaptic complexesthreading

More Related Videos

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient
08:06

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient

Published on: September 3, 2014

31.5K
Preparation of Synaptoneurosomes from Mouse Cortex using a Discontinuous Percoll-Sucrose Density Gradient
08:30

Preparation of Synaptoneurosomes from Mouse Cortex using a Discontinuous Percoll-Sucrose Density Gradient

Published on: September 17, 2011

32.0K

Related Experiment Videos

Last Updated: Oct 7, 2025

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements
08:50

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements

Published on: May 12, 2023

2.4K
Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient
08:06

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient

Published on: September 3, 2014

31.5K
Preparation of Synaptoneurosomes from Mouse Cortex using a Discontinuous Percoll-Sucrose Density Gradient
08:30

Preparation of Synaptoneurosomes from Mouse Cortex using a Discontinuous Percoll-Sucrose Density Gradient

Published on: September 17, 2011

32.0K

Area of Science:

  • Molecular Biology
  • Biophysics

Background:

  • Protein-DNA complex assembly is crucial for genetic processes.
  • Mechanisms of synaptosome assembly remain largely unknown.
  • Existing models for single-site search do not explain synaptosome formation.

Purpose of the Study:

  • To elucidate the molecular mechanisms of synaptosome assembly.
  • To visualize the DNA site search process by SfiI enzyme.
  • To propose a novel site-search model for synaptic protein-DNA systems.

Main Methods:

  • Utilized the restriction enzyme SfiI as an experimental system.
  • Applied time-lapse, high-speed atomic force microscopy (AFM).
  • Directly visualized SfiI enzyme's DNA site search process.

Main Results:

  • Observed sliding, jumping, and segmental transfer for single-site SfiI-DNA complexes.
  • Identified threading and site-bound segment transfer as synaptosome-specific pathways.
  • Visualized sliding and jumping pathways for loop-dissociated complexes.

Conclusions:

  • Proposed a new site-search model for synaptic protein-DNA systems.
  • Demonstrated distinct search mechanisms for single-site and synaptic complexes.
  • Provided direct visualization of complex DNA-protein interaction dynamics.