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

Membrane Asymmetry Regulating Transporters01:19

Membrane Asymmetry Regulating Transporters

6.4K
Enzymes like flippase, floppase, and scramblase transfer phospholipids from one layer to another in the membrane, thereby affecting membrane asymmetry.
Flippase
Eukaryotic flippases are type-IV P-type ATPases or P4-ATPases belonging to P-type ATPase family proteins that are membrane-bound pumps involved in the ATP-mediated transport of ions and molecules across the membrane. Flippases flip specific phospholipids from the outer to the inner leaflet of a membrane. All P4-ATPases have one...
6.4K
Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

6.0K
The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
6.0K
Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

3.5K
Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
3.5K
GPI Anchoring of Proteins in the ER Membrane01:29

GPI Anchoring of Proteins in the ER Membrane

4.8K
GPI-anchoring is a post-translational, reversible protein modification that is ubiquitous in eukaryotes. Such proteins are primarily present on the exoplasmic leaflet of the plasma membrane.
GPI-anchor structure
A sequence of 11 enzymatic reactions results in the synthesis of the complete GPI anchor consisting of a hydrophobic and a hydrophilic portion. The hydrophobic portion comprises phosphatidylinositol, while the hydrophilic part comprises polar groups like phosphoethanolamine,...
4.8K
Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

6.1K
In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
6.1K
Mechanisms of Membrane Domain Formation00:59

Mechanisms of Membrane Domain Formation

3.5K
Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with...
3.5K

You might also read

Related Articles

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

Sort by
Same author

Author Correction: Computational design of synthetic receptors with programmable signalling activity for enhanced cancer T cell therapy.

Nature biomedical engineering·2025
Same author

Computational design of synthetic receptors with programmable signalling activity for enhanced cancer T cell therapy.

Nature biomedical engineering·2025
Same author

The effect of hydration and dynamics on the mass density of single proteins.

The Journal of chemical physics·2025
Same author

Filamin C dimerisation is regulated by HSPB7.

Nature communications·2025
Same author

Modeling Realistic Clay Systems with <i>ClayCode</i>.

Journal of chemical theory and computation·2024
Same author

Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition.

Proceedings of the National Academy of Sciences of the United States of America·2024

Related Experiment Video

Updated: Nov 16, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

614

Transmembrane Protein Docking with JabberDock.

Lucas S P Rudden1, Matteo T Degiacomi1

  • 1Department of Physics, Durham University, South Road, DH1 3LE Durham, United Kingdom.

Journal of Chemical Information and Modeling
|February 26, 2021
PubMed
Summary
This summary is machine-generated.

We developed JabberDock, a new computational tool for predicting membrane protein structures. Our method achieves a 75% success rate, significantly advancing membrane protein-protein docking capabilities.

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

754
Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
08:15

Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

Published on: May 10, 2024

775

Related Experiment Videos

Last Updated: Nov 16, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

614
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

754
Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease
08:15

Author Spotlight: Network Pharmacology and Molecular Docking to Decipher the Action of Jiawei Shengjiang San Against Diabetic Kidney Disease

Published on: May 10, 2024

775

Area of Science:

  • Biochemistry and structural biology
  • Computational biology
  • Drug discovery

Background:

  • Transmembrane proteins are crucial for biological processes, representing 20-30% of the proteome.
  • They are key targets in drug design, yet their structural data is scarce (4% of PDB) due to isolation challenges.
  • Existing membrane protein docking tools have limited accuracy compared to soluble protein predictors.

Purpose of the Study:

  • To address the knowledge gap in membrane protein structures.
  • To develop and validate a novel computational pipeline for membrane protein-protein docking.
  • To improve the success rate of predicting transmembrane protein complex structures.

Main Methods:

  • Development of JabberDock, a software for docking membrane proteins.
  • Utilizing shapes representing membrane protein structure and dynamics in a biphasic environment.
  • Testing JabberDock on a benchmark of 20 transmembrane protein dimers.

Main Results:

  • JabberDock achieved a 75.0% success rate in predicting transmembrane dimer structures.
  • The pipeline accurately models membrane protein structure and dynamics.
  • Demonstrated competitive performance against existing membrane protein docking tools.

Conclusions:

  • JabberDock offers a significant advancement in membrane protein-protein docking.
  • The tool can help elucidate the structure of membrane protein complexes.
  • Improved docking accuracy facilitates drug design targeting transmembrane proteins.