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

Structure of Porins01:21

Structure of Porins

3.0K
Mitochondria, chloroplasts, and gram-negative bacteria have transmembrane, beta-barrel proteins called porins to mediate the free diffusion of ions and metabolites across the membrane. Mitochondrial porin precursors contain conserved amino acid sequences called beta signals at their C-terminal. Beta signals have a  motif of PoXGXXHyXHy (Po-Polar, X-Any amino acid, G-Glycine, Hy-LargeHydrophobic), which are crucial for precursor recognition to initiate precursor assembly. Beta-barrel...
3.0K
Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

5.3K
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...
5.3K
Protein Networks02:26

Protein Networks

3.9K
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,...
3.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Fluid Mosaic Model01:19

Fluid Mosaic Model

11.6K
Scientists identified the plasma membrane in the 1890s and its principal chemical components (lipids and proteins) by 1915. The model for plasma membrane structure, proposed in 1935 by Hugh Davson and James Danielli, was the first model to be widely accepted in the scientific community. The model was based on the plasma membrane's "railroad track" appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembled a sandwich...
11.6K
Porin Insertion in the Outer Mitochondrial Membrane01:12

Porin Insertion in the Outer Mitochondrial Membrane

3.0K
Porins are beta-barrel proteins translocated to the mitochondrial outer membrane through the TOM complex into the intermembrane space. Porin precursors bind TIM chaperones within the intermembrane space and are guided to the Sorting and Assembly Machinery complex or SAM complex on the outer mitochondrial membrane.
Three models describe the assembly of porins by the SAM complex and their insertion into the outer membrane. Model 1 suggests that porins are assembled outside the SAM channel as the...
3.0K

You might also read

Related Articles

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

Sort by
Same author

Establishment of a novel system for photothermal removal of ampicillin under near-infrared irradiation: Persulfate activation, mechanism, pathways and bio-toxicology.

Journal of colloid and interface science·2023
Same author

Systematic analysis and expression of Gossypium 2ODD superfamily highlight the roles of GhLDOXs responding to alkali and other abiotic stress in cotton.

BMC plant biology·2023
Same author

Polybrominated diphenyl ethers in water, suspended particulate matter, and sediment of reservoirs and their tributaries in Shenzhen, a mega city in South China.

Environmental science and pollution research international·2023
Same author

Light plays a critical role in the accumulation of chlorogenic acid in Lonicera macranthoides Hand.-Mazz.

Plant physiology and biochemistry : PPB·2023
Same author

Molecular insights into enhanced nitrogen removal induced by trace fluoroquinolone antibiotics in an anammox system.

Bioresource technology·2023
Same author

Screening of Active Ingredients from Wendan Decoction in Alleviating Palmitic Acid-Induced Endothelial Cell Injury.

Molecules (Basel, Switzerland)·2023

Related Experiment Video

Updated: Jun 28, 2025

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

11.7K

Graphical models for identifying pore-forming proteins.

Nan Xu1, Theodore W Kahn2, Theju Jacob2

  • 1Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.

Proteins
|April 15, 2024
PubMed
Summary

This study introduces a novel graphical model to identify novel pore-forming toxins (PFTs) by analyzing protein structures, overcoming limitations of sequence-based methods for agricultural pest control applications.

Keywords:
graphical modelinsecticidal proteinsprotein structure

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K
From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
09:55

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins

Published on: July 4, 2016

13.4K

Related Experiment Videos

Last Updated: Jun 28, 2025

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

11.7K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K
From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
09:55

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins

Published on: July 4, 2016

13.4K

Area of Science:

  • Proteomics
  • Structural Biology
  • Computational Biology

Background:

  • Pore-forming toxins (PFTs) create pores in cell membranes, with potential applications in agriculture.
  • Current methods for discovering new PFTs rely on sequence homology and fail to identify novel proteins with low sequence similarity.
  • Identifying novel PFTs requires structure-based approaches, but limited known PFT structures hinder computational methods like deep learning.

Purpose of the Study:

  • To develop a computational method for identifying novel pore-forming toxins based on structural similarity, overcoming limitations of sequence-based approaches.
  • To enable the discovery of new PFTs with low sequence identity for biotechnological applications, such as agricultural pest control.

Main Methods:

  • A sample-efficient graphical model was developed using consensus secondary structures to build protein structure graphs.
  • A semi-Markov conditional random fields model was employed for protein sequence segmentation.
  • An efficient framework was created to screen the UniRef50 database (43 million proteins) for potential PFT candidates.

Main Results:

  • The proposed method successfully distinguishes structurally similar proteins even with low sequence identity (pairwise identity < 0.4).
  • This structural approach surpasses traditional methods like Hidden Markov Models (HMMs) in identifying distantly related proteins.
  • The framework facilitates efficient extraction of relevant proteins from large-scale genomic databases.

Conclusions:

  • The developed graphical model and sequence segmentation approach offer a powerful tool for discovering novel pore-forming toxins based on structural features.
  • This method significantly advances the identification of PFTs beyond sequence homology, opening new avenues for biotechnological innovation in agriculture and beyond.