Related Experiment Video
Updated: Jun 7, 2026
14:29
Visualization of Bacterial Toxin Induced Responses Using Live Cell Fluorescence Microscopy
Published on: October 1, 2012
Function inferences from a molecular structural model of bacterial ParE toxin
Luiz Carlos Bertucci Barbosa1, Saulo Santesso Garrido, Anderson Garcia
1Institute of Chemistry, UNESP - Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil.
Bioinformation
|October 27, 2010
Summary
Researchers modeled the 3D structure of the bacterial ParE toxin, a component of toxin-antitoxin systems. This structural model aids in understanding its function and designing new molecules for further studies.
Area of Science:
- Structural biology
- Molecular biology
- Bacterial genetics
Background:
- Toxin-antitoxin (TA) systems enhance plasmid stability in bacteria.
- ParE is a toxin in the RelE/ParE superfamily, targeting E. coli DNA gyrase.
- No crystallographic structure for ParE toxin was previously available.
Purpose of the Study:
- To generate a 3D structural model of the E. coli ParE toxin.
- To analyze the structural characteristics and potential active sites of ParE.
- To provide a basis for future structure-function studies and drug design.
Main Methods:
- Comparative molecular homology modeling using MODELLER.
- Energy minimization with CHARMM.
- Model validation using PROCHECK and VERIFY3D.
- Structural similarity searches with DALI server.
- Active site identification using CASTp program.
Main Results:
- A validated 3D model of E. coli ParE toxin was successfully built.
- Ramachandran plot analysis showed 96.8% of residues in favored/allowed regions.
- Structural similarity was found with RelE and YoeB families.
- A potential homologous active site was identified.
Conclusions:
- The predicted 3D model offers insights into the ParE toxin structure.
- The model can guide rational design for structure-function studies.
- Further research is needed to confirm nuclease and replication inhibitory activities.
Related Concept Videos
01:12Bacterial Toxins
Bacterial toxins are sophisticated virulence factors that enable pathogenic bacteria to interact with, invade, and damage host tissues. These toxins fall broadly into two types: protein exotoxins, which are secreted into the environment and target specific host receptors, and lipopolysaccharide endotoxins, which are structural components of the bacterial outer membrane released primarily during bacterial lysis or membrane shedding. Exotoxins generally act more selectively, binding to cell...
01:29Cytoskeletal Proteins in Bacteria
Bacterial cells were initially considered simple, randomly organized structures lacking a cytoskeleton. However, the discovery of cytoskeleton homologs in bacteria led to the change of this opinion. Bacterial cytoskeletal filaments regulate the cell shape, cell polarity, cell division, and partitioning of plasmids during cell division. It was later discovered that bacterial cytoskeletal proteins, mainly actin and tubulin homologs, are diverse compared to their eukaryotic counterparts. On the...
01:28Regulation of Bacterial Virulence
Pathogenic bacteria employ a range of regulatory mechanisms to modulate the expression of virulence genes in response to environmental and host-derived signals. These mechanisms ensure that virulence factors are expressed only under favorable conditions, thereby optimizing infection and survival strategies.Mechanisms of Virulence RegulationKey regulatory strategies include:Two-Component Systems: These consist of a membrane-bound sensor kinase and a cytoplasmic response regulator. Environmental...
01:22Botulism
Botulism is a life-threatening neuroparalytic condition caused by botulinum neurotoxin, which is produced by the bacterium Clostridium botulinum, a Gram-positive, spore-forming, obligate anaerobe.In adults, the toxin enters the body in different ways: in foodborne botulism, the preformed toxin is absorbed in the intestine. In wound botulism, spores grow in injured tissue and release the toxin into the blood. Infant botulism differs mechanistically from adult forms. In infants, botulism commonly...
01:21Structure of Porins
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 precursors...
01:17Gram-negative Bacterial Protein Secretion Systems
Gram-negative bacteria utilize sophisticated protein secretion systems to transport proteins across their double-membrane envelope into the extracellular environment or host cells. Based on their mechanism of action, these systems are classified into one-step and two-step pathways.One-Step Secretion Systems (Types I, III, IV, and VI)One-step secretion systems bypass the periplasm entirely, forming a continuous channel that spans both the inner and outer membranes:Type I Secretion System (T1SS):...