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Related Concept Videos

Structure of Porins01:21

Structure of Porins

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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...
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Protein Complex Assembly02:41

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

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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
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Porin Insertion in the Outer Mitochondrial Membrane01:12

Porin Insertion in the Outer Mitochondrial Membrane

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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.
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Fluid Mosaic Model01:19

Fluid Mosaic Model

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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...
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Multi-pass Transmembrane Proteins and β-barrels01:09

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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.
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From Constructs to Crystals &#8211; Towards Structure Determination of &#946;-barrel Outer Membrane Proteins
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Structural Modeling of T9SS Outer Membrane Proteins and Their Complexes.

Christian D Lorenz1, Michael A Curtis2, James A Garnett3

  • 1Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK.

Methods in Molecular Biology (Clifton, N.J.)
|March 13, 2024
PubMed
Summary

This study presents an in silico modeling method for type 9 secretion system outer membrane proteins. This computational approach aids in understanding these proteins and their complexes when experimental production is challenging.

Keywords:
AlphaFoldAlphaFold multimerBacterial envelopeMD simulationsMembrane-embedded β-barrel proteinsOMPsProtein secretionT9SS

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Area of Science:

  • Microbiology
  • Structural Biology
  • Bioinformatics

Background:

  • The type 9 secretion system (T9SS) is crucial for protein transport and attachment in Gram-negative bacteria.
  • Outer membrane proteins (OMPs) are essential components of the T9SS, mediating protein translocation and surface anchoring.
  • Experimental production of T9SS OMPs can be difficult, limiting structural and functional studies.

Purpose of the Study:

  • To describe a computational method for in silico modeling of T9SS OMPs and their complexes.
  • To validate the developed modeling protocols.
  • To provide a resource for studying OMPs when recombinant protein production is challenging.

Main Methods:

  • In silico modeling of T9SS outer membrane proteins.
  • Computational modeling of OMP complexes.
  • Model validation techniques.

Main Results:

  • A validated method for in silico modeling of T9SS OMPs was established.
  • The modeling approach proved effective for T9SS OMP complexes.
  • The protocols are applicable to OMPs involved in other cellular processes.

Conclusions:

  • In silico modeling offers a viable alternative for studying T9SS OMPs and their complexes.
  • This computational strategy facilitates research when experimental methods are hindered.
  • The developed protocols have broader applications for studying outer membrane proteins.