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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
Mechanisms of Membrane-bending01:15

Mechanisms of Membrane-bending

The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
Membrane bending can happen due to intrinsic changes in lipid composition or extrinsic association with different proteins. The proteins involved...

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Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic

Chaim A Schramm1, Brett T Hannigan, Jason E Donald

  • 1Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Structure (London, England : 1993)
|May 15, 2012
PubMed
Summary

We developed a new method to predict how membrane proteins interact with cell membranes. This approach helps understand protein stability and function, aiding in protein design and drug discovery.

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Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Membrane-associated proteins present unique challenges due to complex hydrophobic and hydrophilic environments.
  • Understanding their interactions with lipid bilayers is crucial for various biological processes.

Purpose of the Study:

  • To develop a computational method for predicting the cross-membrane behavior of proteins.
  • To provide insights into the stability and functional mechanisms of membrane proteins.

Main Methods:

  • Created a nonredundant database to compute knowledge-based asymmetric cross-membrane potentials.
  • Utilized per-residue distributions of C(β), C(γ), and functional group atoms.
  • Predicted transmembrane and peripheral regions from genomic sequences and protein structures.

Main Results:

  • Generated pseudo-energy topological landscapes to assess positional stability.
  • Successfully predicted mechanisms for antimicrobial peptides, transmembrane proteins, and viral fusion proteins.
  • Quantitatively reproduced experimental effects of point mutations on dual-topology proteins.

Conclusions:

  • The developed method effectively parameterizes the cross-membrane propensity of membrane proteins and peptides.
  • This facilitates structural refinement, characterization, prediction, and design of membrane-associated proteins.
  • The functional group potential and membrane-exposed residues are key indicators for detecting native-like structures.