Related Experiment Video
Updated: May 23, 2026
10:49
Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
Published on: March 5, 2017
On graphical representation of trans-membrane proteins.
M Randić1, M Novič, A Roy Choudhury
1National Institute of Chemistry, Ljubljana, Slovenia. mrandic@msn.com
SAR and QSAR in Environmental Research
|March 22, 2012
Summary
This study introduces a new graphical method to represent proteins using amino acid adjacency matrices. This approach generates protein binary codes for use as descriptors, particularly for trans-membrane proteins.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Proteins are fundamental molecules with complex structures.
- Understanding protein structure is crucial for biological function.
- Current protein representation methods have limitations.
Purpose of the Study:
- To develop a novel graphical representation for proteins.
- To create protein binary codes as descriptors.
- To apply this method to trans-membrane proteins.
Main Methods:
- Constructing a protein map from an amino acid adjacency matrix.
- Interpreting matrix elements as sequentially labeled graph vertices.
- Connecting nearest vertices to neighbors with smaller labels.
- Developing protein binary codes from the graphical representation.
Main Results:
- A novel graphical protein representation was successfully developed.
- Protein binary codes were constructed as potential descriptors.
- The method was illustrated using segments of trans-membrane proteins.
Conclusions:
- The novel graphical representation offers a new way to visualize protein structure.
- Protein binary codes can serve as effective descriptors.
- This method shows promise for analyzing proteins, including trans-membrane proteins.
Related Concept Videos
01:25Single-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...
01:29Insertion of Multi-pass Transmembrane Proteins in the RER
The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
01:26Insertion of Single-pass Transmembrane Proteins in the RER
Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These...
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These...
01:09Multi-pass Transmembrane Proteins and β-barrels
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 G-protein-linked receptors (GPCRs) and...
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as G-protein-linked receptors (GPCRs) and...
01:28Protein Translocation Machinery on the ER Membrane
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 translocon complex.
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 translocon complex.
01:20Cotranslational Protein Translocation
Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...