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Related Concept Videos

Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

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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...
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Insertion of Single-pass Transmembrane Proteins in the RER01:26

Insertion of Single-pass Transmembrane Proteins in the RER

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Insertion of Multi-pass Transmembrane Proteins in the RER01:29

Insertion of Multi-pass Transmembrane Proteins in the RER

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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...
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Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

5.1K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

6.0K
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...
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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TMP- SSurface2: A Novel Deep Learning-Based Surface Accessibility Predictor for Transmembrane Protein Sequence.

Zhe Liu1,2,3, Yingli Gong4, Yuanzhao Guo2

  • 1School of Computer Science and Engineering, Changchun University of Technology, Changchun, China.

Frontiers in Genetics
|April 1, 2021
PubMed
Summary
This summary is machine-generated.

Researchers developed TMP-SSurface2, an AI tool that accurately predicts transmembrane protein (TMP) surfaces from amino acid sequences. This advancement improves drug discovery by enhancing our understanding of TMP structures and interactions.

Keywords:
attention mechanismdeep learninglong short term memoryrelative accessible surface areatransmembrane protein

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Transmembrane proteins (TMPs) are crucial membrane proteins involved in vital biological processes.
  • TMP surfaces are key targets for drug development due to their roles in molecular binding.
  • Determining TMP structures is challenging, necessitating advanced computational approaches.

Purpose of the Study:

  • To present TMP-SSurface2, an improved artificial intelligence-based tool for predicting TMP surface residues.
  • To enhance the accuracy of TMP surface prediction using only protein sequences.

Main Methods:

  • Utilized an attention-enhanced Bidirectional Long Short Term Memory (BiLSTM) network.
  • Leveraged AI for sequence-based prediction, eliminating the need for feature engineering.
  • Evaluated performance on an independent test dataset.

Main Results:

  • Achieved higher prediction accuracy compared to previous versions.
  • Improved Pearson correlation coefficients (CC) from 0.58 to 0.66.
  • Demonstrated the efficiency of TMP-SSurface2 in predicting TMP surfaces.

Conclusions:

  • TMP-SSurface2 represents significant progress in TMP structure modeling using primary sequences.
  • The tool offers a promising approach for accurately identifying TMP surfaces.
  • TMP-SSurface2 is publicly available for research use.