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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 Multi-pass Transmembrane Proteins in the RER01:29

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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 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
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...
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Membrane Asymmetry Regulating Transporters01:19

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Enzymes like flippase, floppase, and scramblase transfer phospholipids from one layer to another in the membrane, thereby affecting membrane asymmetry.
Flippase
Eukaryotic flippases are type-IV P-type ATPases or P4-ATPases belonging to P-type ATPase family proteins that are membrane-bound pumps involved in the ATP-mediated transport of ions and molecules across the membrane. Flippases flip specific phospholipids from the outer to the inner leaflet of a membrane. All P4-ATPases have one...
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Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

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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.
α-Helix containing multi-pass transmembrane proteins
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Primary Active Transport01:29

Primary Active Transport

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In contrast to passive transport, active transport involves a substance being moved through membranes in a direction against its concentration or electrochemical gradient. There are two types of active transport: primary active transport and secondary active transport. Primary active transport utilizes chemical energy from ATP to drive protein pumps embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would...
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Updated: Jul 19, 2025

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
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TMKit: a Python interface for computational analysis of transmembrane proteins.

Jianfeng Sun1, Arulsamy Kulandaisamy2, Jinlong Ru3

  • 1Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Headington, Oxford OX3 7LD, UK.

Briefings in Bioinformatics
|August 18, 2023
PubMed
Summary
This summary is machine-generated.

Researchers can now analyze transmembrane proteins more effectively with TMKit, a new open-source Python toolkit. TMKit offers specialized computational tools for sequence and structure analysis, addressing a critical gap in bioinformatics.

Keywords:
bioinformaticsfeature extractionprotein interaction interfacessequence analysisstructural biologytransmembrane proteins

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Transmembrane proteins are crucial for cellular functions like signal transduction and communication.
  • Existing computational tools lack specialization for transmembrane protein analysis, creating a research gap.

Purpose of the Study:

  • To introduce TMKit, an open-source Python programming interface for specialized transmembrane protein data analysis.
  • To provide a comprehensive toolkit for database wrangling, feature engineering, and visualization of transmembrane proteins.

Main Methods:

  • Development of TMKit, a modular and scalable Python interface.
  • Integration of seqNetRR, a high-performance computing library for residue connection analysis.
  • Implementation of tools for mutational, domain, and topological feature engineering and visualization of protein-protein interaction interfaces.

Main Results:

  • TMKit provides a unified platform for diverse transmembrane protein analyses.
  • The seqNetRR library enables rapid assignment of correlation matrix-based features.
  • The toolkit facilitates efficient processing and analysis of transmembrane protein data.

Conclusions:

  • TMKit addresses the need for specialized computational tools in transmembrane protein research.
  • This open-source toolkit enhances the study of transmembrane protein sequences and structures.
  • TMKit is publicly available to support the research community.