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Related Concept Videos

ABC Transporters: Exporter01:31

ABC Transporters: Exporter

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ATP-binding cassette or ABC transporter is the largest superfamily of integral membrane proteins. The transporters have transmembrane-binding domains (TMDs) and nucleotide-binding domains (NBDs). The TMDs are specific to their substrates, whereas the NBDs are similar to engines that complete ATP hydrolysis to complete the substrate transport. They can be full transporters consisting of two TMDs and NBDs, half transporters with one TMD and NBD, while some encoded with a single TMD or NBD are...
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ATP-binding cassette or ABC transporters are a class of ATP-driven pumps that hydrolyze ATP to move solutes across the membrane. They can be grouped into importers and exporters. While exporters are present in all domains of life, importers exist only in bacteria and some plants.
In bacteria, based on the number of transmembrane helices and the chemical nature of their substrates, the ABC importers can be divided into three types:
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ATP Driven Pumps I: An Overview01:27

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ATP-driven pumps, also known as transport ATPases, are integral membrane proteins. They have binding sites for ATP located on the membrane's cytosolic side and the ion-conducting domain in the transmembrane region. These pumps use the free energy released from ATP hydrolysis to move the solutes across cell membranes against an electrochemical gradient.
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Carrier-Mediated Transport01:06

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Carrier-mediated transport is a pivotal process in drug absorption, particularly for lipid-insoluble drugs, and encompasses facilitated diffusion and active transport. Facilitated diffusion allows drugs to move along their concentration gradient without energy expenditure, while active transport utilizes ATP to drive drug movement against this gradient.
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The Significance of Membrane Transport01:44

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The transport of solutes across the cell membrane is essential for metabolic processes, like maintaining cell size and volume, generating the action potential, exchanging nutrients and gases, etc. Membrane transport can be either passive or active. It can be simple diffusion, facilitated, or mediated transport aided by transport proteins such as transporters and channels.
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Membrane Transporters01:31

Membrane Transporters

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Transporters are essential membrane transport proteins with functions related to cell nutrition, homeostasis, communication, etc. Approximately 7% of all genes in the human genome code for transporters or transporter-related proteins.
Transporters are mainly composed of alpha-helices, built from bundles of ten or more helices traversing the plasma membrane. The solute-binding sites are located midway, where some of the helices are broken or distorted, making space for the binding site through...
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DeepRTCP: Predicting ATP-Binding Cassette Transporters Based on 1-Dimensional Convolutional Network.

Zhaoxi Zhang1, Juan Wang1,2, Jiameng Liu1

  • 1School of Computer Science, Inner Mongolia University, Hohhot, China.

Frontiers in Cell and Developmental Biology
|February 18, 2021
PubMed
Summary

DeepRTCP accurately identifies ATP-binding cassette (ABC) transporters, crucial for nutrient absorption and waste removal. This novel deep learning method significantly improves upon existing techniques for classifying these vital transmembrane proteins.

Keywords:
ABC transportersPSSMcross validationdeep convolutional neural networktripeptide composition

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • ATP-binding cassette (ABC) transporters are essential membrane proteins involved in nutrient uptake and the excretion of harmful substances.
  • Their role in transmembrane transport of macromolecules makes their accurate identification critical for biological research.

Purpose of the Study:

  • To introduce DeepRTCP, a novel computational method for the accurate identification and classification of ABC transporters.
  • To evaluate the performance of DeepRTCP against existing state-of-the-art methods.

Main Methods:

  • DeepRTCP utilizes a deep convolutional neural network combined with sequence-derived features.
  • Features include reduced amino acid alphabet-based tripeptide composition and Position-Specific Scoring Matrix (PSSM).
  • A curated dataset, ABC_2020, comprising recently identified ABC transporters from UniProt was used for training and validation.

Main Results:

  • DeepRTCP achieved an average accuracy of 95.96% through 10-fold cross-validation.
  • The method demonstrated a significant improvement of 9.29% in accuracy compared to the current leading prediction methods.
  • The constructed ABC_2020 dataset provides a valuable resource for ABC transporter research.

Conclusions:

  • DeepRTCP is a highly effective and accurate classifier for identifying ABC transporters.
  • The developed method offers reliable guidance for future research on ABC transporter functions and mechanisms.