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Related Concept Videos

Active Transport01:14

Active Transport

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Active transport is a critical biological process that allows cells to move solutes against an electrochemical gradient. This process requires direct energy input and is characterized by its selectivity, saturability, and susceptibility to competitive inhibition.
Primary active transporters, like Na+, K+ and -ATPase, directly utilize ATP to move ions across the membrane. These transporters play significant roles in various physiological processes. For instance, Na+, K+ and -ATPase maintain...
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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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Primary Active Transport01:47

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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 that are embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction...
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Secondary Active Transport01:55

Secondary Active Transport

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One example of how cells use the energy contained in electrochemical gradients is demonstrated by glucose transport into cells. The ion vital to this process is sodium (Na+), which is typically present in higher concentrations extracellularly than in the cytosol. Such a concentration difference is due, in part, to the action of an enzyme “pump” embedded in the cellular membrane that actively expels Na+ from a cell. Importantly, as this pump contributes to the high concentration of...
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Secondary Active Transport01:32

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One example of how cells use the energy contained in electrochemical gradients is demonstrated by glucose transport into cells. The ion vital to this process is sodium (Na+), which is typically present in higher concentrations extracellularly than in the cytosol. Such a concentration difference is due, in part, to the action of an enzyme "pump" embedded in the cellular membrane that actively expels Na+ from a cell. Importantly, as this pump contributes to the high concentration of...
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Membrane Transporters01:31

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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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ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual

Semmy Wellem Taju1, Syed Muazzam Ali Shah1, Yu-Yen Ou1

  • 1Department of Computer Science & Engineering, Yuan Ze University, Chungli, 32003, Taiwan.

Computational Biology and Chemistry
|July 3, 2021
PubMed
Summary

This study introduces a novel Support Vector Machine (SVM) approach using Bidirectional Encoder Representations from Transformers (BERT) to classify active transport proteins. The method accurately distinguishes protein types involved in cellular transport mechanisms.

Keywords:
Active transportContextual representationsContextualized word embeddingsMembrane proteinsPrimary active transportSecondary active transport

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Bioinformatics

Background:

  • Active transport, essential for cellular function, moves substances against concentration gradients using energy and transport proteins.
  • Classifying transmembrane transport proteins is crucial for understanding cellular regulation.
  • Primary and secondary active transport represent key mechanisms involving protein-mediated substance movement.

Purpose of the Study:

  • To classify proteins involved in primary and secondary active transport using advanced machine learning.
  • To introduce a novel method for representing protein sequences through contextualized word embeddings.
  • To leverage Bidirectional Encoder Representations from Transformers (BERT) for feature extraction in protein sequence analysis.

Main Methods:

  • Utilized a Support Vector Machine (SVM) classifier.
  • Employed contextualized word embeddings from BERT to represent protein sequences.
  • Extracted fixed feature vectors from BERT's hidden layers to capture amino acid context and relations.

Main Results:

  • Achieved high classification accuracies: 85.44% (Class-1), 88.74% (Class-2), and 92.84% (Class-3) via five-fold cross-validation and independent testing.
  • Demonstrated superior performance compared to other feature extraction methods.
  • Effectively classified the two main types of active transport proteins.

Conclusions:

  • The proposed BERT-based SVM method accurately classifies active transport proteins.
  • Contextualized protein sequence representation enhances the understanding of amino acid roles.
  • This approach offers improved performance for classifying transmembrane transport proteins.