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Related Concept Videos

The Significance of Membrane Transport01:44

The Significance of Membrane Transport

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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.
Transporters facilitate either an active or passive movement of solutes. They can allow a single-molecule transport down its...
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Physiological Pharmacokinetic Models: Incorporating Hepatic Transporter-Mediated Clearance01:07

Physiological Pharmacokinetic Models: Incorporating Hepatic Transporter-Mediated Clearance

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Drug transporters are critical in drug absorption, distribution, and excretion processes. They should be included in physiological-based pharmacokinetic (PBPK) models, which help predict human drug disposition. However, predicting this is challenging during drug development, especially when liver transport is involved. However, with a realistic representation of body transport processes, an accurate model may be possible.
A recent model describes pravastatin's hepatobiliary excretion,...
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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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Nonlinear Pharmacokinetics: Role of Transporters01:27

Nonlinear Pharmacokinetics: Role of Transporters

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A drug's nonlinear kinetics can be influenced by a diverse range of transporter proteins that serve as crucial players in drug distribution. These transporters, found within cells, can enhance or reduce local drug concentrations by facilitating the influx or efflux of drugs. For instance, the expression of xenobiotic transporters can be influenced by factors such as age and gender, potentially impacting the linearity of drug response.
Polymorphisms occurring in drug transporters can alter...
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Carrier-Mediated Transport01:06

Carrier-Mediated Transport

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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.
Active transport involves two types of membrane-spanning transporters: uptake and efflux. Uptake transporters are expressed in the small...
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ABC Transporters: Importer01:27

ABC Transporters: Importer

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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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Related Experiment Video

Updated: Sep 11, 2025

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
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High-Throughput Metabolic Profiling for Model Refinements of Microalgae

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Transporter annotations are holding up progress in metabolic modeling.

John Casey1, Brian Bennion1, Patrik D'haeseleer2

  • 1Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory, Livermore, CA, United States.

Frontiers in Systems Biology
|August 14, 2025
PubMed
Summary
This summary is machine-generated.

Accurate transporter annotations are crucial for microbial metabolic models. Improving transporter function prediction will enhance understanding of microbe interactions and applications in medicine and engineering.

Keywords:
flux balance analysisfunctional genomicsmetabolic modelingmicrobial community modelingtransporter annotation

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Area of Science:

  • Microbiology
  • Systems Biology
  • Metabolic Engineering

Background:

  • Mechanistic, constraint-based models are vital for microbial metabolic analysis.
  • Accurate transporter annotations are essential for predicting microbe-microbe and microbe-environment interactions.
  • Current transporter annotations face challenges including non-specific substrate assignments and ambiguity in localization and directionality.

Purpose of the Study:

  • To summarize experimental and computational approaches for determining transporter function.
  • To outline future directions for integrating experimental and computational methods.
  • To emphasize the need for high-throughput functional characterization of transporters.

Main Methods:

  • Review of existing experimental techniques for transporter characterization.
  • Overview of computational strategies for transporter annotation and prediction.
  • Discussion of data integration approaches.

Main Results:

  • Progress in both experimental and computational methods for transporter functional assignment has been made.
  • Significant challenges remain in achieving comprehensive and accurate transporter annotations.
  • The integration of experimental and computational approaches offers a promising path forward.

Conclusions:

  • Investment in high-throughput functional characterization is critical for advancing predictive tools.
  • Improved transporter predictions will lead to more accurate genome-scale metabolic network reconstructions.
  • Enhanced predictions will benefit diverse fields including personalized medicine, metabolic engineering, and microbial ecology.