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Related Concept Videos

The Significance of Membrane Transport01:44

The Significance of Membrane Transport

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...
Membrane Transporters01:31

Membrane Transporters

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...
Primary Active Transport01:29

Primary Active Transport

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 not...
ABC Transporters: Importer01:27

ABC Transporters: Importer

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:
Carrier-Mediated Transport01:06

Carrier-Mediated Transport

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...
ABC Transporters: Exporter01:31

ABC Transporters: Exporter

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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Characterization of Membrane Transporters by Heterologous Expression in E. coli and Production of Membrane Vesicles
13:16

Characterization of Membrane Transporters by Heterologous Expression in E. coli and Production of Membrane Vesicles

Published on: December 31, 2019

Annotation-based inference of transporter function.

Thomas J Lee1, Ian Paulsen, Peter Karp

  • 1Artificial Intelligence Center, SRI International, Menlo Park, CA, USA. tomlee@ai.sri.com

Bioinformatics (Oxford, England)
|July 1, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method to computationally infer transporter protein activities and construct transport reactions from genome annotations. This approach enhances metabolic network analysis and comparative studies across organisms.

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Transporter proteins play crucial roles in cellular transport.
  • Current methods for analyzing transporter functions are limited by free-text protein names.
  • Computational manipulation of transporter activities requires standardized descriptions.

Purpose of the Study:

  • To develop a computational method for inferring and constructing transport reactions from protein names.
  • To enable advanced computational analyses of transporter activities and metabolic networks.
  • To facilitate comparative studies of transport capabilities across different organisms.

Main Methods:

  • Analysis of individual protein names within genome annotations.
  • Encoding transporter activities into declarative transport reactions.
  • Implementation within the PathoLogic software, part of Pathway Tools.

Main Results:

  • Achieved 0.93 precision and 0.90 recall in identifying transporter proteins.
  • Obtained 67.5% accuracy in predicting complete transport reactions, rising to 82.5% with generalized predictions.
  • Demonstrated potential for database queries, metabolic map generation, anomaly detection, and comparative analyses.

Conclusions:

  • The developed method effectively infers transport reactions from protein names.
  • This facilitates computational analysis and interpretation of transporter functions.
  • The approach aids in understanding and comparing metabolic and transport networks across species.