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Redox Reactions01:27

Redox Reactions

Redox reactions are vital biochemical processes that underpin energy metabolism in cells. These reactions involve the transfer of electrons between molecules, occurring in tandem as oxidation and reduction. Oxidation refers to the loss of electrons, while reduction denotes their gain. This coupling ensures the seamless flow of electrons through metabolic pathways. For example, in bacterial metabolism, glucose undergoes oxidation to carbon dioxide, while oxygen is simultaneously reduced to...
Redox Reactions01:24

Redox Reactions

Oxidation-reduction or redox reactions involve the transfer of electrons from one molecule or atom to another. When an atom gains an electron, another atom must lose an electron, meaning oxidation and reduction must occur together. Since the redox occurs in pairs, the atom that gets oxidized is also called the reducing agent or reductant, and the atom that is reduced is also called the oxidizing agent or oxidant. A straightforward way to remember the definitions of oxidation and reduction is...
Oxidation and Reduction of Organic Molecules01:19

Oxidation and Reduction of Organic Molecules

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions, which occur at the same time. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called redox reactions.
The removal of an electron from a molecule, results in a...
Phase I Reactions: Reductive Reactions01:27

Phase I Reactions: Reductive Reactions

Phase I biotransformation reductive reactions are chemical processes that modify drugs by introducing or revealing polar functional groups via reduction. Enzymes called reductases catalyze these reactions, playing a pivotal role in drug metabolism by transforming lipophilic drugs into more polar, water-soluble metabolites for easy excretion. An essential type of reductive reaction is the carbonyl group reduction, where aldehydes and ketones are reduced to alcohols. An example is the...
Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.
Phase I Oxidative Reactions: Overview01:19

Phase I Oxidative Reactions: Overview

Phase I biotransformation, or functionalization, is a crucial chemical process that converts drugs and other xenobiotics into more water-soluble forms, facilitating expulsion from the body. It involves oxidative, reductive, and hydrolytic reactions that add or unveil polar functional groups on lipophilic substrates. Key players in phase I reactions are the mixed-function oxidases. Situated in liver cell microsomes, these enzymes predominantly carry out drug metabolism. They require molecular...

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Related Experiment Video

Updated: May 23, 2026

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase
10:01

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase

Published on: December 4, 2017

TrAnsFuSE refines the search for protein function: oxidoreductases.

Arye Harel1, Paul Falkowski, Yana Bromberg

  • 1Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Science, Rutgers the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, USA. harel@marine.rutgers.edu

Integrative Biology : Quantitative Biosciences From Nano to Macro
|April 7, 2012
PubMed
Summary

We developed TrAnsFuSE, a novel method to identify oxidoreductase enzyme domains in unannotated sequences, improving accuracy by 11-14% over existing tools. This advances our understanding of ancient enzyme evolution and function.

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Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry
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Related Experiment Videos

Last Updated: May 23, 2026

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase
10:01

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase

Published on: December 4, 2017

Measuring Trans-Plasma Membrane Electron Transport by C2C12 Myotubes
10:27

Measuring Trans-Plasma Membrane Electron Transport by C2C12 Myotubes

Published on: May 4, 2018

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry
12:07

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry

Published on: March 24, 2012

Area of Science:

  • Biochemistry and Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Non-equilibrium catalysis by oxidoreductases, utilizing transition metals, is crucial for biological macromolecule element flux.
  • These ancient enzyme domains, originating in microbes, are difficult to identify due to sequence divergence.
  • Current homology-based methods for annotating uncharacterized protein sequences have limitations in accuracy and reliability.

Purpose of the Study:

  • To develop a robust method for identifying redox enzyme domains in large, unannotated sequence datasets.
  • To improve the accuracy of protein function annotation transfer for oxidoreductases.
  • To enhance the study of evolutionary relationships and functional diversity of these critical enzymes.

Main Methods:

  • Developed TrAnsFuSE, a computational approach combining profile-based searches with catalytic site annotations.
  • Validated annotations of 104 InterPro domains involved in transition metal-mediated redox reactions.
  • Utilized experimentally identified catalytic residues to refine sequence alignment-based function annotations.

Main Results:

  • TrAnsFuSE demonstrated 11% and 14% higher accuracy than PSI-BLAST and InterPro, respectively.
  • The method proved robust, achieving higher accuracy with comparable coverage when including metal-binding sites.
  • Successfully identified redox domains across diverse oxidoreductases, primarily those using iron, copper, and molybdenum.

Conclusions:

  • TrAnsFuSE significantly enhances the detection accuracy of redox domains in unannotated sequences.
  • This method facilitates the study of vast amounts of genomic and metagenomic data.
  • Improves understanding of oxidoreductase evolution and function, particularly ancient metalloenzymes.