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Related Concept Videos

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...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme-linked Receptors01:00

Enzyme-linked Receptors

Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Engineering oxidoreductases: maquette proteins designed from scratch.

Bruce R Lichtenstein1, Tammer A Farid, Goutham Kodali

  • 1Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, U.S.A. lichtenstein@gmail.com

Biochemical Society Transactions
|May 24, 2012
PubMed
Summary

Synthetic biology creates custom protein maquettes to understand essential oxidoreductase functions. This approach simplifies complex natural enzymes, revealing fundamental requirements for oxidation-reduction catalysis.

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Area of Science:

  • Biochemistry
  • Synthetic Biology
  • Protein Engineering

Background:

  • Natural enzymes, particularly oxidoreductases, present complex structures and functions obscured by evolutionary history.
  • Understanding the fundamental requirements for enzyme function is challenging due to intertwined molecular details.

Purpose of the Study:

  • To simplify the study of oxidoreductase function by removing evolutionary complexities.
  • To identify the necessary and sufficient requirements for biocatalytic oxidation and reduction reactions.

Main Methods:

  • Utilizing a synthetic biology approach to construct de novo protein maquettes.
  • Designing and iteratively building sturdy, versatile three- and four-α-helical structural platforms expressible in bacteria.
  • Incorporating natural redox cofactors and synthetic analogues into maquette structures.
  • Directing maquette assembly to specific environments (membranes, surfaces) using external polarity, charge-patterning, and linkers.

Main Results:

  • Developed a family of protein maquettes with robust and adaptable structural platforms.
  • Demonstrated the ability to incorporate diverse redox cofactors and synthetic analogues.
  • Achieved functional assembly of maquettes on various surfaces and in membranes.
  • Observed maquettes engaging in light harvesting, charge separation, dioxygen binding, and basic oxidative chemistry.

Conclusions:

  • This synthetic approach effectively decouples protein structure from specific evolutionary constraints, enabling exploration of fundamental enzyme function.
  • Protein maquettes provide a simplified yet versatile platform for studying and engineering oxidation-reduction catalysis.
  • The methodology allows for the design of functional protein systems for applications in biocatalysis and materials science.