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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Measurement of Heme Synthesis Levels in Mammalian Cells
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Evolutionary relationships between heme-binding ferredoxin α + β barrels.

Giriraj Acharya1, Gurmeet Kaur1, Srikrishna Subramanian2

  • 1CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India.

BMC Bioinformatics
|April 20, 2016
PubMed
Summary

This study reveals two distinct ways ferredoxin-like proteins form alpha+beta barrels, impacting how they bind heme and related molecules. These findings suggest evolutionary links between barrel structures and heme-binding sites.

Keywords:
Barrel packingHemeHemoproteinIron metabolismProtein evolution

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Area of Science:

  • Structural biology
  • Protein evolution
  • Biochemistry

Background:

  • The alpha+beta barrel superfamily comprises diverse, evolutionarily related proteins.
  • Barrel structures form via domain dimerization or fusion.
  • Heme binding is crucial for the function of many superfamily members.

Purpose of the Study:

  • To analyze heme-binding sites and barrel topologies within the alpha+beta barrel superfamily.
  • To understand the structural basis of heme accommodation in these proteins.

Main Methods:

  • Comparative structural analysis of heme-binding alpha+beta barrels.
  • Examination of ferredoxin-like domain packing modes.

Main Results:

  • Identified two distinct modes of ferredoxin-like domain packing in alpha+beta barrels (Type-1/IsdG-like and Type-2/OxdA-like).
  • Demonstrated the ability of these barrels to bind heme or siroheme in at least three different configurations.
  • Characterized heme-binding pockets within different barrel types.

Conclusions:

  • Provided insights into evolutionary relationships between the two barrel packing topologies.
  • Linked observed heme-binding sites to specific barrel structures.