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Related Concept Videos

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Related Experiment Video

Updated: May 23, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Collective dynamics differentiates functional divergence in protein evolution.

Tyler J Glembo1, Daniel W Farrell, Z Nevin Gerek

  • 1Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona, United States of America.

Plos Computational Biology
|April 6, 2012
PubMed
Summary
This summary is machine-generated.

This study integrates protein structure and dynamics to understand steroid receptor evolution. It reveals that functionally similar proteins share dynamic subspaces, aiding in predicting mutations for new functions.

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Identification of Functional Protein Regions Through Chimeric Protein Construction
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Identification of Functional Protein Regions Through Chimeric Protein Construction

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Last Updated: May 23, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Identification of Functional Protein Regions Through Chimeric Protein Construction
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Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Area of Science:

  • Molecular evolution
  • Structural biology
  • Biophysics

Background:

  • Protein evolution studies traditionally focus on sequence analysis and functional assays.
  • Structural and dynamic aspects of protein evolution remain under-explored.
  • Steroid receptors provide a model system for studying evolutionary divergence.

Purpose of the Study:

  • To elucidate the molecular principles governing the evolutionary divergence of steroid receptor proteins.
  • To incorporate structural and dynamic information into molecular evolution studies.
  • To investigate the relationship between protein dynamics, function, and evolutionary pathways.

Main Methods:

  • Utilized the Zipping and Assembly Method with FRODA (ZAMF) for predicting ancestral protein structures.
  • Achieved high accuracy in structure prediction, with ~2.7 Å all-atom RMSD compared to crystal structures.
  • Employed essential dynamics analysis to investigate conformational dynamics and identify collective motions.

Main Results:

  • Predicted structures of three evolutionarily diverged ancestral steroid receptor proteins.
  • Demonstrated that evolutionarily diverged proteins within the same family do not share the same dynamic subspace.
  • Showed that proteins with similar functions cluster together in dynamic space, distinct from functionally diverged proteins.
  • Identified mutations significantly impacting protein dynamics, successfully predicting those necessary for evolving new functions and recovering ancestral ones.

Conclusions:

  • Protein structure and dynamics are crucial for understanding evolutionary divergence.
  • Shared dynamic subspaces correlate with shared protein function, offering insights into evolutionary trajectories.
  • The ZAMF method and dynamic analysis provide a powerful framework for studying protein evolution and predicting functional changes.