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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...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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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Related Experiment Video

Updated: May 21, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Analytic markovian rates for generalized protein structure evolution.

Ivan Coluzza1, James T MacDonald, Michael I Sadowski

  • 1Department of Physics, University of Vienna, Vienna, Austria. ivan.coluzza@univie.ac.at

Plos One
|June 14, 2012
PubMed
Summary
This summary is machine-generated.

This study models protein evolution using a Markovian process to understand constraints on mutations. Compact protein structures with many hydrogen bonds are more likely to evolve.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Understanding protein evolution requires defining constraints on mutations that maintain organism fitness.
  • These constraints can originate from various factors, influencing evolutionary pathways.

Purpose of the Study:

  • To present a model for constrained evolutionary trajectories using a Markovian process.
  • To analyze the transition rates between topologically intermediate protein structures.

Main Methods:

  • Constructed artificial protein-like structures as topological intermediates between natural proteins.
  • Utilized a coarse-grained representation for protein structures.
  • Derived an analytic formulation for transition rates between intermediate structures.

Main Results:

  • Identified compact structures with a high number of hydrogen bonds as more probable evolutionary outcomes.
  • Demonstrated that the number and type of intermediate steps dictate the overall evolutionary constraint.

Conclusions:

  • The developed model provides insights into constrained evolutionary trajectories in proteins.
  • Knowledge of transition rates facilitates the study of complex evolutionary pathways and protein structure evolution.