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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...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 18, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Comparing models of evolution for ordered and disordered proteins.

Celeste J Brown1, Audra K Johnson, Gary W Daughdrill

  • 1Department of Biological Sciences, University of Idaho, USA. celesteb@uidaho.edu

Molecular Biology and Evolution
|November 20, 2009
PubMed
Summary
This summary is machine-generated.

Disordered proteins evolve differently than ordered proteins, showing greater evolutionary change and fewer constraints. Their amino acid frequencies correlate with solvent-exposed regions in ordered proteins.

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

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Last Updated: Jun 18, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

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Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

Area of Science:

  • Protein evolution
  • Structural bioinformatics
  • Molecular evolution

Background:

  • Most protein evolution models assume rigid 3D structures.
  • Disordered proteins lack fixed structures and sample diverse conformations.
  • Disordered proteins have different evolutionary constraints due to lack of long-range interactions.

Purpose of the Study:

  • To develop and compare evolutionary models for disordered and ordered proteins.
  • To investigate differences in evolutionary constraints and substitution patterns.
  • To explore the structural basis of disordered protein evolution.

Main Methods:

  • Constructed protein substitution matrices using homologous sequences.
  • Inferred separate matrices for disordered and ordered proteins at varying sequence similarity levels.
  • Compared amino acid frequencies of disordered proteins with ordered protein secondary structures.

Main Results:

  • Disordered and ordered protein substitution matrices differed significantly across all similarity levels.
  • Disordered proteins showed a higher propensity for evolutionary changes, including non-conservative substitutions.
  • Disordered proteins generally face fewer evolutionary constraints, with exceptions like conserved tryptophan and tyrosine residues crucial for interfaces.
  • Amino acid frequencies in disordered proteins correlated strongly with solvent-exposed loops and turns in ordered proteins.

Conclusions:

  • Disordered proteins exhibit distinct evolutionary dynamics compared to ordered proteins.
  • The findings support a model where disordered proteins may structurally resemble solvent-exposed regions of ordered proteins.
  • Evolutionary constraints on disordered proteins are less stringent, but specific residues remain highly conserved for functional roles.