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Intrinsically Disordered Proteins

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 Proteins

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...

Conservation of Protein Domains Over Different Proteins

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...

Conservation of Protein Domains

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...

Conserved Binding Sites

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 Sites

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...

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Related Experiment Video

Updated: May 8, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Protein domain definition should allow for conditional disorder.

Kavestri Yegambaram¹, Esther M M Bulloch, Richard L Kingston

¹School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.

Protein Science : a Publication of the Protein Society

|August 22, 2013

Summary

Protein structure is conditional, not binary. This study redefines protein domains by their potential to fold, accommodating environmental influences and distinguishing them from intrinsically disordered regions.

Keywords:

RNA-dependent RNA polymerase coupled binding and folding intrinsic protein disorder mumps virus protein stability rubulaviruses stabilizing osmolytes trimethylamine N-oxide

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

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

Published on: July 14, 2015

Related Experiment Videos

Last Updated: May 8, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

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

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

Published on: July 14, 2015

Area of Science:

Biochemistry
Structural Biology
Molecular Biology

Background:

Proteins are often classified as either structured or disordered, a binary approach with limitations.
Protein folding is conditional on the physiochemical environment, meaning structure can change with conditions.
Existing classifications fail to account for proteins that can fold under certain conditions but are disordered otherwise.

Purpose of the Study:

To challenge the binary classification of proteins as structured or disordered.
To propose a new definition for protein structural domains based on their capacity to adopt a specific tertiary structure.
To differentiate between conditional disorder and intrinsic disorder in protein regions.

Main Methods:

Experimental study of small binding domains from mumps virus RNA polymerase.
Analysis of a protein family exhibiting a structural continuum (folded, partially folded, unstructured).
Assessment of conditional disorder and the capacity for folding under varying environmental conditions.

Main Results:

The studied protein family displayed conditional disorder; all members could access the same folded state under appropriate conditions.
A definition emphasizing conformational stability inaccurately divided the protein domain family.
The observed structural continuum highlights the environmental dependence of protein folding.

Conclusions:

Protein structural domains should be defined by their ability to adopt a specific tertiary structure, regardless of environmental conditions.
This definition accommodates the conditional nature of protein folding and clarifies the distinction from intrinsically disordered regions.
A more nuanced understanding of protein structure is crucial for accurate biological interpretation.