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Related Concept Videos

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 Organization01:13

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.
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...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Discrete-continuous duality of protein structure space.

Ruslan I Sadreyev1, Bong-Hyun Kim, Nick V Grishin

  • 1Howard Hughes Medical Institute, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

Current Opinion in Structural Biology
|June 2, 2009
PubMed
Summary
This summary is machine-generated.

The protein structure space is both discrete and continuous. Evolutionary relationships form distinct protein fold "islands," but geometric similarities allow continuous paths between any structures.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • The protein structure space has been debated as either discrete (separate folds) or continuous (traversable paths).
  • Recent evidence suggests a more complex landscape than previously understood, challenging traditional discrete models.
  • Understanding the organization of protein structures is crucial for predicting function and evolution.

Purpose of the Study:

  • To reconcile the discrete and continuous views of protein structure space.
  • To investigate the complementary nature of evolutionary and geometric descriptions of protein structures.
  • To analyze the connectivity and organization of the protein universe.

Main Methods:

  • Analysis of protein structure databases.
  • Quantification of geometric similarities between protein structures.
  • Examination of evolutionary relationships and structural prototypes.
  • Development of similarity cutoffs to establish connectivity.

Main Results:

  • Protein structure space exhibits a dual nature: discrete in an evolutionary context and continuous geometrically.
  • Evolutionary connections are primarily limited to distinct protein fold prototypes, resembling 'islands' of stability.
  • Geometric similarity measures reveal continuous pathways connecting seemingly distant protein structures through intermediates.
  • Traceable evolutionary links between major structural groups are sparse.

Conclusions:

  • The discrete and continuous descriptions of protein structure space are not mutually exclusive but complementary.
  • Evolutionary history shapes distinct protein fold families, while geometric principles allow for continuous structural variation.
  • The protein universe can be viewed as a landscape with discrete evolutionary islands connected by continuous geometric pathways.