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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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 Organization01:24

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: Jul 4, 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

Effective connectivity profile: a structural representation that evidences the relationship between protein

Ugo Bastolla1, Angel R Ortíz, Markus Porto

  • 1Centro de Biología Molecular Severo Ochoa, (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain. ubastolla@cbm.uam.es

Proteins
|June 7, 2008
PubMed
Summary

We introduce the effective connectivity profile (EC), a novel network-based method to represent protein structures. This profile accurately predicts protein sequence properties and reveals insights into protein dynamics and modularity.

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Last Updated: Jul 4, 2026

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Published on: July 14, 2015

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

Published on: July 16, 2017

Area of Science:

  • * Bioinformatics
  • * Computational Biology
  • * Structural Biology

Background:

  • * Protein structure complexity necessitates simplified representations for analyzing sequence-structure relationships.
  • * Existing 1D profiles capture aspects like buriedness or secondary structure but have limitations for complex proteins.
  • * Understanding the statistical inverse folding problem is crucial for predicting sequence properties from structure.

Purpose of the Study:

  • * To define and validate the effective connectivity (EC) profile as a novel, network-theoretical representation of protein topology.
  • * To demonstrate the EC profile's ability to predict sequence-level properties, such as average hydrophobicity and amino acid distributions.
  • * To explore the EC profile's utility in understanding protein dynamics, modularity, and structure similarity.

Main Methods:

  • * Development of the effective connectivity (EC) profile based on the protein contact matrix.
  • * Simulation using the structurally constrained neutral (SCN) model of protein evolution.
  • * Analysis of sequence-structure pairs from the Protein Data Bank (PDB).
  • * Correlation analysis with experimental data (e.g., temperature factors) and structural properties.

Main Results:

  • * The EC profile accurately predicts average hydrophobicity and amino acid distributions for homologous protein families, even with limited sequence data.
  • * EC profile predictions are robust across various mutation processes and protein types (single- and multi-domain).
  • * EC components show a strong inverse correlation with experimental temperature factors, indicating constrained dynamics.
  • * EC profile exhibits a natural measure of modularity correlating with domain count and can serve as a protein structure similarity measure.

Conclusions:

  • * The EC profile offers an analytical solution to the statistical inverse folding problem, linking protein sequence and structure.
  • * It generalizes and improves upon existing structural profiles, especially for modular and long proteins.
  • * EC profile provides novel insights into protein dynamics and domain organization.
  • * EC profile similarity serves as an effective metric for protein structure alignment.