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Related Concept Videos

Protein Networks

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 Networks

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 Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

Protein-protein Interfaces

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 Diffusion in the Membrane

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

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Related Experiment Video

Updated: Jul 14, 2026

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

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

Published on: July 16, 2017

Network analysis of protein dynamics.

Csaba Böde¹, István A Kovács, Máté S Szalay

¹Department of Biophysics and Radiation Biology, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary. csabi@puskin.sote.hu

|May 29, 2007

Summary

Complex systems are analyzed using network topology. Protein structures reveal small-world networks, with hubs controlling protein function and dynamics, offering insights into biological processes.

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Area of Science:

Biophysics
Systems Biology
Structural Biology

Background:

The network paradigm offers a powerful framework for understanding complex systems.
Protein structures can be represented as molecular networks to analyze their topology and dynamics.

Purpose of the Study:

To review topological analyses of protein structures as molecular networks.
To explore the role of network hubs and central elements in protein function and stability.
To assess the utility of conformational and energy networks for predicting protein folding and dynamics.

Main Methods:

Topological analysis of protein structures.
Network centrality measures to identify key elements.
Assessment of conformational and energy networks.

Main Results:

Protein structures exhibit small-world network characteristics.
Central network elements are often located in active centers and ligand-binding sites, influencing protein dynamics.
Hubs and central nodes play critical roles in enzyme activity, allosteric regulation, motor function, signal transduction, and protein stability.

Conclusions:

Network analysis provides valuable insights into protein structure-function relationships.
Conformational and energy networks show promise for simplifying complex energy landscapes and predicting protein behavior.
Future advancements in modular analysis, centrality measures, and network dynamics will expand this field.