Related Experiment Video
Updated: Jun 28, 2026
07:33
Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
Cavities and atomic packing in protein structures and interfaces
Shrihari Sonavane1, Pinak Chakrabarti
1Department of Biochemistry, Bose Institute, Calcutta, India.
Plos Computational Biology
|November 14, 2008
Summary
Protein cavities and interfaces were analyzed. Larger protein structures and interfaces contain more cavities, which are less spherical and more enriched in larger protein-protein interaction sites.
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Protein structures contain internal cavities and cavities form at protein-protein interfaces.
- Obligate protein interactions (heterocomplexes) and non-obligate interactions (homodimers) differ in their interface characteristics.
Purpose of the Study:
- To comparatively analyze cavities within protein tertiary structures and at protein-protein interfaces.
- To investigate the relationship between cavity volume, protein size, and residue composition.
Main Methods:
- Comparative analysis of protein tertiary structures and protein-protein interfaces.
- Utilized Voronoi volume calculations to assess residue packing.
- Quantified cavity volume, shape, solvation, and residue lining.
Main Results:
- Cavity volume increases with protein or interface size.
- Larger cavities are less spherical, more solvated, and enriched at interfaces.
- Interfaces exhibit approximately twice the cavity frequency compared to tertiary structures for similar atom counts.
- Beta-strands are more prevalent in lining cavities than turns or loops.
Conclusions:
- Cavity characteristics differ significantly between protein interiors and interfaces.
- Protein-protein interfaces have a higher density of cavities, influencing molecular interactions and solvation.
- Understanding these cavity properties is crucial for protein design and drug discovery.
Related Concept Videos
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
02:04Protein-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...
02:04Protein-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...