Related Experiment Video
Updated: May 30, 2026
08:38
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
Published on: March 3, 2015
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO
George R Bickerton1, Alicia P Higueruelo, Tom L Blundell
1Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK. grbickerton@dundee.ac.uk
BMC Bioinformatics
|August 2, 2011
Summary
PICCOLO is a new database detailing protein-protein interactions at the atomic level. It enables large-scale analysis of protein interfaces and supports detailed inspection of specific systems.
Area of Science:
- Structural Biology
- Biochemistry
- Bioinformatics
Background:
- Understanding cellular processes requires characterizing intermolecular interactions in multi-protein assemblies.
- Standard representations inadequately describe these complex interactions.
- Structural studies generate vast data on protein assemblies.
Purpose of the Study:
- To present PICCOLO, a comprehensive relational database for structurally characterized protein-protein interactions.
- To facilitate large-scale analyses of protein-protein interface properties.
- To support detailed investigation of specific protein interaction systems.
Main Methods:
- Developing a relational database (PICCOLO) to capture protein-protein interaction details.
- Describing interactions at atomic, residue, and polypeptide chain levels.
- Characterizing physico-chemical properties using distance and angle terms to define 12 interaction types (e.g., van der Waals, hydrogen bonds, hydrophobic contacts).
Main Results:
- PICCOLO database contains over 260 million interacting atom pairs from 38,202 protein complexes.
- Analysis of residue propensity and interface contact preferences using a large dataset.
- Demonstration of PICCOLO's capability for both large-scale analysis and detailed inspection.
Conclusions:
- PICCOLO provides a detailed resource for studying protein-protein interactions.
- The database supports advanced analyses of protein interface properties.
- A web interface is available for accessing the PICCOLO database.
Related Concept Videos
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...
02:26Protein 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,...
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,...
02:26Protein 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,...
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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.
01:57Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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