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Related Concept Videos

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 Complexes with Interchangeable Parts01:57

Protein 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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein 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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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 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 17, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Interaction geometry involving planar groups in protein-protein interfaces.

Rudra Prasad Saha1, Rajasri Bhattacharyya, Pinak Chakrabarti

  • 1Department of Biochemistry, Bose Institute, Calcutta 700 054, India.

Proteins
|January 16, 2007
PubMed
Summary

Protein interactions maintain similar geometries and hydrogen bonds during folding and binding at biological interfaces. However, these interactions are less common in non-specific crystal lattice interfaces.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Area of Science:

  • Structural biology
  • Biochemistry
  • Protein-protein interactions

Background:

  • Planar residue interactions in protein tertiary structures exhibit nonrandom geometry.
  • These interactions form conventional and nonconventional hydrogen bonds (e.g., X--H...pi, X--H...O).

Purpose of the Study:

  • To investigate if similar interaction geometries are preserved at protein-protein interfaces.
  • To compare hydrogen bond types and percentages in biological versus crystal lattice interfaces.

Main Methods:

  • Analysis of interaction geometries involving planar residues in protein structures.
  • Comparison of hydrogen bond types and frequencies across protein structures, biological interfaces (homodimers, heterocomplexes), and crystal lattice interfaces.

Main Results:

  • Interaction geometries and hydrogen bond percentages are similar in protein structures and biological interfaces.
  • These interactions are significantly less prevalent in non-specific crystal lattice interfaces.
  • C--H...O interactions are common across all interface types analyzed.

Conclusions:

  • Chemical interactions during protein folding and binding are similar to those at biological interfaces.
  • Weaker hydrogen bond interactions contribute less to the stability of crystal lattice interfaces due to a depletion of aromatic residues.