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Related Concept Videos

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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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: Jun 29, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Shape complementarity of protein-protein complexes at multiple resolutions.

Qing Zhang1, Michel Sanner, Arthur J Olson

  • 1Department of Molecular Biology, The Scripps Research Institute 10550 North Torrey Pines Road, mail MB-5, La Jolla, California 92037, USA.

Proteins
|October 8, 2008
PubMed
Summary

Surface smoothing in protein docking can preserve shape complementarity. Medium resolution smoothing retains 88% of complementarity, while low resolution improves consistency between bound and unbound protein states.

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein complexes feature highly complementary interfaces.
  • Computational docking predicts protein complex structures using surface complementarity.
  • Conformational changes in proteins during association can hinder docking accuracy.

Purpose of the Study:

  • To systematically evaluate the impact of surface smoothing on shape complementarity in protein-protein interfaces.
  • To investigate how different resolutions of smoothed surfaces affect the prediction of protein complex structures.

Main Methods:

  • Generated multiresolution blurred surfaces for 66 protein-protein complexes using Gaussian functions.
  • Quantified shape complementarity by analyzing surface mesh vertex distances.
  • Compared complementarity between crystallographic complexes and those modeled from unbound structures.

Main Results:

  • Medium resolution smoothing (blobbyness = -0.9) preserved ~88% of shape complementarity compared to atomic resolution.
  • Low resolution smoothing (blobbyness = -0.3) increased consistency between bound and unbound protein conformations.
  • Reduced Gaussian densities for flexible atoms further refined surface complementarity.

Conclusions:

  • Surface smoothing is a viable strategy to mitigate conformational changes in protein docking.
  • Optimizing surface resolution is crucial for accurate prediction of protein-protein complex structures.
  • Smoothed surfaces offer a balance between detail and robustness for docking protocols.