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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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jun 1, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Protein-protein HADDocking using exclusively pseudocontact shifts.

Christophe Schmitz1, Alexandre M J J Bonvin

  • 1Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan, The Netherlands.

Journal of Biomolecular NMR
|June 1, 2011
PubMed
Summary

This study integrates long-range pseudocontact shift (PCS) restraints into HADDOCK for enhanced macromolecular structure determination. The method efficiently predicts protein complex structures, even with noisy data, and determines novel complex structures using PCS data alone.

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Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
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Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Related Experiment Videos

Last Updated: Jun 1, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) is crucial for determining macromolecular structures.
  • Macromolecular assemblies present challenges for traditional structure determination methods.
  • Pseudocontact shifts (PCS) offer long-range structural information.

Purpose of the Study:

  • To enhance macromolecular assembly structure determination using NMR.
  • To implement long-range PCS restraints within the HADDOCK protein docking software.
  • To validate the method's efficiency and applicability.

Main Methods:

  • Integration of PCS restraints into the HADDOCK package.
  • Application to a model system: lanthanide-labeled E. coli DNA polymerase III ε186 domain with HOT domain.
  • Testing with varying levels of noise and conformational flexibility.
  • Structure determination using PCS data exclusively.

Main Results:

  • HADDOCK successfully docked bound protein partners with high accuracy (RMSD < 1 Å), even with significant noise.
  • Challenges remain for docking proteins with conformational changes in their free states (RMSD 3.1-3.9 Å).
  • The structure of ε186 in complex with the HOT-homologue θ subunit was determined using only PCS data.

Conclusions:

  • The implemented PCS restraints significantly improve HADDOCK's capability for structure determination of macromolecular assemblies.
  • The method is robust and efficient, providing accurate structural models.
  • This approach enables the determination of novel protein complex structures using PCS as the sole experimental input.