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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 Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
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...

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Related Experiment Video

Updated: Jul 8, 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

Preferred side-chain constellations at antiparallel coiled-coil interfaces.

Erik B Hadley1, Oliver D Testa, Derek N Woolfson

  • 1Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.

Proceedings of the National Academy of Sciences of the United States of America
|January 11, 2008
PubMed
Summary
This summary is machine-generated.

New rules for protein folding reveal complex helix-helix interactions. Understanding these

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

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

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Last Updated: Jul 8, 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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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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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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Predicting protein structure from sequence is crucial for biology and protein design.
  • Antiparallel dimeric coiled coils are common protein structural motifs.
  • Knobs-into-holes (KIH) packing describes helix-helix interfaces in coiled coils.

Purpose of the Study:

  • To decipher and rationalize new rules for helix-helix interfaces in antiparallel dimeric coiled coils.
  • To investigate the energetic importance of vertical interactions within the KIH motif.
  • To identify favorable side-chain interactions, termed 'constellations'.

Main Methods:

  • Experimental analysis of protein structures.
  • Analysis of the Protein Data Bank (PDB).
  • Investigating both lateral and vertical interactions within the KIH motif.

Main Results:

  • Identified energetically important vertical interactions within the KIH motif.
  • Database and experimental analyses agree on preferred vertical combinations.
  • Defined 'constellations' as favorable side-chain interactions driving coiled-coil stability.

Conclusions:

  • Coiled-coil interactions exhibit greater complexity than previously understood.
  • Vertical interactions play a significant energetic role in KIH packing.
  • The identified constellations provide a framework for understanding and predicting coiled-coil structures.