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Related Concept Videos

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

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Protein Folding01:22

Protein Folding

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Protein Organization01:13

Protein Organization

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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.
Protein Organization01:13

Protein Organization

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Updated: Jun 4, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Side-chain conformational changes upon Protein-Protein Association.

Anatoly M Ruvinsky1, Tatsiana Kirys, Alexander V Tuzikov

  • 1Center for Bioinformatics, The University of Kansas, Lawrence, KS 66047, USA.

Journal of Molecular Biology
|March 1, 2011
PubMed
Summary
This summary is machine-generated.

Protein side chains undergo distinct conformational changes during binding, with longer chains exhibiting larger transitions. This impacts protein-protein interactions and guides better computational modeling of molecular flexibility.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Last Updated: Jun 4, 2026

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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

Area of Science:

  • Structural biology
  • Computational biophysics
  • Biochemistry

Background:

  • Protein-protein association involves critical conformational changes in amino acid side chains.
  • Understanding these dynamics is essential for deciphering binding mechanisms and improving molecular modeling.

Purpose of the Study:

  • To systematically analyze large-scale conformational changes in protein side chains upon association.
  • To investigate the relationship between side chain length, flexibility, and interface alterations.
  • To evaluate current protein docking approaches for modeling side-chain dynamics.

Main Methods:

  • Large-scale analysis of protein-protein complex structures.
  • Comparison of conformational changes in side chains based on length and dihedral angles.
  • Analysis of interface area changes (polar and nonpolar).
  • Comparison of X-ray structures with protein docking decoy sets.

Main Results:

  • Side chain conformational changes differ based on length; longer chains (≥3 dihedral angles) show larger transitions, while shorter chains exhibit local adjustments.
  • The dihedral angle furthest from the backbone typically undergoes the most significant change.
  • Protein association increases both polar and nonpolar interface areas, with a greater increase in nonpolar area, enhancing hydrophobic contributions.
  • Core-to-surface transitions are more frequent than surface-to-core transitions for specific residues.

Conclusions:

  • Protein side chain flexibility plays a crucial role in protein-protein binding, influencing interface thermodynamics.
  • Observed conformational changes provide insights for refining protein docking protocols and enhancing side-chain conformational sampling.
  • The study highlights the importance of accurately modeling side-chain dynamics for predicting protein complex formation.