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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...
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Valence Bond Theory02:42

Valence Bond Theory

Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)01:22

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Noncovalent Attractions in Biomolecules02:35

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Debye–Huckel–Onsager Conductance Equation01:28

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Dynamic features of homodimer interfaces calculated by normal-mode analysis.

Yuko Tsuchiya1, Kengo Kinoshita, Shigeru Endo

  • 1Division of Life Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-Ku, Tokyo 112-8610, Japan.

Protein Science : a Publication of the Protein Society
|August 14, 2012
PubMed
Summary

Dynamic analysis of protein interfaces reveals that interface area and dimer formation nature significantly influence protein-protein interactions. Larger interfaces and complex formations reduce dynamic flexibility, impacting protein function.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Understanding protein-protein interactions is crucial for biological processes.
  • Dynamic features of protein interfaces are key to interaction mechanisms.

Purpose of the Study:

  • To dynamically characterize 517 nonredundant homodimer interfaces using normal-mode analysis (NMA).
  • To investigate the relationship between interface properties and dynamic characteristics.

Main Methods:

  • Performed NMA on homodimers and their protomers.
  • Decomposed atomic motion vectors into internal and external components.
  • Calculated averaged correlation coefficients (ACCs) for interface atom pairs.

Main Results:

  • ACCs decrease exponentially with increasing interface area and r-value (interface area/subunit surface area).
  • For small/medium r-values without entanglement, ACCs increase upon dimer formation.
  • Large r-values and intersubunit entanglements (interwinding dimers) show no ACC increase and distinct motion correlations.

Conclusions:

  • Interface area and dimer formation nature dictate dynamic properties of protein interfaces.
  • External motions are critical for distinguishing dimer interface dynamics, especially in interwinding dimers.