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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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Updated: May 8, 2026

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

Reassessing buried surface areas in protein-protein complexes.

Devlina Chakravarty1, Mainak Guharoy, Charles H Robert

  • 1Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India.

Protein Science : a Publication of the Protein Society
|August 13, 2013
PubMed
Summary

Protein-protein complex interfaces show significant differences between buried surface area (BSA) and accessible surface area (ASA) loss upon association (DSA) due to conformational changes. These changes impact binding energy, highlighting the importance of dynamic structural analysis in protein interactions.

Keywords:
binding free energyconformation changesprotein-protein interactionsolvent accessible surface

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • The interface in protein-protein complexes is often characterized by buried surface area (BSA).
  • Accessible surface area (ASA) lost upon association is termed dissociation-induced surface area loss (DSA).
  • Conformational changes can cause differences between BSA and DSA.

Purpose of the Study:

  • To evaluate the DSA in protein-protein complexes.
  • To quantify the differences between BSA and DSA.
  • To investigate the impact of conformational changes on protein-protein interfaces.

Main Methods:

  • Analysis of 144 protein-protein complexes from the Protein-Protein Interaction Affinity Database.
  • Measurement of ASA for interface atoms in both bound and unbound states.
  • Comparison of BSA and DSA to assess conformational changes.

Main Results:

  • Differences between BSA and DSA exceeding 20% were observed.
  • A systematic bias was found, with bound state ASA being 3.3% greater than unbound state ASA.
  • BSA was, on average, 7% greater than DSA, even in complexes with minimal conformational changes.

Conclusions:

  • Conformational changes significantly affect the interface area calculations in protein-protein complexes.
  • Local movements optimize inter-component contacts at the expense of internal contacts.
  • These interface dynamics may influence binding free energy, impacting protein interaction stability.