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Updated: Jul 26, 2026
10:37
Protein Complex Affinity Capture from Cryomilled Mammalian Cells
Published on: December 9, 2016
A systematic study of low-resolution recognition in protein--protein complexes
I A Vakser1, O G Matar, C F Lam
1Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA. vakseri@musc.edu
Summary
Low-resolution recognition is prevalent in protein-protein complexes, with over half exhibiting this interaction. This finding, based on a large database analysis, suggests widespread structural flexibility in protein binding.
Area of Science:
- Structural biology
- Computational biology
- Biochemistry
Background:
- Protein-protein interactions are fundamental to cellular processes.
- Understanding protein recognition mechanisms is crucial for drug discovery and systems biology.
- Previous studies suggested low-resolution recognition plays a role, but its prevalence was unclear.
Purpose of the Study:
- To investigate the prevalence of low-resolution recognition in a large-scale database of protein-protein complexes.
- To determine if interface size influences the occurrence of low-resolution recognition.
Main Methods:
- A comprehensive, nonredundant database of 475 cocrystallized protein-protein complexes was curated.
- The GRAMM docking program was employed to simulate low-resolution recognition by removing atomic details.
- Molecular images were systematically docked to assess interaction patterns.
Main Results:
- Low-resolution recognition was identified in 52% of the analyzed protein-protein complexes.
- Complexes with larger interface areas (>4,000 Ų) showed a higher prevalence of low-resolution recognition (76%).
- Limitations in current tools suggest the actual prevalence may be even greater.
Conclusions:
- Low-resolution recognition is a widespread phenomenon in protein-protein interactions.
- The study provides strong evidence for the broad-scale significance of low-resolution recognition in structural biology.
- Further research with advanced tools is warranted to fully elucidate the extent of low-resolution recognition.
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