ArticleScientific reports2015
A structural dissection of large protein-protein crystal packing contacts.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- ESpma: A method for assessing biological/non-biological interfaces using point-clouds-based structural features and protein language models.Protein science : a publication of the Protein Society · 2026Article
- Beyond contacts: The important role of the support region in protein complex assembly.Protein science : a publication of the Protein Society · 2026Article
- Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology.The protein journal · 2025Review
- Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.Acta crystallographica. Section D, Structural biology · 2025Article
- Thermotolerant class A acid phosphatase active across broad pH range and diverse substrates.Protein science : a publication of the Protein Society · 2025Article
- Investigation of structural and dynamic properties of the Butyrophilin BTN3A1/BTN2A1 cytoplasmic complex byFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning.Biomolecules · 2025Review
- Residue-Specific Epitope Mapping of the PD-1/Nivolumab Interaction Using X-ray Footprinting Mass Spectrometry.Antibodies (Basel, Switzerland) · 2024Article
- An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering.Nature communications · 2023Article
- Strong non-ideality effects at low protein concentrations: considerations for elongated proteins.European biophysics journal : EBJ · 2023Article
- 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins.Frontiers in molecular biosciences · 2023Article
- Simple mechanisms for the evolution of protein complexity.Protein science : a publication of the Protein Society · 2022Review
- Human CEACAM1 N-domain dimerization is independent from glycan modifications.Structure (London, England : 1993) · 2022Article
- Bridging the N-terminal and middle domains in FliG of the flagellar rotor.Current research in structural biology · 2022Article
- Antibody interfaces revealed through structural mining.Computational and structural biotechnology journal · 2022Article
- Article
- Interhelical interactions within the STIM1 CC1 domain modulate CRAC channel activation.Nature chemical biology · 2021Article
- Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM.Biophysical journal · 2020Article
- Structure basis of the FERM domain of kindlin-3 in supporting integrin αIIbβ3 activation in platelets.Blood advances · 2020Article
- Engineering protein assemblies with allosteric control via monomer fold-switching.Nature communications · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed.
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