ArticlePLoS computational biology2008
Cavities and atomic packing in protein structures and interfaces.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 91 citations in OpenAlex.
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- Statistical Analysis of the Role of Cavity Flexibility in Thermostability of Proteins.Polymers · 2024Article
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- Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography.IUCrJ · 2022Article
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- Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.Biophysical journal · 2020Article
- Pressure Reveals Unique Conformational Features in Prion Protein Fibril Diversity.Scientific reports · 2019Article
- Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.Proteins · 2018Article
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- Exceptionally potent and broadly cross-reactive, bispecific multivalent HIV-1 inhibitors based on single human CD4 and antibody domains.Journal of virology · 2014Article
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.Nucleic acids research · 2013Article
- Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.BMC pharmacology & toxicology · 2013Article
- Protein pocket and ligand shape comparison and its application in virtual screening.Journal of computer-aided molecular design · 2013Article
- Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.PloS one · 2013Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 A(3) of cavity volume is found to accommodate single water, with another 40-45 A(3) needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in beta-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein-protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein-protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.