ArticleActa crystallographica. Section D, Structural biology2016
Empirical power laws for the radii of gyration of protein oligomers.
Article in Acta crystallographica. Section D, Structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- Parametric Studies of Polyacrylamide Adsorption on Calcite Using Molecular Dynamics Simulation.Molecules (Basel, Switzerland) · 2025Article
- Design of multi-epitope vaccine candidate based on OmpA, CarO and ZnuD proteins against multi-drug resistantHeliyon · 2024Article
- Development of Self-Assembled Biomimetic Nanoscale Collagen-like Peptide-Based Scaffolds for Tissue Engineering: An In Silico and Laboratory Study.Biomimetics (Basel, Switzerland) · 2023Article
- Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine againstFrontiers in molecular biosciences · 2023Article
- Assignment of structural domains in proteins using diffusion kernels on graphs.BMC bioinformatics · 2022Article
- Topological bio-scaling analysis as a universal measure of protein folding.Royal Society open science · 2022Article
- AlphaFold illuminates half of the dark human proteins.Current opinion in structural biology · 2022Review
- Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach.PLoS neglected tropical diseases · 2022Article
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- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations.Entropy (Basel, Switzerland) · 2020Article
- Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7.Biophysical journal · 2019Article
- Determination of protein oligomeric structure from small-angle X-ray scattering.Protein science : a publication of the Protein Society · 2018Review
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Abstract
The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2-6 and 8. The power-law exponents for oligomers span a narrow range of 0.38-0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.
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