ArticleBiophysical journal2016
Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Amyloid-International journal of molecular sciences · 2023Article
- Polymer Physics-Based Classification of Neurons.Neuroinformatics · 2023Article
- Dissecting the cosegregation probability from genome architecture mapping.Biophysical journal · 2022Article
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.Nucleic acids research · 2020Article
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.Biophysical journal · 2019Article
- Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci.PLoS computational biology · 2018Article
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.Biophysical journal · 2017Article
- Flory theory of randomly branched polymers.Soft matter · 2017Article
- Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.RNA (New York, N.Y.) · 2017Article
- Ensemble View of RNAs and Proteins: Loops, Knots, Territories, and Evolution.Biophysical journal · 2016Article
- Extruding Loops to Make Loopy Globules?Biophysical journal · 2016Article
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Abstract
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have territorial organization with signatures pointing to metastability, we analyzed the biomolecular structures deposited in the Protein Data Bank and found that the intrachain contact probabilities, P(s) as a function of the arc length s, decay in power-law ∼s(-γ) over the intermediate range of s, 10 ≲ s ≲ 110. We found that the contact probability scaling exponent is γ ≈ 1.11 for large RNA (N > 110), γ ≈ 1.41 for small-sized RNA (N < 110), and γ ≈ 1.65 for proteins. Given that Gaussian statistics is expected for a fully equilibrated chain in polymer melts, the deviation of γ-value from γ = 1.5 for the subchains of large RNA in the native state suggests that the chain configuration of RNA is not fully equilibrated. It is visually clear that folded structures of large-sized RNA (N ≳ 110) adopt crumpled structures, partitioned into modular multidomains assembled by proximal sequences along the chain, whereas the polypeptide chain of folded proteins looks better mixed with the rest of the structure. Our finding of γ ≈ 1 for large RNA might be an ineluctable consequence of the hierarchical ordering of the secondary to tertiary elements in the folding process.
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