ArticleScientific reports2015
Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads.
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 8 papers.
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8 citing papers in PubMed, 41 citations in OpenAlex.
- Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface.Entropy (Basel, Switzerland) · 2022Article
- Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations.Entropy (Basel, Switzerland) · 2020Article
- Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins.Journal of biosciences · 2020Review
- The BackMAP Python module: how a simpler Ramachandran number can simplify the life of a protein simulator.PeerJ · 2018Article
- To be disordered or not to be disordered: is that still a question for proteins in the cell?Cellular and molecular life sciences : CMLS · 2017Review
- Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions.Journal of molecular modeling · 2017Article
- Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins.Journal of computer-aided molecular design · 2017Article
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3 authors at 1 institution in 1 country.
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Abstract
This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory's isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method.
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