ArticleProceedings of the National Academy of Sciences of the United States of America2020
The structure of protein dynamic space.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. 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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Who cites it
8 citing papers in PubMed.
- The Spatial Distribution of Local Mobility in Folded Proteins.The journal of physical chemistry. B · 2026Article
- Techniques for Bioinformatic Applications in Protein Dynamics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.Proteins · 2024Article
- Comprehensive analysis of pepper (Capsicum annuum) RAV genes family and functional identification of CaRAV1 under chilling stress.BMC genomics · 2024Article
- B-factor prediction in proteins using a sequence-based deep learning model.Patterns (New York, N.Y.) · 2023Article
- 3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors.Journal of cheminformatics · 2023Article
- The dynamic basis of structural order in proteins.Proteins · 2022Article
- Uses and Abuses of the Atomic Displacement Parameters in Structural Biology.Methods in molecular biology (Clifton, N.J.) · 2022Article
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2 authors.
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Abstract
We use a bioinformatic description of amino acid dynamic properties, based on residue-specific average B factors, to construct a dynamics-based, large-scale description of a space of protein sequences. We examine the relationship between that space and an independently constructed, structure-based space comprising the same sequences. It is demonstrated that structure and dynamics are only moderately correlated. It is further shown that helical proteins fall into two classes with very different structure-dynamics relationships. We suggest that dynamics in the two helical classes are dominated by distinctly different modes--pseudo-one-dimensional, localized helical modes in one case, and pseudo-three-dimensional (3D) global modes in the other. Sheet/barrel and mixed-α/β proteins exhibit more conventional structure-dynamics relationships. It is found that the strongest correlation between structure and dynamic properties arises when the latter are represented by the sequence average of the dynamic index, which corresponds physically to the overall mobility of the protein. None of these results are accessible to bioinformatic methods hitherto available.
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