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Tytuł:
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The structure of protein dynamic space.
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Autorzy:
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Rackovsky S; Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853; .; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642.
Scheraga HA; Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853; .
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Źródło:
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Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2020 Aug 18; Vol. 117 (33), pp. 19938-19942. Date of Electronic Publication: 2020 Aug 05.
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Typ publikacji:
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Journal Article; Research Support, N.I.H., Extramural
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Język:
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English
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Imprint Name(s):
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Original Publication: Washington, DC : National Academy of Sciences
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MeSH Terms:
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Proteins/*chemistry
Computational Biology ; Protein Structure, Secondary
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References:
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Grant Information:
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R01 GM014312 United States GM NIGMS NIH HHS
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Contributed Indexing:
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Keywords: B factor; Fourier transform; protein dynamics; structure–dynamics relationships
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Substance Nomenclature:
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0 (Proteins)
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Entry Date(s):
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Date Created: 20200808 Date Completed: 20201029 Latest Revision: 20210206
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Update Code:
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20240105
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PubMed Central ID:
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PMC7443874
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DOI:
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10.1073/pnas.2008873117
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PMID:
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32759212
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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.
Competing Interests: The authors declare no competing interest.