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Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding

Biophysical journal, 2020-04, Vol.118 (7), p.1782-1794 [Peer Reviewed Journal]

2020 ;Copyright © 2020. Published by Elsevier Inc. ;2020. 2020 ;ISSN: 0006-3495 ;EISSN: 1542-0086 ;DOI: 10.1016/j.bpj.2020.01.046 ;PMID: 32130874

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  • Title:
    Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding
  • Author: Li, Hongchun ; Doruker, Pemra ; Hu, Guang ; Bahar, Ivet
  • Subjects: DNA ; DNA Replication ; DNA-Binding Proteins - metabolism ; Ligands
  • Is Part Of: Biophysical journal, 2020-04, Vol.118 (7), p.1782-1794
  • Description: Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.
  • Publisher: United States: Elsevier Inc
  • Language: English
  • Identifier: ISSN: 0006-3495
    EISSN: 1542-0086
    DOI: 10.1016/j.bpj.2020.01.046
    PMID: 32130874
  • Source: Cell Press Free Archives
    MEDLINE
    PubMed Central
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