Allostery through protein-induced DNA bubbles

Scientific Reports
Joseph J TraversoNikolaos K Voulgarakis

Abstract

Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.

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Aug 10, 2015·Current Opinion in Structural Biology·Turkan Haliloglu, Ivet Bahar
Dec 2, 2015·Journal of Chemical Information and Modeling·Tauanne Dias Amarante, Gerald Weber
Mar 30, 2016·Annual Review of Biochemistry·Claes M GustafssonNils-Göran Larsson
Jun 15, 2019·International Journal of Molecular Sciences·Géraldine Farge, Maria Falkenberg
Apr 3, 2019·Physical Review. E·M HillebrandCh Skokos
Jan 21, 2021·Physical Review. E·M HillebrandA R Bishop

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