Allostery through protein-induced DNA bubbles

Traverso, Joseph J.; Manoranjan, Valipuram S.; Bishop, A. R.; Rasmussen, Kim Ø.; Voulgarakis, Nikolaos K.

doi:10.1038/srep09037

Title: Allostery through protein-induced DNA bubbles

Journal Article · Thu Mar 12 04:00:00 UTC 2015 · Scientific Reports

DOI: https://doi.org/10.1038/srep09037 · OSTI ID:1190537

Traverso, Joseph J. ^[1]; Manoranjan, Valipuram S. ^[2]; Bishop, A. R. ^[3]; Rasmussen, Kim Ø. ^[3]; Voulgarakis, Nikolaos K. ^[4]

Washington State Univ., Richland, WA (United States). Dept. of Mathematics and Dept. of Mechanical Engineering.
Washington State Univ., Richland, WA (United States). Dept. of Mathematics.
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Washington State Univ., Pullman, WA (United States). Dept. of Mathematics.

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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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1190537

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Vol. 5; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Acetylation and phosphorylation of human TFAM regulate TFAM–DNA interactions via contrasting mechanisms King, Graeme A.; Hashemi Shabestari, Maryam; Taris, Kees-Karel H. Nucleic Acids Research, Vol. 46, Issue 7 https://doi.org/10.1093/nar/gky204	journal	March 2018
Organization of DNA in Mammalian Mitochondria Farge, Géraldine; Falkenberg, Maria International Journal of Molecular Sciences, Vol. 20, Issue 11 https://doi.org/10.3390/ijms20112770	journal	June 2019

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