Allostery through protein-induced DNA bubbles

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

doi:10.1038/srep09037

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Allostery through protein-induced DNA bubbles

Journal article

Open access

Peer reviewed

Allostery through protein-induced DNA bubbles

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

Scientific reports, Vol.5(1), pp.9037-9037

03/12/2015

DOI: https://doi.org/10.1038/srep09037

Handle:

https://hdl.handle.net/2376/104603

PMCID: PMC4356955

PMID: 25762409

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https://doi.org/10.1038/srep09037View

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Abstract

Protein Aggregates

Transcription Factors - chemistry

DNA, Mitochondrial - metabolism

Allosteric Regulation

DNA - metabolism

DNA-Binding Proteins - chemistry

DNA-Binding Proteins - metabolism

Transcription Factors - metabolism

DNA - chemistry

Algorithms

Mitochondrial Proteins - metabolism

Models, Biological

Mitochondrial Proteins - chemistry

Protein Binding

DNA, Mitochondrial - chemistry

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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Title: Allostery through protein-induced DNA bubbles
Creators: Joseph J Traverso - 1] Department of Mathematics, Washington State University, Richland, WA 99354, USA Department of Mechanical Engineering, Washington State University, Richland, WA 99354, USA
Valipuram S Manoranjan - Department of Mathematics, Washington State University, Pullman, WA 99163, USA
A R Bishop - Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Kim Ø Rasmussen - Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Nikolaos K Voulgarakis - Department of Mathematics, Washington State University, Richland, WA 99354, USA
Publication Details: Scientific reports, Vol.5(1), pp.9037-9037
Academic Unit: Mathematics and Statistics, Department of
Publisher: England
Identifiers: 99900546969901842
Language: English
Resource Type: Journal article