Biochemical and Biophysical Research Communications

Journal Information
ISSN / EISSN : 0006291X / 10902104
Current Publisher: Elsevier BV (10.1016)
Former Publisher: Elsevier BV (10.1006)
Total articles ≅ 89,885
Google Scholar h5-index: 64
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Biochemical and Biophysical Research Communications, Volume 530; doi:10.1016/s0006-291x(20)31594-1

So Yeon Cho, Sung-Il Yoon
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.09.011

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Céline Salaud, Arturo Alvarez-Arenas, Fanny Geraldo, Juan Belmonte-Beitia, Gabriel F. Calvo, Catherine Gratas, Claire Pecqueur, Delphine Garnier, Victor Pérez-Garcià, François M. Vallette, et al.
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.101

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Alaa Al Helaili, Sung Jin Park, Michael J. Beyak
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.045

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Jinwoo Park, Tae Woo Jung, Yoon Hee Chung, Eon Sub Park, Ji Hoon Jeong
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.09.019

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Xueli Zhang, Dongyu Li, Xushan Zhu, Youwang Wang, Ping Zhu
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.088

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Jialu Qiao, Weiling Li, Jian Bao, Qian Peng, Dongmei Wen, Jianing Wang, Binlian Sun
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.09.042

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Hyo Jung Kim
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.070

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Liqiang Dai, Jin Yu
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.004

Abstract:
Oncogenic protein Myc serves as a transcription factor to control cell metabolisms. Myc dimerizes via leucine zipper with its associated partner protein Max to form a heterodimer structure, which then binds target DNA sequences to regulate gene transcription. The regulation depends on Myc-Max binding to DNA and searching for target sequences via diffusional motions along DNA. Here, we conduct structure-based molecular dynamics (MD) simulations to investigate the diffusion dynamics of the Myc-Max heterodimer along DNA. We found that the heterodimer protein slides on the DNA in a rotation-uncoupled manner in coarse-grained simulations, as its two helical DNA binding basic regions (BRs) alternate between open and closed conformations via inchworm stepping motions. In such motions, the two BRs of the heterodimer step across the DNA strand one by one, with step sizes reaching about half of a DNA helical pitch length. Atomic MD simulations of the Myc-Max heterodimer in complex with DNA have also been conducted. Hydrogen bond interactions are revealed between the two BRs and two complementary DNA strands, respectively. In the non-specific DNA binding, the BR from Myc shows an onset of stepping on one association DNA strand and starts detaching from the other strand. Overall, our simulation studies suggest that the inchworm stepping motions of the Myc-Max heterodimer can be achieved during the protein diffusion along DNA.
Jianfu Li, Chunyan Zhao, Shi Hu, Xiaoyun Song, Mengli Lv, Dan Yao, Qingwei Song, Kaijing Zuo
Biochemical and Biophysical Research Communications; doi:10.1016/j.bbrc.2020.08.025

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