气候变化领域集成服务门户(CCPortal): Accurate modeling of DNA conformational flexibility by a multivariate Ising model

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DOI	10.1073/pnas.2021263118
	Accurate modeling of DNA conformational flexibility by a multivariate Ising model
	Liebl K.; Zacharias M.
发表日期	2021
ISSN	00278424
卷号	118 期号:15
英文摘要	The sequence-dependent structure and deformability of DNA play a major role for binding of proteins and regulation of gene expression. So far, most efforts to model DNA flexibility are based on unimodal harmonic stiffness models at base-pair resolution. However, multimodal behavior due to distinct conformational substates also contributes significantly to the conformational flexibility of DNA. Moreover, these local substates are correlated to their nearest-neighbor substates. A description for DNA elasticity which includes both multimodality and nearest-neighbor coupling has remained a challenge, which we solve by combining our multivariate harmonic approximation with an Ising model for the substates. In a series of applications to DNA fluctuations and protein-DNA complexes, we demonstrate substantial improvements over the unimodal stiffness model. Furthermore, our multivariate Ising model reveals a mechanical destabilization for adenine (A)-tracts to undergo nucleosome formation. Our approach offers a wide range of applications to determine sequence-dependent deformation energies of DNA and to investigate indirect readout contributions to protein-DNA recognition. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	DNA deformability; Indirect readout; Nearest-neighbor model; Protein-DNA binding
语种	英语
scopus关键词	article; conformational transition; elasticity; molecular recognition; nucleosome; protein DNA binding; rigidity
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/179891
作者单位	Physics Department T38, Technical University of Munich, Garching, 85748, Germany
推荐引用方式 GB/T 7714	Liebl K.,Zacharias M.. Accurate modeling of DNA conformational flexibility by a multivariate Ising model[J],2021,118(15).
APA	Liebl K.,&Zacharias M..(2021).Accurate modeling of DNA conformational flexibility by a multivariate Ising model.Proceedings of the National Academy of Sciences of the United States of America,118(15).
MLA	Liebl K.,et al."Accurate modeling of DNA conformational flexibility by a multivariate Ising model".Proceedings of the National Academy of Sciences of the United States of America 118.15(2021).