A Generalized conformational energy function of DNA derived from molecular dynamics simulations

Yamasaki, Satoshi*; Terada, Toru*; Shimizu, Kentaro*; Kono, Hidetoshi; Sarai, Akinori*

Nucleic Acids Research, 37(20), p.e135_1 - e135_9, 2009/09

https://doi.org/10.1093/nar/gkp718

Sequence-dependent DNA deformability studied using molecular dynamics simulations

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

Nucleic Acids Research, 35(18), p.6063 - 6074, 2007/09

https://doi.org/10.1093/nar/gkm627

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base-pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base-pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base-pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

DNA deformability and hydration studied by molecular dynamics simulation

Yonetani, Yoshiteru*; Kono, Hidetoshi; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

Molecular Simulation, 33(1-2), p.103 - 107, 2007/01

https://doi.org/10.1080/08927020601052971

DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics simulations of these two sequences, and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove than the flexible TTAA. The result suggests that the hydration water molecules play a critical role for determining the sequence dependent deformability of DNA conformation.

Role of inter and intramolecular interactions in protein-DNA recognition

Gromiha, M. M.*; Siebers, J. G.*; Selvaraj, S.*; Kono, Hidetoshi; Sarai, Akinori*

Gene, 364, p.108 - 113, 2005/12

https://doi.org/10.1016/j.gene.2005.07.022

no abstracts in English

Protein-DNA recognition patterns and predictions

Sarai, Akinori*; Kono, Hidetoshi

Annual Review of Biophysics and Biomolecular Structure, 34, p.379 - 398, 2005/06

https://doi.org/10.1146/annurev.biophys.34.040204.144537

no abstracts in English

Balance of direct readout and indirect readout contributions to protein-DNA recognition

Kono, Hidetoshi; Kumar, S.*; Ahmad, S.*; Arazo-Bravo, M. J.*; Fujii, Satoshi*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Indirect readout by DNA binding proteins; Analysis of sequence dependent conformation by molecular dynamics simulation

Fujii, Satoshi*; Arazo-Bravo, M. J.*; Takenaka, Shigeori*; Kono, Hidetoshi; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Free energy landscape for interactions between DNA bases and protein side chains

Yoshida, Tomoki*; Doi, Hideo*; Aida, Misako*; Kono, Hidetoshi; Kumar, S.*; Gromiha, M. M.*; Sarai, Akinori*

no journal, , 

no abstracts in English

Sequence context dependent flexibility of DNA studied by molecular dynamics simulation

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

DNA sequence-dependent deformability associated with hydration; Implication for indirect readout in protein-DNA interactions

Kono, Hidetoshi; Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

no journal, , 

Proteins recognize specific DNA sequences not only through direct contact between amino acids and base-pairs, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetramericsequences sandwiched between CGCG sequences. We found that the average conformation and deformability of the tetramers can be highly sequence dependent. Even the tetrameric sequences having the same dimeric sequence at the center showed the distinct deformabilities dependent on the bases on either end of the tetramers. Such conformations of tetramers were found to be associated with hydration. The tetrameric sequences with AT at their center, for instance, generally were rigid and highly hydrated. The rigidity among the tetramers was affected by the flanking bases and also correlated with the amount of hydration which we defined as number of water molecules bridging two bases belonging to different chains in minor groove. These results suggest that hydration of DNA is responsible for the mechanism of indirect readout during protein-DNA recognition. We also show that the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.