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

DNA sequence specific hydration responsible for conformational flexibility; Molecular dynamics simulation on all possible tetramer sequences

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

no journal, , 

DNA conformation and deformability depend on sequence composition. For example, it is known that a sequence containing contiguous AT steps is more deformable. The variability in DNA conformation and deformability has been believed to be one of important factors in specific recognition of DNA sequence by regulatory proteins. Several factors can be considered to yield the difference in DNA conformation and deformability among distinct DNA sequences. One is the mechanical stiffness inherent in the DNA itself, which is originated from base-pairing hydrogen interactions and base-stacking interactions. Another important factor affecting the DNA conformation and deformability is the hydration. The hydration effect is inevitable when discussing the structural properties of DNA, since DNA is physiologically surrounded by water molecules, and the structure cannot be maintained without water. A characteristic hydration pattern observed for DNA is the spine of water, which is composed of the highly ordered water molecules aligned along the floor of the minor groove. Such a hydration pattern as well as the conformation of DNA is dependent on the sequence. Consequently, the following question arises: How and to what extent does the hydration affect the sequence-dependent deformability of DNA ? To address this question, a comparative study of various DNA sequences is required. Recently, the sequence dependence of DNA conformation and deformability has been studied by MD simulations, where all possible 136 patterns for tetramer were examined. In the present work, we report further analysis of these 136 MD trajectories focused on the hydration water. We compared the both properties of DNA hydration and deformation, and found a possible relationship between them.

DNA sequence dependent deformability and hydration

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

no journal, , 

no abstracts in English

Relationship between DNA conformational flexibility and hydration

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

no journal, , 

no abstracts in English

Sequence dependencies of DNA deformability and hydration in the minor groove

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

no journal, , 

no abstracts in English

Role of indirect readout in protein-DNA recognition assessed by a Bayesian approach

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

no journal, ,