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Articles by Tsuyoshi Terakawa
In vitro reconstitution of chromatin replication recapitulates symmetric histone recycling
Abstract Symmetric histone recycling is vital for maintaining epigenetic inheritance upon eukaryotic DNA replication. Recent genome-wide studies have uncovered key determinants of this process, but how these factors collectively support parental histone transfer remains incompletely understood.
SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path
eLife Assessment This important study presents a well-constructed multiscale simulation framework to investigate ATP-driven DNA translocation by prokaryotic SMC complexes, supporting a segment-capture mechanism. The strength of evidence is convincing, highlighting the necessity of a precise balance between electrostatic interactions and hydrogen bonding, as well as the critical role of kleisin asymmetry in ensuring unidirectional movement.
Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics
Abstract The nucleosome is the fundamental chromatin unit, containing two copies of histones H2A, H2B, H3, and H4 wrapped by ~ 146 bp of core DNA plus linker DNA; addition of linker histone H1 forms a chromatosome. Tetra-acetylation of the H4 N-terminal tail (H4-4Kac) enhances H3 N-tail acetylation by altering their mutual dynamics, but how H1 influences these dynamics remains unclear.
悪しき哲学が物理学の進歩を妨げている｜Tsuyoshi Terakawa
元記事 🧭 概要 理論物理学者カルロ・ロヴェッリがNatureに寄稿した本稿では、現代物理学が**“新しさ至上主義”と誤解された科学哲学に振り回され、根本的な進歩から遠ざかっていると批判しています。多くの理論物理学者が「標準理論の先へ」と躍起になっている一方で、過去数十年の実験的成果は既存理論（標準モデル、一般相対論、量子力学）を次々に強固に裏付けるものばかり。それにもかかわらず、コミュニティは謙虚さを失い、根拠の乏しい理論に人材と資源を浪費しているというのがロヴェッリの指摘です。 🔍 “新理論信仰”の誤りを検証する ここ数十年、物理学は「標準理論の限界」や「その先」を探る試みで溢れてきました。たとえば： 2012年のヒッグス粒子の発見：標準モデルを完全に支持し、“その先”の理論をことごとく否定。 2015年の重力波検出、2017年の中性子星合体観測：一般相対性理論を驚異的に検証。 2022年の量子もつれ実験（量子力学のノーベル賞）：量子理論の正しさを示し、“量子力学のその先”の理論に打撃。...
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion
Citation: Gu C, Takada S, Brandani GB, Terakawa T (2025) Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. PLoS Comput Biol 21(4): e1012493. https://doi.org/10.1371/journal.pcbi.1012493 Editor: Benjamin Hall, UCL: University College London, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND Received: September 13, 2024; Accepted: February 19, 2025; Published: April 4, 2025 Copyright: © 2025 Gu et al.
Molecular mechanism of parental H3/H4 recycling at a replication fork - Nature Communications
Abstract In chromatin replication, faithful recycling of histones from parental DNA to replicated strands is essential for maintaining epigenetic information across generations. A previous experiment has revealed that disrupting interactions between the N-terminal tail of Mcm2, a subunit in DNA replication machinery, and a histone H3/H4 tetramer perturb the recycling.
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion
Abstract The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL.
Corrigendum: Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination
This extract was created in the absence of an abstract. Genes & Development 33: 1191–1207 (2019) In the above-mentioned article, …
SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path
Abstract SMC (structural maintenance of chromosomes) protein complexes are ring-shaped molecular motors essential for genome folding. Despite recent progress, the detailed molecular mechanism of DNA translocation in concert with the ATP-driven conformational changes of the complex remains to be clarified. In this study, we elucidated the mechanisms of SMC action on DNA using multiscale molecular dynamics simulations.
Nucleosome crowding in chromatin slows the diffusion but can promote target search of proteins
Abstract Dynamics of nuclear proteins in crowded chromatin has only been poorly understood. Here, we address the diffusion, the target search, and structural dynamics of three proteins in a model chromatin using coarse-grained molecular simulations run on the K computer.
The condensin complex is a mechanochemical motor that translocates along DNA
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The condensin complex is a mechanochemical motor that translocates along DNA
Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. Here, we use single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of ATP hydrolysis-dependent translocation along double-stranded DNA.
Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
Protein binding to DNA changes the DNA’s structure, and altered DNA structure can, in turn, modulate the dynamics of protein binding. This mutual dependency is poorly understood. Here we investigated dynamic couplings among protein binding to DNA, protein sliding on DNA, and DNA bending by applying a coarse-grained simulation method to the bacterial architectural protein HU and 14 other DNA-binding proteins.
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