Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

(2020) Toru Niina et al.   Journal of Chemical Theory and Computation

DNA-loop extruding condensin complexes can traverse one another

(2020) Eugene Kim et al.   NATURE

Cryo-EM structure of the human cohesin-NIPBL-DNA complex

(2020) Zhubing Shi et al.   SCIENCE

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism

(2020) Byung-Gil Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The condensin holocomplex cycles dynamically between open and collapsed states

(2020) Je-Kyung Ryu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Generalized Born Implicit Solvent Models for Biomolecules

(2019) Alexey V. Onufriev et al.   Annual Review of Biophysics

Structural Basis of an Asymmetric Condensin ATPase Cycle

(2019) Markus Hassler et al.   MOLECULAR CELL

Transient DNA Occupancy of the SMC Interarm Space in Prokaryotic Condensin

(2019) Roberto Vazquez Nunez et al.   MOLECULAR CELL

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

(2019) John F Marko et al.   NUCLEIC ACIDS RESEARCH

Mitotic Chromosome Mechanics: How Cells Segregate Their Genome

(2019) Paul Batty et al.   TRENDS IN CELL BIOLOGY

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Braiding topology and the energy landscape of chromosome organization proteins

(2019) Dana Krepel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes

(2018) Masahiro Shimizu et al.   Journal of Chemical Theory and Computation

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Towards a Unified Model of SMC Complex Function

(2018) Markus Hassler et al.   CURRENT BIOLOGY

Deciphering the structure of the condensin protein complex

(2018) Dana Krepel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization

(2017) Marie-Laure Diebold-Durand et al.   MOLECULAR CELL

The condensin complex is a mechanochemical motor that translocates along DNA

(2017) Tsuyoshi Terakawa et al.   SCIENCE

Overall Shapes of the SMC-ScpAB Complex Are Determined by Balance between Constraint and Relaxation of Its Structural Parts

(2017) Katsuhiko Kamada et al.   STRUCTURE

Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic

(2016) Jorine M. Eeftens et al.   Cell Reports

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

(2015) Shoji Takada et al.   ACCOUNTS OF CHEMICAL RESEARCH

Structural Basis for Dimer Formation of Human Condensin Structural Maintenance of Chromosome Proteins and Its Implications for Single-stranded DNA Recognition

(2015) Susumu Uchiyama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding

(2015) Young-Min Soh et al.   MOLECULAR CELL

Reconstitution of mitotic chromatids with a minimum set of purified factors

(2015) Keishi Shintomi et al.   NATURE CELL BIOLOGY

Coarse-grained modeling of DNA curvature

(2014) Gordon S. Freeman et al.   JOURNAL OF CHEMICAL PHYSICS

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

(2014) Tsuyoshi Terakawa et al.   Journal of Chemical Theory and Computation

Weak Frustration Regulates Sliding and Binding Kinetics on Rugged Protein–DNA Landscapes

(2013) Amir Marcovitz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

(2012) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Frustration in protein-DNA binding influences conformational switching and target search kinetics

(2011) A. Marcovitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Video imaging of walking myosin V by high-speed atomic force microscopy

(2010) Noriyuki Kodera et al.   NATURE

Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins

(2010) Julia J. Griese et al.   NUCLEIC ACIDS RESEARCH

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

(2010) P. L. Privalov et al.   NUCLEIC ACIDS RESEARCH

Structure and DNA-binding activity of the Pyrococcus furiosus SMC protein hinge domain

(2010) Julia J. Griese et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS