Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

D Chowdhury - Physics Reports, 2013 - Elsevier
A molecular motor is made of either a single macromolecule or a macromolecular complex.
Just like their macroscopic counterparts, molecular motors “transduce” input energy into …

Statics and dynamics of strongly charged soft matter

H Boroudjerdi, YW Kim, A Naji, RR Netz… - Physics reports, 2005 - Elsevier
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged.
This makes them water soluble, which is of great importance in technological application …

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

CA Brackley, S Taylor, A Papantonis… - Proceedings of the …, 2013 - National Acad Sciences
Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and
dissociate; in the absence of any explicit interaction between proteins, or between …

The physics of chromatin

H Schiessel - Journal of Physics: Condensed Matter, 2003 - iopscience.iop.org
Recent progress has been made in the understanding of the physical properties of
chromatin—the dense complex of DNA and histone proteins that occupies the nuclei of plant …

Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme

I Whitehouse, C Stockdale, A Flaus… - … and cellular biology, 2003 - Taylor & Francis
The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-
remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal …

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

VB Teif, K Rippe - Nucleic acids research, 2009 - academic.oup.com
Nucleosome positions on the DNA are determined by the intrinsic affinities of histone
proteins to a given DNA sequence and by the ATP-dependent activities of chromatin …

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

A Arneodo, C Vaillant, B Audit, F Argoul… - Physics Reports, 2011 - Elsevier
Understanding how chromatin is spatially and dynamically organized in the nucleus of
eukaryotic cells and how this affects genome functions is one of the main challenges of cell …

Nucleosome dynamics: sequence matters

B Eslami-Mossallam, H Schiessel… - Advances in colloid and …, 2016 - Elsevier
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming
nucleosomes. Even though the histone proteins that make up the core of nucleosomes are …

Dynamic properties of nucleosomes during thermal and ATP-driven mobilization

A Flaus, T Owen-Hughes - Molecular and cellular biology, 2003 - Taylor & Francis
The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move
along DNA via either thermal or enzyme-driven movements. Here we have monitored the …

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

T Niina, GB Brandani, C Tan… - PLoS computational …, 2017 - journals.plos.org
While nucleosome positioning on eukaryotic genome play important roles for genetic
regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not …