Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models

How hydrophobic drying forces impact the kinetics of molecular recognition

(2013) J. Mondal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

(2012) Tadashi Ando et al.   JOURNAL OF CHEMICAL PHYSICS

Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse?

(2012) Jingyuan Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains

(2012) Tsuyoshi Terakawa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Dancing on DNA: Kinetic Aspects of Search Processes on DNA

(2011) Anahita Tafvizi et al.   CHEMPHYSCHEM

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

(2011) Joseph A. Morrone et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

(2010) Tamara Frembgen-Kesner et al.   BIOPHYSICAL JOURNAL

Hydrodynamic effects in proteins

(2010) Piotr Szymczak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

An end to 40 years of mistakes in DNA–protein association kinetics?

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

(2009) Tamara Frembgen-Kesner et al.   Journal of Chemical Theory and Computation

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Nonspecifically bound proteins spin while diffusing along DNA

(2009) Paul C Blainey et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nanoscale Forces and Their Uses in Self-Assembly

(2009) Kyle J. M. Bishop et al.   Small

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

Protein Sliding along DNA: Dynamics and Structural Characterization

(2008) Ohad Givaty et al.   JOURNAL OF MOLECULAR BIOLOGY

Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA†

(2008) Biman Bagchi et al.   JOURNAL OF PHYSICAL CHEMISTRY B