High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins

HMG1 and 2: architectural DNA-binding proteins.

HMG1 and 2 (high mobility group proteins 1 and 2; renamed HMGB1 and 2) contain two DNA-binding HMG-box domains (A and B) and a long acidic C-terminal domain. They bind DNA without sequence specificity, but have a high affinity for bent or distorted DNA, and bend linear DNA. The individual A and B boxes (which, although broadly similar, show both structural and functional differences) exhibit ma...

Facilitated diffusion of DNA-binding proteins.

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is...

Direct Visualization of Single-Molecule DNA-Binding Proteins Along DNA to Understand DNA–Protein Interactions

Minor groove-binding architectural proteins: structure, function, and DNA recognition.

To date, high-resolution structures have been solved for five different architectural proteins complexed to their DNA target sites. These include TATA-box-binding protein, integration host factor (IHF), high mobility group I(Y)[HMG I(Y)], and the HMG-box-containing proteins SRY and LEF-1. Each of these proteins interacts with DNA exclusively through minor groove contacts and alters DNA conforma...

Facilitated diffusion of DNA-binding proteins: Simulation of large systems.

The recently introduced method of excess collisions to estimate reaction times of protein-DNA systems in the presence of facilitated diffusion ("sliding") requires a cell of full system size. This bottleneck is avoided with a modification, by which a set of empirical parameters is calibrated using numerical simulations of a small test system. Once this is done, reaction times for systems of arb...