Synopsis: Protein diffusion

The shapes of “binding proteins” contribute to the ease with which they can diffuse along DNA until they reach a specific sequence.
Synopsis figure
Illustration: Alan Stonebraker

Proteins that selectively bind to DNA play an active part in regulating transcription and separating double stranded DNA into single strands.

The binding protein finds its attachment point—a sequence of specific nucleotides—by a process of diffusing in the volume around the DNA and along the DNA strand itself. However, the ease with which the protein diffuses along the DNA until it finds the right sequence is surprising, given that the positively charged proteins should be attracted to the typically negatively charged DNA at any site along the strand.

Writing in Physical Review Letters, Vincent Dahirel and colleagues at Université Paris 6, France, demonstrate with simulations how geometry—namely, the relative shapes of the DNA and binding protein—affects the electrostatic force between the two molecules and the ease with which the protein can diffuse.

Dahirel et al. model the DNA as a solid cylinder and the protein as a variety of solid shapes with different curvatures: a sphere, a cylinder, and a cylinder or square block with a concave “nook.” Both molecules are assumed to be in an ionic solution.

What the group finds is that when the protein surface compliments that of the DNA, that is, it is convex with a similar curvature, there is a repulsive electrostatic force between the molecules at very short distances. The finding provides an explanation that reconciles the site specificity of the protein with its ability to diffuse easily: the protein is attracted to the vicinity of the DNA, but doesn’t adhere until it reaches the site with the right sequence, where hydrogen bonds overcome the short-range repulsive force. – Jessica Thomas


More Features »


More Announcements »

Subject Areas

Biological Physics

Previous Synopsis


Height matters

Read More »

Next Synopsis

Related Articles

Focus: Membrane Holes Can Shrink, Grow, or Stay Put
Soft Matter

Focus: Membrane Holes Can Shrink, Grow, or Stay Put

Pores in a polymer film do not change size over time if they have just the right diameter, according to experiments. Read More »

Focus: How Cells Remember Who They Are
Biological Physics

Focus: How Cells Remember Who They Are

A theoretical model of chromosome strands as polymers explains why chemical markers on genes can survive from one cell generation to the next. Read More »

Synopsis: Flocks Without Memory
Biological Physics

Synopsis: Flocks Without Memory

Moving particles with no memory can group together in complex flock configurations using only instantaneous cues.   Read More »

More Articles