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Biomedical subjects

R Bruinsma

Publications and source records attributed to R Bruinsma.

At least 19 recordsLinked to original sources
PubMed1999

DNA-protein cooperative binding through variable-range elastic coupling.

Cooperativity plays an important role in the action of proteins bound to DNA. A simple mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations, is proposed. These proteins are not in direct physical contact. DNA segments intercalating bound proteins are modeled as a worm-like chain, which is free to deform in two dimensions. The tension-controlled protein-protein interaction is the consequence of two effects produced by the protein binding. The first is the introduction of a bend in the host DNA and the second is the modification of the bending modulus of the DNA in the immediate vicinity of the bound protein. The interaction between two bound proteins may be either attractive or repulsive, depending on their relative orientation on the DNA. Applied tension controls both the strength and the range of protein-protein interactions in this model. Properties of the cooperative interaction are discussed, along with experimental implications.

Biophysical Phenomena↗
PubMed1998

Elasticity theory of the B-DNA to S-DNA transition.

We propose in this note a simple model--the two-state Worm Like Chain--to describe the elasticity of the recently discovered stress-induced transformation from B-DNA to S-DNA. The model reduces for low tractions to the well-known Worm Like chain theory, which is used to describe the elastic properties of B-DNA, while in the limit of high chain-bending moduli it reduces to the two-state Ising model proposed by Cluzel et al. for the B-S transition [Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J-L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794]. Our model can be treated analytically to produce an explicit form of the force-extension relationship which agrees reasonably with the observations. We use the model to show that conformational fluctuations of the chain play a role also for the B to S transformation.

DNA↗
PubMed1998

Motion of RNA polymerase along DNA: a stochastic model.

RNA polymerase is a key transcription enzyme that moves along a DNA double helix to polymerize an RNA transcript. Recent progress in micromechanical experiments permits quantitative studies of forces and motion generated by the enzyme. We present in this paper a chemical kinetics description of RNA polymerase motion. The model is based on a classical chemical kinetics description of polymerization reactions driven by a free energy gain that depends on forces applied externally at the catalytic site. The RNA polymerase controlled activation barrier of the reaction is assumed to be strongly dependent on inhibitory internal strains of the RNA polymerase molecule. The sequence sensitivity of RNA polymerase is described by a linear coupling between the height of the activation barrier and the local DNA sequence. Our model can simulate optical trap experiments and allows us to study the dynamics of chemically halted complexes that are important for footprinting studies. We find that the effective stall force is a sequence-dependent, statistical quantity, whose distribution depends on the observation time. The results are consistent with the experimental observations to date.

Base Sequence↗
PubMed1994

Self-assembly of membrane junctions.

We present a mechanism for the aggregation of mobile intermembrane junctions, such as the connexon dyad of gap junctions. The model demonstrates that intermembrane repulsion provides a powerful self-assembly pressure. If the membrane repulsion is strong enough to prevent membrane adhesion, then the self-assembly pressure is of effective infinite range.

Cell Communication↗