http://www.bio21.bas.bg/ibf/PC_review.pdf

Phases and phase transitions of the phosphatidylcholines

The DNA in sperm and certain viruses is condensed by arginine-rich proteins into toroidal subunits, a form of packaging that inactivates their entire genome. Individual DNA molecules were manipulated with an optical trap to examine the kinetics of torus formation induced by the binding of protamine and a subset of its DNA binding domain, Arg6. Condensation and decondensation experiments with λ-phage DNA show that toroid formation and stability are influenced by the number of arginine-rich anchoring domains in protamine. The results explain why protamines contain so much arginine and suggest that these proteins must be actively removed from sperm chromatin after fertilization.

https://zenodo.org/record/1231163/files/article.pdf

Protamine-Induced Condensation and Decondensation of the Same DNA Molecule

The kinetics of protein-nucleic acid interactions are discussed with particular emphasis on the effects of salt concentration and valence on the observed rate constants. A general review is given of the use of experimentally determined salt dependences of observed kinetic parameters as a tool to probe the mechanism of interaction. Quantitative analysis of these salt dependences, through the application of polyelectrolyte theory, can be used to distinguish reactions which occur in a single step from those reactions which involve distinct intermediates. For those rate constants which display a large salt dependence, in either the association or dissociation reaction, this is due to the high concentration of counterions (e.g., Na+) in the vicinity of the nucleic acid which are subsequently released (or bound in the case of dissociation) at some point before the rate limiting step of the reaction. A general discussion of other features which affect protein-nucleic acid kinetics, such as nucleic acid length and the ratio of nonspecific to specific DNA binding sites (in the case of sequence specific binding proteins), is also given. The available data on the nucleic acid binding kinetics of small ligands (ions, dyes, oligopeptides), nonspecific binding proteins (T4 gene 32 protein, fd gene 5 and Escherichia coli SSB), and sequence specific binding proteins (lac repressor, RNA polymerase, Eco RI restriction endonuclease) are discussed with emphasis on the interpretation of the experimentally determined salt dependences.

Kinetics of protein-nucleic acid interactions: use of salt effects to probe mechanisms of interaction.

Many biologically important proteins bind nonspecifically, and often cooperatively, to single-or double-stranded nucleic acid lattices in discharging their physiological functions. This binding can generally be described in thermodynamic terms by three parameters: n, the binding site size; K, the intrinsic binding constant; omega, the binding cooperativity parameter. The experimental determination of these parameters often appears to be straightforward but can be fraught with conceptual and methodological difficulties that may not be readily apparent. In this paper we describe and analyze a number of approaches that can be used to measure these protein-nucleic acid interaction parameters and illustrate these methods with experiments on the binding of T4-coded gene 32 (single-stranded DNA binding) protein to various nucleic acid lattices. We consider the following procedures: (i) the titration of a fixed amount of lattice (nucleic acid) with added ligand (protein); (ii) the titration of a fixed amount of ligand with added lattice; (iii) the determination of ligand binding affinities at very low levels of lattice saturation; (iv) the analysis of ligand cluster size distribution on the lattice; (v) the analysis of ligand binding to lattices of finite length. The applicability and limitations of each approach are considered and discussed, and potential pitfalls are explicitly pointed out.

Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: experimental approaches to the determination of thermodynamic parameters.

Salt-dependent changes in the DNA binding co-operativity of Escherichia coli single strand binding protein

Thermodynamics and kinetics of co-operative protein-nucleic acid binding: I. General aspects of analysis of data

Kinetic investigations on the phase transition of phospholipid bilayers.

labelled histone H1 . The titration data were analysed in terms of the large ligand model. The stoichiometric number, n = 65 ± 10 bases/Hi, was independent of NaCl concentration (0.02 - 0.35 M). The nucleation and the co- ~ operative binding constants, K' and K, and the cooperativity parameter q were # sensitive to salt concentration; K = 3.6 + 0.8 x 107 M~1 and q = 1.1 ± 0.4 x 103 at 0.2 M NaCl. The dependence of K' on NaCl concentration revealed that »* 6 Na+ ions were released from DNA upon complex formation. An extrapolation of K' to 1M NaCl yielded a small value, K1 = 5 + 2 M"1. Thus the binding of H1 i is essentially electrostatic, being compatible with its independence of tem- perature. A calculation of K' based on the counterion release reproduced the salt concentration dependence of K'. Therefore, the binding of H1 is of an electrostatic territorial type. Thus, H1 may move along the DNA chain to a ~X certain extent, when both salt concentration and the degree of saturation are sufficiently low. The condition is so restricted that the sliding would not •r play an important role ^ii vivo. It was concluded from the DNA concentration independent binding isotherm that H1 can cooperatively bind onto a single DNA ** molecule. A simple power law dependence of the cooperativity parameter q upon NaCl concentration was found; qoc(NaCl)h with h = 0.72, though the physical basis of this dependence remains unknown.

Cooperative interaction of histone H1 with DNA.

Thermodynamics and kinetics of co-operative protein-nucleic acid binding: II. Studies on the binding between protamine and calf thymus DNA

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2884%2981360-5

Fumiyuki Watanabe

Papers

Thermodynamics and kinetics of co-operative protein-nucleic acid binding: I. General aspects of analysis of data

Kinetic investigations on the phase transition of phospholipid bilayers.

Cooperative interaction of histone H1 with DNA.

Thermodynamics and kinetics of co-operative protein-nucleic acid binding: II. Studies on the binding between protamine and calf thymus DNA

Condensation of polynucleosome by histone H1 binding.