DNA Replication and Cell Cycle Progression Regulatedby Long Range Interaction between Protein Complexes bound to DNA

Long Range Force between Pre-Replication Complexes (Pre-RC) in DNA Controls Replication and Cell Cycle Progression

A nonstationary interaction, that controls DNA replication and the cell cycle, is derived from a manybody physics model in a chemically open T cell. The model predicts a long range force F'(ξ)=-(κ/2) ξ(1-ξ)(2-ξ) between the pre-replication complexes (pre-RCs) bound by DNA, ξ=ϕ/N being the relative displacement of preRCs, ϕ the number of pre-RCs, N the threshold for initiation, and κ the compressibility modulus in thelattice of pre-RCs which behaves like an elastically braced string. Initiation of DNA replication is induced by a switch of sign of F'(ξ), from attraction (-)and assembly in the G(1) phase (0 < ϕ < N), to repulsion (+) and partialdisassembly in the S phase (N < ϕ < 2N), with release of licensing factors from the pre-RCs, thus explaining prevention of re-replication. Replication is terminated by a switch of sign of F at ϕ = 2N, when all primed replicons are duplicated once, and F(0)=0 corresponds to a resting cell in absence of driving force at ϕ = 0. The switch of sign of force at ϕ = N also explains the dynamic instability in growing microtubules (MTs), as well as switch in the interleukin-2 (IL2) interaction with its receptor in late G(1), at the restriction point. Shape, slope and scale of the response curves derived agree well with experimental data from dividing T cells and polymerizing MTs, the variable length of which is due to anonlinear dependence of the growth amplitude on the initial concentrations of tubulin dimers and guanosine-tri-phosphate (GTP).

Lyotropic ion channel current model compared with ising model

Trans-membrane currents in ligand-gated ion channels are calculated in a non-equilibrium, chemically open whole cell system. The model is lyotropic in the sense that dynamics and parameters such as ligand concentration for half-maximal response (scale of response), and threshold for firing in neurons, are nonlinear functions of the reactant concentrations. The derived total current fits recorded data significantly better than those derived from mass action, Ising, and other equilibrium type models, in which the derived response can be displaced from the assessed response by several orders in the ligand concentration. A comparison of the model obtained with an Ising-like model provides a methodology to obtain the non-equilibrium scaling dependence of Ising-like models on the reactant concentrations.

Monte Carlo simulation for statistical mechanics model of ion-channel cooperativity in cell membranes

Voltage-gated ion channels are key molecules for the generation and propagation of electrical signals in excitable cell membranes. The voltage-dependent switching of these channels between conducting and nonconducting states is a major factor in controlling the transmembrane voltage. In this study, a statistical mechanics model of these molecules has been discussed on the basis of a two-dimensional spin model. A new Hamiltonian and a new Monte Carlo simulation algorithm are introduced to simulate such a model. It was shown that the results well match the experimental data obtained from batrachotoxin-modified sodium channels in the squid giant axon using the cut-open axon technique.

Model of DNA dynamics and replication

Before DNA replication can be initiated a definite number of adenosine triphosphate (ATP) containing pre-replication protein complexes (pre-RCs) must be assembled and bound to DNA like in a super-critical mass. A chemically driven dynamics of the Ginzburg-Landau (GL) type is derived, using the non-equilibrium equation for binding of pre-RCs to DNA and a probabilistic conformational distribution of these protein complexes. This dynamics, in which the DNA-protein system behaves like a nonlinear elastically braced string (NEBS), can control the cell cycle via conformational transitions such that G(2) cells contain exactly twice as much DNA as G(1) cells. After adjustment of previously-made derivations, the model is compared with cell growth data from the T lymphocyte MLA-144.

Dynamic simulation of active/inactive chromatin domains

In the present study a model for the compactification of the 30 nm chromatin fibre into higher order structures is suggested. The idea is that basically every condensing agent (HMG/SAR, HP1, cohesin, condensin, DNA-DNA interaction …) can be modeled as an effective attractive potential of specific chain segments. This way the formation of individual 1 Mbp sized rosettes from a linear chain could be observed. We analyse how the size of these rosettes depends on the number of attractive segments and on the segment length. It turns out that 8-20 attractive segments per 1 Mbp domain produces rosettes of 300-800 nm in diameter. Furthermore, our results show that the size of the rosettes is relatively insensitive to the segment length.

Ligand-gated ion channel currents in a nonstationary lyotropic model

Transmembrane currents in ligand-gated ion channels are calculated in a nonstationary, chemically open whole cell system or patch of a membrane. The model is lyotropic in the sense that dynamics, and parameters such as the ligand concentration for half-maximal response (scale of response), and threshold for firing, such as in neurons, become nonlinear functions of the reactant concentrations. The derived total currents fit recorded data significantly better than those derived from mass action, Ising, and other stationary type models, in which the derived response is often displaced from the assessed response by several orders in the ligand concentration. Also, the derived slope of response is in perfect agreement with the values assessed.