Activation of tubulin assembly into microtubules upon a series of repeated femtosecond laser impulses

Computational Investigation of the Ordered Water System Around Microtubules: Implications for Protein Interactions

The existence of an exclusion zone in which particles of a colloidal suspension in water are repelled from hydrophilic surfaces has been experimentally demonstrated in numerous studies, especially in the case of Nafion surfaces. Various explanations have been proposed for the origin of this phenomenon, which is not completely understood yet. In particular, the existence of a fourth phase of water has been proposed by G. Pollack and if this theory is proven correct, its implications on our understanding of the properties of water, especially in biological systems, would be profound and could give rise to new medical therapies. Here, a simple approach based on the linearized Poisson-Boltzmann equation is developed in order to study the repulsive forces mediated by ordered water and involving the following interacting biomolecules: 1) microtubule and a tubulin dimer, 2) two tubulin dimers and 3) a tubulin sheet and a tubulin dimer. The choice of microtubules in this study is motivated because they could be a good candidate for the generation of an exclusion zone in the cell and these models could be a starting point for detailed experimental investigations of this phenomenon.

Integration of intracellular signaling: Biological analogues of wires, processors and memories organized by a centrosome 3D reference system

BACKGROUND

Myriads of signaling pathways in a single cell function to achieve the highest spatio-temporal integration. Data are accumulating on the role of electromechanical soliton-like waves in signal transduction processes. Theoretical studies strongly suggest feasibility of both classical and quantum computing involving microtubules.

AIM

A theoretical study of the role of the complex composed of the plasma membrane and the microtubule-based cytoskeleton as a system that transmits, stores and processes information.

METHODS

Theoretical analysis presented here refers to (i) the Penrose-Hameroff theory of consciousness (Orchestrated Objective Reduction; Orch OR), (ii) the description of the centrosome as a reference system for construction of the 3D map of the cell proposed by Regolini, (iii) the Heimburg-Jackson model of the nerve pulse propagation along axons' lipid bilayer as soliton-like electro-mechanical waves.

RESULTS AND CONCLUSION

The ideas presented in this paper provide a qualitative model for the decision-making processes in a living cell undergoing a differentiation process.

OUTLOOK

This paper paves the way for the real-time live-cell observation of information processing by microtubule-based cytoskeleton and cell fate decision making.

New horizons of adenosinetriphosphate energetics arising from interaction with magnesium cofactor

MD DFT:B3LYP (6-31G** basis set, T = 310 K) method is used to study interactions [singlet (S) and triplet (T) reaction paths] between adenosinetriphosphate, ATP(4-), and [Mg(H(2)O)(6)](2+) in water environment, modeled with 78 water molecules. Computations reveal the appearance of low and high-energy states (stable, quasi-stable, and unstable), assigned to different spin symmetries. At the initial stage of interaction, ATP donates a part of its negative charge to the Mg complex making the Mg slightly charged. As a result, the original octahedral Mg complex loses two (S state) or four (T state) water molecules. Moving along S or T potential energy surfaces (PESs), Mg(H(2)O)(4 )or Mg(H(2)O)(2) display different ways of complexation with ATP. S path favors the formation of a stable chelate with the O1-O2 fragment of ATP triphosphate tail, whereas T path favors producing a single-bonded complex with the O2. The latter, being unstable, undergoes a further conversion into a spin-separated complex, also unstable, and two metastable S complexes, which finally arise in two stable, low-energy and high-energy, chelates. The spin-separated complex experiences rapid decomposition resulting in the production of a highly reactive adenosinemonophosphate ion-radical *AMP, early observed in the CIDNP experiment (Tulub 2006). Biological consequences of the findings are discussed.

Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail

A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.