Molecular mechanisms on interactions between oxygen co-ordinated metal polyhedra and biochemical compounds

Abstract

Information is presented on the structural and functional properties of phosphates in "biochemical systems. Phosphates follow four structural formation principles: (1) linkage of phosphate units via oxygen co-ordinated metal ion polyhedra, (2) establishment of chains, (3) cross linkages of chains resulting in corrugated layers, and (4) cross linkages of layers resulting in distinct three-dimensional molecular networks. One Iinkage type does not require nor exclude another Iinkage type. On the basis of this concept on the associations of phosphate tetrahedra and metal ion oxygen polyhedra, a revised molecular model for DNA is proposed. Metal ion oxygen polyhedra excercise control on the shape of the DNA, and thus may introduce the stretching of the polymer chains This can be considered the ultimate reason why a single stranded DNA will associate itself readily with another single stranded DNA resulting in a double helix. In contrast, the coupling of a single stranded DNA by itself in making a sharp bend (loop) will not take place due to the stabilization of the structure by means of the metal ion oxygen polyhedra backbone. This model also explains thefunctional properties of the nucleic acids, for instance, the oxide chains and layers will favor proton jumps, and in the presence of a differential potential, they will form proton conduction bands. The molecular organization, as introduced by the association of metal ion coordination polyhedra with the PO4 groups, plays also a significant role in membrane dynamics. Analogous to the ion co-ordination interactions of polyphosphoric acids, the fixation of metal ions at the P-O surface and of membranes will result in a distinct molecular geometry as a whole. In this way, the membranes will act as dynamic molecular sieves, whereby the mesh size and the functional characteristics of these molecular sieves is determined by the flexible interplay of metals and the individual phospholipid compounds contained in the membranes. TP (111-P) is characterized for its ability to form a co-ordination polyhedron with polyvalent cations. In this way it resembles polyphosphates and differs from 1-P and 11-P. Triphosphate exhibits two significant properties: (1) terminal chain degradation, i.e. the release of terminal PO4 groups and formation of PO3 radicals which is controlled by external electrical forces,and (2) affinity to all cations by means of metal ion oxygen polyhedra and the establishment of an exchange affinity series for all metal ions. Concerning the biosynthesis of polysaccharides, proteins, and the nucleic acids, three conditions have to be fulfilled;. (1) acitvation of the react ion partner, (2) maximum efficiency and minimum error, and (3) well-defined control of the reactions in terms of kinetics and transportation mechanism. All three requirements are most effectively executed by triphosphates. The controlled formation of the reactive P03 radicaI not only activates the reaction partner, but also eliminates by means of the phosphate formation, the OH and O groups from the reaction system and this with extraordinary efficiency and elegance. In biochemical reactions, this role is commonly exercised by ATP.