Mechanical and geometrical properties of three-dimensional structures of long biological macromolecules

Projektinformationen

ID Finanzhilfevereinbarung: INTAS-94-0643

Projekt abgeschlossen

Startdatum 1 Mai 1995

Enddatum 31 Oktober 1997

Finanziert unter

• International Association for the promotion of cooperation with scientists from the independent states of the former Soviet Union (INTAS), 1993-

Gesamtkosten € 0,00

EU-Beitrag € 33 980,00

Koordiniert durch

Technische Universität Wien
Austria

Exploitable results

Properties of three-dimensional structures of long biological macromolecules

The project studied the cord-like objects of molecular biology: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) macromolecules. The three-dimensional shapes of nucleic acids were investigated by employing a model of a thin, linearly elastic rod. An equilibrium configuration of such a rod, submitted to external forces and moments at its end only, obeys equations identical to those governing the rotation of a gyrostat spinning about a fixed point in a gravitational field (the Kirchloff analogy). It is known that DNA molecules often exist in their closed form with the ends of each strand joined together. The linking number may be changed under the action of specific enzymes called topoisomerases. The closed molecules with different linking numbers can take different shapes in the three-dimensional space. Various complex shapes bifurcate from the flat circular ring. The stability analysis of such a ring was carried out. The condition for supercoiling instability was obtained for a rod with non-circular cross section and with large twisting rate. The continuous rod model was applied to a problem of reconstruction of spatial structure of an RNA molecule. A numerical procedure was developed for computation of 3-dimensional conformations of loops. This was carried out by solving the corresponding boundary value problem. The approach developed is usable for identification of effective elastic coefficients and average characteristics of the relaxed RNA chain by using known free energy data. Several whole molecules of RNA were assembled and their three dimensional structures were obtained. The comparison of their shapes with the available results of X-ray analysis reveals a good correspondence. The model may catch the biologically important features of the conformation. It may also serve as an initial approximation to start a much more time consuming procedure of the shape computation at the base or atomic level.