Chapter 1 The geometry of molecules: Basic principles and nomenclatures

Establishment of order in the flow of genetic information in cells

The activities related to the flow of genetic information encoded in DNA in a cell are very orderly. This order, in a living cell, is achieved through specific, but noncovalent, interactions of varieties of structurally dynamic macromolecules under constantly changing physiological conditions. Hence, it is expected that there should be some force that can stabilize the multicomponent reaction processes and establish (or maintain) order in genetic regulatory functions under far-from-equilibrium conditions. The genetic regulatory functions in a cell, however, are believed to be energetically coupled. Expression of genes in a cell is often modulated under changing environmental conditions, raising the possibility of a state controlled nature of the genetic regulatory functions. Adenosine triphosphate (ATP) is the major free-energy contributor for these energy-consuming cellular activities. Enzymatic transfer of high-energy phosphate group from ATP to other reactive components is considered to be the chief mode of energy-transduction in a cell for various biosynthetic processes, as well as other activities related to the flow of information. In an effort to find a solution of the paradox, we assessed the contribution of physiological state of a cell in the process of maintaining order in genetic regulatory functions. As an approach, we systematically perturbed the normal energy flow of a cellular system (bovine aortic endothelial [BAE] cell) by a protein kinase inhibitor (staurosporine), and then followed the expression patterns of several constitutively-expressed protein-encoding genes to measure the effects. Staurosporine, as a function of its concentration, disintegrated the membrane structure of these cells, and eventually caused their death. These secondary consequences of staurosporine treatment offered two additional grossly altered physiological states of the cell to study. Under all of these dramatically altered energy states of the system, an extreme degree of functional coherence prevailed at every level of genetic regulatory function. Integrity at the level of gene transcription remained unaffected. Degradation rate of specific mRNA remained unaltered. Translational activities involving varieties of mRNA species continued in an well-ordered manner. Other state changes, resulting from nutrient and metabolic starvation, or inhibition of oxidative phosphorylation, in addition to the staurosporine treatments, also failed to disintegrate these ordered activities. The steady-state levels of specific mRNA underwent certain changes in these conditions, however, without maintaining any proportional relationships with the staurosporine concentrations applied or the ATP levels in the cell. These results thus led us to propose that the internal energy or a certain intrinsic property of the participating components, rather than the physiological state of the cell, acts as the dominant force in maintaining order and stability of genetic regulatory functions in a cell. Kinetic analyses under different energy states of the cell also supported the hypothesis, and further demonstrated the autoregulatory nature of the genetic order establishment. All of these results suggest a process of molecular self-organization as the fundamental principle for genetic regulation in a cellular system.

The concept of molecular structure in structure-activity relationship studies and drug design

We can justify the use of any model, method, or algorithm if we clearly state our goals, understand the basis of our procedures, and fully appreciate the true nature and limitations of the results. As we have illustrated here, the creation of new wisdom may appear to be a consequence of our labors. There are cases, however, where this creation may be only an illusion. In any analysis of structure-activity, property-activity, or structure-property relationships, the degree of understanding of the nature of the starting data therefore determines the level of confidence ascribable to any result and prediction. This is, in essence, the message of our inquisitive meditations on the deep nature of structure-activity relationships.