Intermolecular interactions-From some general features to conformational autocatalysis

摘要

The intermolecular interaction is ubiquitous and influences the results of virtually every chemical or physical experiment. There are some important questions left in the theory of intermolecular interaction. One of such questions is: what kind of objects do interact. In the article, we recall a kind of unusual symmetry requirement in a physical theory related to this question. Also, we introduce a gradation of such choices of the interacting subsystems leading eventually to the concept of the most natural choice. Electrostatics plays a special role in the intermolecular interaction. We discuss why electrostatics remains important even if other interactions are strong. Next, the electrostatic interactions are shown to be important in the three-dimensional (3D) structure of proteins occurring in Nature. Predicting the molecule's lowest-energy conformation or configuration represents a formidable task. There were many attempts to solve this problem for protein molecules, for which it is believed their native conformation corresponds to the lowest free energy. The challenge to find this conformation from a given sequence of amino acids (AAs) is known as a "second genetic code." In fact all of these attempts are based on some smoothing of the energy landscape. In the article, some of these smoothing techniques are described, which finally turned out to be highly successful in finding native structures of globular proteins. When discussing the contributions to the conformational energy the importance of the electrostatic interactions has been stressed. In particular, it turned out that the dipole moments of the NH and of the CO bonds in proteins functioning in nature are oriented to good accuracy along the local intramolecular electric field. Thanks to an enormous effort of the protein folding community it is possible to predict the native 3D structure of globular proteins. It is also possible to design such AA sequences, which fold to the desired protein 3D structure. A certain reliable theoretical technique of protein folding has been used to study a possibility of conformational autocatalysis. It turned out that such an effect has been predicted for a small protein of 32 AAs, with carefully designed AA sequence. This may be seen as a model of the prion disease propagation.