A brief review is made of empirical methods for prediction of three aspects of protein conformation: (i) secondary structures, (ii) packing of secondary structures and (iii) surface and interior of globular proteins. The physical assumptions implicit in these empirical methods are analyzed. To explain the effectiveness of these empirical methods, "a consistency principle" is proposed which asserts that the various conformational energy terms contributing to the stability of native conformations are consistent with each other and therefore individually consistent with the native conformations. The low resolving power of the short-range interactions necessitates a prediction algorithm with a feedback mechanism by which the long-range interactions are involved in the determination of local structures. Such an algorithm should appear to simulate a folding process in which the intrinsic instability of small local structures serves as a built-in mechanism to overcome the low resolving power of the short-range interactions.
Proteins from thermophiles have higher thermostability than homologus proteins from mesophiles. This higher thermostability is an intrinsic property which must depend on the sequence of amino acid residues. The thermostability of thermostable proteins is due to additive hydrophobic interactions, hydrogen bonding, ionic interactions or a combination of these factors. To elucidate the role of individual amino acid resideues in conformational stability, the stabilities of wild-type and mutant proteins differing by a single amino acid residue were compared. In the case of the tryptophan synthase α-subunit from E. coli., the conformational stability (ΔdG)of seven proteins with different substituents at the same position in the interior of the protein was found to be correlated with the hydrophobicity of the substituent amino acid residue. The differences in ΔdG among the wild-type and mutant proteins seemed to be caused mainly by the entropic factor, because enthalpy changes of the proteins were the same.
In the field of physiology, it has generally been Considered that changes in the phase boundary potential do not affect membrane potentials. The present review shows that the phase boundary potential directly contributes to the membrane potential of a number of cells. (1) The K+-channels of mouse neuroblastoma (N-18 cells) are open at high external K+-concentration but closed at low K+-concentration including the physiological one. Under physiological conditions, the resting membrane potentials of N-18 cells stem significantly from the phase boundary potentials. Theoretical consideration shows that changes in the phase boundary potentials directly affect the membrane potential when no selective channels are open. (2) Changes in the phase boundary potential also contribute to the receptor potentials in taste cells, olfactory cells and Tetrahymena as well as to the resting potentials of these cells: adsorption of chemical stimuli on the receptor membranes of these cells induces changes in the phase boundary potential, which leads to depolarization of the cells.