The Snake Cube Puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of folding of proteins into their sequence-specific native three-dimensional structures. The problem of protein folding is reviewed very briefly by comparing it with the problem of genetic code. It is stressed that the folding process is basically a physical phenomenon. The consistency principle advocated nearly 40 years ago to explain the folding mechanism is briefly reviewed. The result obtained by using the models provides a semi-quantitative manifestation of the consistency principle.
Cl–-pump rhodopsin is the second discovered microbial rhodopsin and functions as light-driven Cl– pump. The physiological significance of the Cl– pump has not been fully resolved. However, its functional mechanism has been studied as a model system of anion transporters. In this review, the variation and functional mechanisms of Cl–-pump rhodopsins were summarized. After 2014, novel Cl–-pump groups were discovered in marine and terrestrial bacteria and were revealed to have unique characteristics. The most recently identified protein has close similarity with the H+-pump rhodopsin and begins to pump H+ outwardly by only a single amino acid replacement.
Ciliates are microorganisms found in water environments that feed by accumulating close to solid-liquid interfaces such as pond bottom and waterweed surface. The ability of swimming ciliates to remain near surfaces is crucial for efficient nutrient acquisition. Here, we investigated the dynamics of the near-surface swimming behavior. In our experiments, the cilia of these ciliates lost their propelling activity when encountering a surface, suggesting they have a mechano-sensing system, and the ciliate slid along the surface. Our simulations revealed that not only the loss of ciliary activity but also the cell body aspect ratio was critical for this sliding motion.