Herein we report that the 18-base telomeric oligodeoxynucleotides (ODNs) designed from the Lactobacillus rhamnosus GG genome promote differentiation of skeletal muscle myoblasts which are myogenic precursor cells. We termed these myogenetic ODNs (myoDNs). The activity of one of the myoDNs, iSN04, was independent of Toll-like receptors, but dependent on its conformational state. Molecular simulation and iSN04 mutants revealed stacking of the 13–15th guanines as a core structure for iSN04. The alkaloid berberine bound to the guanine stack and enhanced iSN04 activity, probably by stabilizing and optimizing iSN04 conformation. We further identified nucleolin as an iSN04-binding protein. Results showed that iSN04 antagonizes nucleolin, increases the levels of p53 protein translationally suppressed by nucleolin, and eventually induces myotube formation by modulating the expression of genes involved in myogenic differentiation and cell cycle arrest. This study shows that bacterial-derived myoDNs serve as aptamers and are potential nucleic acid drugs directly targeting myoblasts.

Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest freeenergy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature.

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