To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal peptide from p53 confirming its performance nearly equal to the original REST.

Molecular evolution based on mutagenesis is widely used in protein engineering. However, optimal proteins are often difficult to obtain due to a large sequence space. Here, we propose a novel approach that combines molecular evolution with machine learning. In this approach, we conduct two rounds of mutagenesis where an initial library of protein variants is used to train a machine-learning model to guide mutagenesis for the second-round library. This enables us to prepare a small library suited for screening experiments with high enrichment of functional proteins. We demonstrated a proof-of-concept of our approach by altering the reference green fluorescent protein (GFP) so that its fluorescence is changed into yellow. We successfully obtained a number of proteins showing yellow fluorescence, 12 of which had longer wavelengths than the reference yellow fluorescent protein (YFP). These results show the potential of our approach as a powerful method for directed evolution of fluorescent proteins.

early in vivo studies demonstrated the involvement of a tumor-suppressing transcription factor, p53, into cellular droplets such as Cajal and promyelocytic leukemia protein bodies, suggesting that the liquid-liquid phase separation (LLPS) might be involved in the cellular functions of p53. To examine this possibility, we conducted extensive investigations on the droplet formation of p53 in vitro. First, p53 itself was found to form liquid-like droplets at neutral and slightly acidic pH and at low salt concentrations. Truncated p53 mutants modulated droplet formation, suggesting the importance of multivalent electrostatic interactions among the N-terminal and C-terminal domains. Second, FRET efficiency measurements for the dimer mutants of p53 revealed that distances between the core domains and between the C-terminal domains were modulated in an opposite manner within the droplets. Third, the molecular crowding agents were found to promote droplet formation, whereas ssDNA, dsDNA, and ATP, to suppress it. Finally, the p53 mutant mimicking posttranslational phosphorylation did not form the droplets. We conclude that p53 itself has a potential to form droplets that can be controlled by cellular molecules and by posttranslational modifications, suggesting that LLPS might be involved in p53 function. Tumor suppressor p53 is a multifunctional transcription factor that induces cell cycle arrest, DNA repair or apoptosis upon binding to its target DNA sequence. In 50% of human cancers, mutations on p53 are found to hamper its binding to the target sequence. Accordingly, extensive investigations have been conducted to characterize the functions as well as malfunctions of p53. However, an important aspect of p53, namely its involvement in liquid-like droplets, is still largely unresolved. In fact, p53 has long been known to be uptaken into cellular droplets such as Cajal and promyelocytic leukemia protein (PML) bodies. In this report, we describe that p53 itself can form liquid-like droplets upon the control of solution conditions, suggesting a possible involvement of the p53 droplets in the cellular environment. The primary function of p53 is the accommodation of various posttranslational modifications, termed activation, which in turn triggers the search for and the binding to its target DNA sequence, leading to the expression of downstream genes 1. p53 is composed of the N-terminal (NT) (residues 1-95), the core (95-293), the linker (293-326), the tetramerization (Tet) (326-357), and the C-terminal (CT) (357-393) domains. p53 slides along nonspecific DNA by attaching the CT domain to the DNA and by hopping the core domain 2-4. The sliding of p53 occurs in two modes 5,6 , in which the CT, core and linker domains are differently in contact with the DNA 7. The recognition efficiency of the target sequence by the sliding p53 is low, but is enhanced by the activation of p53 8. Furthermore, the sliding p53 can transfer from one DNA strand to another using the CT domain 9. In addition,

The poor aqueous solubility of drug substances hampers their broader applications. This paper describes a de novo strategy to increase the aqueous solubility of drug substances using an arginine-assisted solubilization system (AASS) with alkyl gallates as model drug substances. Solubility experiments of alkyl gallates showed that arginine greatly increases the aqueous solubility of different alkyl gallates, whose aqueous solubilities differ widely. In contrast, lysine showed marginal effects on alkyl gallates solubility. Molecular dynamic simulation indicated a greater interaction of arginine with alkyl gallates than that of lysine, which reflects favorable interaction between the guanidinium group of arginine and the aromatic ring of alkyl gallates. Such interaction apparently disrupts association of alkyl gallate molecules, leading to solubilization. These results indicate AASS as a promising approach to solubilize poorly soluble drug substances containing aromatic ring structures.