A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution

Functional-renormalization-group approach to classical liquids with short-range repulsion: A scheme without repulsive reference system

The renormalization-group approaches for classical liquids in previous works required a repulsive reference such as a hard-core one when applied to systems with short-range repulsion. The need for the reference is circumvented here by using a functional-renormalization-group approach for integrating the hierarchical flow of correlation functions along a path of variable interatomic coupling. We introduce the cavity distribution functions to avoid the appearance of divergent terms and choose a path to reduce the error caused by the decomposition of higher order correlation functions. We demonstrate using exactly solvable one-dimensional models that the resulting scheme yields accurate thermodynamic properties and interatomic distribution at various densities when compared to integral-equation methods such as the hypernetted chain and the Percus-Yevick equation, even in the case where our hierarchical equations are truncated with the Kirkwood superposition approximation, which is valid for low-density cases.

Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals

Myoglobin (Mb) is highly concentrated in the myocytes of diving mammals such as whales and seals, in comparison with land animals, and its molecular evolution has played a crucial role in their deep-sea adaptation. We previously resurrected ancestral whale Mbs and demonstrated the evolutional strategies for higher solubility under macromolecular crowding conditions. Pinnipeds, such as seals and sea lions, are also expert diving mammals with Mb-rich muscles. In the present study, we resurrected ancestral pinniped Mbs and investigated their biochemical and structural properties. Comparisons between pinniped and whale Mbs revealed the common and distinctive strategies for the deep-sea adaptation. The overall evolution processes, gaining precipitant tolerance and improving thermodynamic stability, were commonly observed. However, the strategies for improving the folding stability differed, and the pinniped Mbs exploited the shielding of hydrophobic surfaces more effectively than the whale Mbs.

Water-mediated interactions destabilize proteins

Proteins are folded to avoid exposure of the nonpolar groups to water because water‐mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins—which is a well‐accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free‐energy calculation for a thermodynamic cycle of a protein folding using a liquid‐state density functional theory. Here, the solvation‐free energy for a leucine zipper formation was examined in the coiled‐coil protein GCN4‐p1, a typical model for hydrophobic interactions, which demonstrated that water‐mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.

Self-consistent construction of bridge functional based on the weighted density approximation

A parameter-free bridge functional is presented using a weighted density approximation (WDA). The key point of this scheme is the utilization of Baxter's relation connecting the second-order direct correlation function (DCF) to the higher-order DCF with the density derivative. The free energy density required for the WDA is determined in a self-consistent manner using Baxter's relation and Percus's test particle method. This self-consistent scheme enables us to employ any type of potential model for simple liquids. The new functional is applied to calculate density distribution functions for the inhomogeneous fluids interacting via the hard-sphere, Lennard-Jones, and hard-core Yukawa potentials under an external field from a planar wall and a slit pore.

Theoretical analysis on thermodynamic stability of chignolin

Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.

Tracing whale myoglobin evolution by resurrecting ancient proteins

Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.