Hydration sphere structure of proteins: A theoretical study

Theoretical Study of Fe3+ and Ni2+ Ion Interactions in Ethaline as the Deep Eutectic Solvent and Water Solutions Using Molecular Dynamics, Quantum Theory of Atoms in Molecules, and Non-Covalent Interactions

Deep eutectic solvents (DES) have several advantages compared to water and traditional solvents, making them an alternative, especially in applications that require better solvation, greater thermal stability, and a lower environmental impact. This study aimed to analyze the behavior of Fe3+ and Ni2+ ions in two quantities of water (300 and 5580 molecules) and in a eutectic solvent based on choline chloride and ethylene glycol (1ChCl:2EG). The computational methods used involved molecular dynamics, quantum theory of atoms in molecules (QTAIM), and noncovalent interactions simulations. Analysis of the radial distribution function multiplied by the number density [g(r)ρ] and the cumulative number (CN) indicated that the interactions between the metal ions and the water molecules were strongest for the systems with the most water. QTAIM determined the bond critical point, the electron density [ρ(r)], the Laplacian of the electronic density [∇2ρ(r)], and the electron localization function (η, ELF), allowing the interactions to be analyzed. Polarizability of the metal ions in both water and ethaline was compared; the increasing order of polarizability was Fe3+ < Ni2+ < Fe2+, with Fe3+ being the least polarizable due to its high charge and smaller ionic radius. In the mixed systems with Fe2+ or Fe3+ added to Ni2+, the metal species with the same charge competed similarly in water and DES. The intermolecular forces in DES are weaker due to the solvent's lower polarity and dielectric constant than water. In the systems with the highest water content (5580 molecules), Fe3+ ions were surrounded by the largest water molecules, followed by Fe2+ and Ni2+. These results may help to better understand the solvation and behavior of these ions in different media, which has implications for use in electrodeposition, batteries, and corrosion inhibition.

An integrated serum pharmacochemistry, network pharmacology, and metabolomics strategy: A study on raw and wine-processed Paeoniae Radix Alba in promoting blood circulation to alleviate blood stasis

Paeoniae Radix Alba (PRA) is a traditional Chinese medicine that can be processed with wine to achieve an enhanced effect of promoting blood circulation, thus alleviating blood stasis. However, to date, the changes in the bioactive compounds of PRA before and after wine-processing, as well as the mechanisms of action and the effects on ameliorating blood stasis syndrome (BSS), have not been adequately investigated. Therefore, we systematically elucidated the material basis and mechanisms of action of PRA in the treatment of BSS before and after wine processing by integrating serum pharmacochemistry, network pharmacology, and metabolomics approaches. The wine processing method significantly affected 11 components of PRA, including gallic acid, ethyl gallate, paeoniflorin, and 3-O-methylellagic acid 4-O-β-D-glucopyranoside. Benzoylpaeoniflorin and desbenzoylpaeoniflorin are key serum components of PRA both before and after wine processing. SRC and GAPDH are the central targets through which benzoylpaeoniflorin and desbenzoylpaeoniflorin exert their ameliorative effects on BSS, respectively. The metabolomics results indicated that six metabolic pathways-pyrimidine metabolism, ascorbate and aldarate metabolism, steroid hormone biosynthesis, pentose and glucuronate interconversions, tryptophan metabolism, and lysine degradation-play important roles in the amelioration of BSS by PRA and WPRA. 2'-Deoxycytidine, cortexolone, dihydrocortisol, L-gulonic gamma-lactone, L-uridine, D-ribulose, 4-trimethylammoniobutanoic acid, and indoleacetic acid have been identified as potential biomarkers for the amelioration of BSS by PRA and WPRA. The present study significantly contributes to elucidating the processing mechanism of PRA in "promoting blood circulation to remove blood stasis through wine processing".

DeepCys: Structure-based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains

Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In-silico predictions complement the experiments to meet the need of functional characterization. Multiple Cys function prediction algorithm is scarce, in contrast to specific function prediction algorithms. Here we present a deep neural network-based multiple Cys function prediction, available on web-server (DeepCys) (https://deepcys.herokuapp.com/). DeepCys model was trained and tested on two independent datasets curated from protein crystal structures. This prediction method requires three inputs, namely, PDB identifier (ID), chain ID and residue ID for a given Cys and outputs the probabilities of four cysteine functions, namely, disulphide, metal-binding, thioether and sulphenylation and predicts the most probable Cys function. The algorithm exploits the local and global protein properties, like, sequence and secondary structure motifs, buried fractions, microenvironments and protein/enzyme class. DeepCys outperformed most of the multiple and specific Cys function algorithms. This method can predict maximum number of cysteine functions. Moreover, for the first time, explicitly predicts thioether function. This tool was used to elucidate the cysteine functions on domains of unknown functions belonging to cytochrome C oxidase subunit-II like transmembrane domains. Apart from the web-server, a standalone program is also available on GitHub (https://github.com/vam-sin/deepcys).

A review of solvent freeze-out technology for protein crystallization

In this review, we summarize important advances in solvent freeze-out (SFO) technology for protein crystallization, including the background of SFO, its fundamental principle, and some crucial conditions and factors for optimizing SFO technology.

Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes

VirE2 from Agrobacterium tumefaciens is a single-stranded (ss) DNA-binding protein involved in delivery of ssT-DNA (single-stranded transfer DNA) from the agrobacterial Ti plasmid into the eukaryotic cell nucleus. The crystallized part of VirE2 was studied by X-ray diffraction, and the noncrystallized parts of the C- (40 amino acid residues [aars]) and N- (111 aars) termini of the protein, which are presumably disordered, were evaluated by computational methods. We did a molecular dynamics simulation of VirE2 without VirE1 and observed no large changes in domain orientation. The interaction of VirE2 with ssDNA and formation of ssDNA-VirE2 complexes in silico were studied. We also used computer-aided methods to design model complexes consisting from two- and four-subunit VirE2 proteins. We examined the implication of disordered sites in formation of two- and four-subunit VirE2 complexes. Formation of VirE2 dimers and tetramers within ssDNA-VirE2 complexes was demonstrated by computational methods. Using the Platinum program, we found that hydrophilic amino acids were predominant on the surface of the four-subunit VirE2 complex.

Cell theory, intrinsically disordered proteins, and the physics of the origin of life

Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.

The spatial range of protein hydration

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.

The geometry of protein hydration

Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Šwater-carbon cutoff and a 4 Šwater-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Ų which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.

Probabilistic analysis for identifying the driving force of protein folding

Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.