Lysozyme−Lysozyme and Lysozyme−Salt Interactions in the Aqueous Saline Solution: A New Square-Well Potential

Liquid-Liquid Phase Separation Prediction of Proteins in Salt Solution by Deep Neural Network

Liquid-liquid phase separation (LLPS) underlies the formation of membrane-free organelles in eukaryotic cells and plays an important role in the development of some diseases. The phase boundary of metastable liquid-liquid phase separation as well as the cloud point temperature of some globular proteins characterize the phase behavior of proteins and have been widely studied theoretically and experimentally. In the present study, we used a regression and classification neural network to deal with the phase behavior of lysozyme and bovine serum albumin (BSA). We predicted the cloud point temperature and solubility of a lysozyme solution containing sodium chloride by regression and the reentrant phase behavior of BSA in YCl₃ solution containing a surfactant dodecyl dimethyl amine oxide (DDAO) by classification. Specifically, our network model is capable of predicting (a) the solubility of lysozyme in the range: pH 4.0-5.4, temperature 0-25 °C, and NaCl concentration 2-7% (w/v); (b) the cloud point temperature of lysozyme in the range: pH 4.0-4.8, NaCl concentration 2-7%, and lysozyme concentration 0-400 mg/mL; and (c) the phase behavior of BSA in the range: DDAO 1-60 mM, BSA 30-100 mg/mL, and YCl₃ 1-20 mM. We experimentally tested the model at some prediction points with a high accuracy, which means that deep neural networks can be applicable in qualitative and quantitive analysis of liquid-liquid phase separation.

Mechanistic differences in the effects of sucrose and sucralose on the phase stability of lysozyme solutions

The effect of two disaccharide analogues, sucrose and sucralose, on the phase stability of aqueous lysozyme solutions has been addressed from a mechanistic viewpoint by a combination of experiment and molecular dynamics (MD) simulations. The influence of the added low molecular weight salts (NaBr, NaI and NaNO₃) was considered as well. The cloud-point temperature measurements revealed a larger stabilizing effect of sucralose. Upon increasing sugar concentration, the protein solutions became more stable and differences in the effect of sucralose and sucrose amplified. It was confirmed that the addition of either of the two sugars imposed no secondary structure changes of the lysozyme. Enthalpies of lysozyme-sugar mixing were exothermic and a larger effect was recorded for sucralose. MD simulations indicated that acidic, basic and polar amino acid residues play predominant roles in the sugar-protein interactions, mainly through hydrogen bonding. Such sugar mediated protein-protein interactions are thought to be responsible for the biopreserative nature of sugars. Our observations hint at mechanistic differences in sugar-lysozyme interactions: while sucrose does not interact directly with the protein's surface for the most part (in line with the preferential hydration hypothesis), sucralose forms hydrogen bonds with acidic, basic and polar amino acid residues at the lysozyme's surface (in line with the water replacement hypothesis).

Singular value decomposition of the radial distribution function for hard sphere and square well potentials

We compute the singular value decomposition of the radial distribution function g(r) for hard sphere, and square well solutions. We find that g(r) decomposes into a small set of basis vectors allowing for an extremely accurate representation at all interpolated densities and potential strengths. In addition, we find that the coefficient vectors describing the magnitude of each basis vector are well described by a low-order polynomial. We provide a program to calculate g(r) in this compact representation for the investigated parameter range.

Improvement of plant protein solubilization and 2-DE gel resolution through optimization of the concentration of Tris in the solubilization buffer

It is important to solubilize acetone-precipitated proteins before isoelectric focusing (IEF) to achieve high resolution 2-DE gels. To resolve the maximum possible number of plant protein spots, we developed an improved solubilization buffer for plant proteins. We demonstrated that the resolution of 2-DE gels increased dramatically as the concentration of Tris-base increased, with maximum solubilization obtained at 200 mM Tris-base (Ly200T). The Ly200T buffer was more effective than the commonly used solubilization buffer containing 40 mM Tris at solubilizing acetone-precipitated plant proteins. Use of the Ly200T buffer to solubilize proteins resulted in an increase in intensity of approximately 30% of plant protein spots in the larger-than-40 kDa region of the gel. The Ly200T buffer also improved the resolution of abundant and basic proteins. Thus, the Ly200T buffer can be used to achieve greater resolution of protein spots in plant proteomics research.

A molecular-thermodynamic model for the interactions between globular proteins in aqueous solutions: applications to bovine serum albumin (BSA), lysozyme, alpha-chymotrypsin, and immuno-gamma-globulins (IgG) solutions

To investigate globular protein-protein and protein-salt interactions in electrolyte solutions, a potential of mean force including hard-core repulsion, van der Waals attraction and electric double layer repulsion is proposed in this work. Both van der Waals attraction and double-layer repulsion are represented using hard spheres with two-Yukawa tails. The explicit analytical solution of osmotic pressure is derived from the first-order mean spherical approximation. From the comparison between the calculated and experimental values of osmotic pressures for aqueous bovine serum albumin (BSA), lysozyme, alpha-chymotrypsin, and immuno-gamma-globulins (IgG) solutions, we found that the proposed model is adequate for the description of the interactions between proteins at low ionic strength and small self-association of protein molecules. At high ionic strength, the charge inversions of protein molecules should be taken into account.

Noncompact crystalline solids in the square-well potential

We reexamine the phase diagram of the square-well potential, using both theoretical and computer-simulation techniques, for not too short ranges of the potential. The phase diagram turns out to contain a variety of crystalline structures, both compact and, interestingly, also noncompact. The latter result from a large increase in negative energy when pairs of particles come at distances within the interaction range, which more than compensates the entropy loss associated with reduced packing. Transitions between these crystalline structures give rise to a surprisingly rich phase diagram.