Antibody association in solution: cluster distributions and mechanisms.

Understanding factors that affect the clustering and association of antibodies molecules in solution is critical to their development as therapeutics. For 19 different monoclonal antibody (mAb) solutions, we measured the viscosities, the second virial coefficients, the Kirkwood-Buff integrals, and the cluster distributions of the antibody molecules as functions of protein concentration. Solutions were modeled using the statistical-physics Wertheim liquid-solution theory, representing antibodies as Y-shaped molecular structures of seven beads each.

The mechanism of self-association of human -D crystallin from molecular dynamics simulations.

The aggregation of human -D crystallin is associated with the age-onset cataract formation. Here, we extensively investigated the self-association mechanism of human -D crystallin through molecular dynamics computer simulations. By mutating the protein surface we found that electrostatic interactions between charged amino acids play a crucial role in its self-association.

Protein Association in Solution: Statistical Mechanical Modeling.

Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics.

Biophysical Principles Emerging from Experiments on Protein-Protein Association and Aggregation.

Protein-protein association and aggregation are fundamental processes that play critical roles in various biological phenomena, from cellular signaling to disease progression. Understanding the underlying biophysical principles governing these processes is crucial for elucidating their mechanisms and developing strategies for therapeutic intervention. In this review, we provide an overview of recent experimental studies focused on protein-protein association and aggregation.

The influence of excipients on the viscosity of monoclonal antibody solutions.

The aggregation propensity of monoclonal antibodies can be modified by adding different cosolutes into the solution. A simple coarse-grained model in the combination with the thermodynamic perturbation theory was used to predict cluster distribution and viscosity of the solutions of IgG4 monoclonal anibody in the presence of L-Arginine Hydrochloride. The data were analysed using binding polynomial to describe the binding of cosolute (Arginine) to the antibody molecule.

CAT-Site: Predicting Protein Binding Sites Using a Convolutional Neural Network.

Identifying binding sites on the protein surface is an important part of computer-assisted drug design processes. Reliable prediction of binding sites not only assists with docking algorithms, but it can also explain the possible side-effects of a potential drug as well as its efficiency. In this work, we propose a novel workflow for predicting possible binding sites of a ligand on a protein surface.

The Effect of Arginine on the Phase Stability of Aqueous Hen Egg-White Lysozyme Solutions.

The effect of arginine on the phase stability of the hen egg-white lysozyme (HEWL) has been studied via molecular dynamics computer simulations, as well as experimentally via cloud-point temperature determination. The experiments show that the addition of arginine increases the stability of the HEWL solutions. The computer simulation results indicate that arginine molecules tend to self-associate.

The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism: A Methodological Approach.

The amyloidophilic dyes thioflavin T and Congo red are small, yet powerful, molecules that allow the in vitro and in vivo detection of amyloid fibrils in protein solutions. Even though Congo red and thioflavin T binding assays are widespread techniques for unveiling amyloid fibers and are gradually replacing the more demanding X-ray diffraction method, handling samples containing amyloid fibrils is still challenging and can lead to false-positive/negative results. Here we describe a relatively straightforward procedure of preparing hen egg-white lysozyme amyloid fibrils in different buffer solutions and their detection with thioflavin T and Congo red, supported by an indispensable method for determining the secondary structure of proteins - circular dichroism.

A new fibrillization mechanism of β-lactoglobulin in glycine solutions.

Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2.

Influence of Low Molecular Weight Salts on the Viscosity of Aqueous-Buffer Bovine Serum Albumin Solutions.

Pharmaceutical design of protein formulations aims at maximum efficiency (protein concentration) and minimum viscosity. Therefore, it is important to know the nature of protein-protein interactions and their influence on viscosity. In this work, we investigated the dependence of the viscosity of BSA in an aqueous 20 mM acetate buffer at pH = 4.

Tetrahedrality, hydrogen bonding and the density anomaly of the central force water model. A Monte Carlo study.

Monte Carlo computer simulations in the canonical and grand canonical statistical ensemble were used to explore the properties of the central force (CF1) water model. The intramolecular structure of the HO molecule is well reproduced by the model. Emphasis was made on hydrogen bonding, and on the tehrahedral, , and translational, , order parameters.

Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model.

Liquid-liquid phase separation (LLPS) of proteins has recently been associated with the onset of numerous diseases. Despite several studies in this area of protein aggregation, buffer-specific effects always seem to be overlooked. In this study we investigated the influence of buffers on the phase stability of hen egg-white lysozyme (HEWL) and its respective protein-protein interactions by measuring the cloud point temperature, second virial coefficient, and interaction diffusion coefficient of several HEWL-buffer solutions (MOPS, phosphate, HEPES, cacodylate) at pH 7.

Studying the mechanism of phase separation in aqueous solutions of globular proteins molecular dynamics computer simulations.

Proteins are the most abundant biomacromolecules in living cells, where they perform vital roles in virtually every biological process. To maintain their function, proteins need to remain in a stable (native) state. Inter- and intramolecular interactions in aqueous protein solutions govern the fate of proteins, as they can provoke their unfolding or association into aggregates.

The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism.

Amyloid fibrils, highly ordered protein aggregates, play an important role in the onset of several neurological disorders. Many studies have assessed amyloid fibril formation under specific solution conditions, but they all lack an important phenomena in biological solutions-buffer specific effects. We have focused on the formation of hen egg-white lysozyme (HEWL) fibrils in aqueous solutions of different buffers in both acidic and basic pH range.

DNA-Polyelectrolyte Complexation Study: The Effect of Polyion Charge Density and Chemical Nature of the Counterions.

Complexes of polycations and DNA, also known as polyplexes, have been extensively studied in the past decade, as potential gene delivery systems. Their stability depends strongly on the characteristics of the polycations, as well as the nature of the added salt. We present here a study of the DNA ionene complexation in which we used fluorescence, UV, and CD spectroscopy, combined with molecular dynamics computer simuations, to systematically examine the influence of the polycation charge density, as well as the influence of the nature of the counterion, on the stability of these systems.

Replica Ornstein-Zernike Theory Applied for Studying the Equilibrium Distribution of Electrolytes across Model Membranes.

By means of replica Ornstein-Zernike theory (supplemented in a few cases by Monte Carlo simulations) we examined the distribution of an annealed primitive model +1:-1 electrolyte in a mixture with uncharged hard spheres, or another model +1:-1 or +2:-1 electrolyte inside and outside the quenched vesicles, decorated by a model membrane, and across the membrane phase. We explored the influence of the size and charge of the annealed fluid on the partition equilibrium, as well as the effect of the vesicle size and membrane interaction parameters (repulsive barrier height, attractive depth, and membrane width). A hydrophobic cation, present in the mixture with NaCl, slightly enhanced the concentration of sodium ions inside the model vesicle, compared to pure NaCl solution.

How Water's Properties Are Encoded in Its Molecular Structure and Energies.

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid.

Modelling the Correlation Between Molecular Electrostatic Potential and pKa on Sets of Carboxylic Acids, Phenols and Anilines.

Calculations of molecular electrostatic potential were correlated with experimental pKa values for different sets of acidic molecules (carboxylic acids, phenols, and anilines) to obtain linear relationships of variable quality. A single tri-parameter model function was constructed to describe the pKa dependence on MEP maxima together with two automatically generated molecular descriptors, namely the counts of carboxylic acid and amine functional groups.

Volumetric and calorimetric properties of aqueous ionene solutions.

The volumetric (partial and apparent molar volumes) and calorimetric properties (apparent heat capacities) of aqueous cationic polyelectrolyte solutions - ionenes - were studied using the oscillating tube densitometer and differential scanning calorimeter. The polyion's charge density and the counterion properties were considered as variables. The special attention was put to evaluate the contribution of electrostatic and hydrophobic effects to the properties studied.

Phase behaviour of a continuous shouldered well model fluid. A grand canonical Monte Carlo study.

The phase behavior of the continuous shouldered well model fluid proposed by Franzese [J. Mol. Liq.

Protein aggregation in salt solutions.

Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein-protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim's thermodynamic perturbation theory.

Tuning the Hydrophobic Interaction: Ultrafast Optical Kerr Effect Study of Aqueous Ionene Solutions.

The molecular origin of the hydrophobic effect continues to be widely studied. Here we design an experiment to tune independently hydrophilic and hydrophobic interactions through the study of a series of aqueous ionene solutions. The dynamics of these solutions are probed using the ultrafast optical Kerr effect, which measures polarizability anisotropy relaxation.

Effects of the translational and rotational degrees of freedom on the hydration of simple solutes.

Molecular dynamics simulations with separate thermostats for rotational and translational motion were used to study the effect of these degrees of freedom on the structure of water around model solutes. To describe water molecules we used the SPC/E model. The simplest solute studied here, the hydrophobe, was represented as a Lennard-Jones particle.