Projects / Programmes
Studies of protein aggregation in aqueous solutions of salts and other soluble additives
| Code |
Science |
Field |
Subfield |
| 1.04.01 |
Natural sciences and mathematics |
Chemistry |
Phyisical chemistry |
| Code |
Science |
Field |
| P400 |
Natural sciences and mathematics |
Physical chemistry |
| Code |
Science |
Field |
| 1.04 |
Natural Sciences |
Chemical sciences |
Protein aggregation, aqueous solutions, liquid-liquid phase separation, influence of additives, Wertheim's theories
Researchers (18)
Organisations (1)
Abstract
Understanding of protein-protein interactions in aqueous solutions, modified by salts and other additives, is central to biology. Under certain conditions protein monomers may associate with each other. The process depends on the protein concentration, temperature, as also the nature and concentration of additives present. Proteins self-assemble to form aggregates leading to either liquid-liquid phase separation, crystallization, or amorphous precipitate.
A traditional approach to analyze the properties of protein solutions has been to adapt colloid theories, such as the Derjaguin–Landau–Verwey–Overbeek theory. In those treatments, proteins are represented as hard spheres that interact through spherically symmetric van der Waals and electrostatic interactions in salt water, using a continuum representation of solvent and the Debye–Huckel screening for salts. While this approach can often give correct trends for the pH and salt concentration dependencies, it cannot account for the salt specific effects, where different salts exhibit widely different powers of protein precipitation. Also, the anisotropy (the interactions are not centrally symmetric) is crucial for protein self assembly; it influences the size and shape of aggregates. Colloidal models are therefore poor representations of the proteins, in particular antibodies. An alternative pursued in literature is the computer modeling. The all-atom computer simulations are useful in pointing out details of various interactions, but the systems, being relevant to biology and pharmacy, are often too big to be handled well enough by explicit-water molecular simulations. Besides that, the well known problem of the force fields exists.
Aggregation modeling requires some coarse-graining, but beyond the DLVO level. An approach, based on the ideas of condensed matter physics, has been forwarded in recent decades. Together with others we have proposed largely analytical models for protein-protein aggregation equilibrium in aqueous salt solutions. Proteins have be modeled as spherical objects, as dumb-bells or Y-shaped molecules, decorated by binding sites on the surface that interact with an attractive square-well potential of depth and width in the range of the hydrogen bond values. Unlike simpler, centrally symmetric, interaction models the binding sites lead orientation interactions between the proteins. We showed in several examples (some of them are already published) that these models, in combination with Wertheim's theories, can be very helpful in predicting the measurable quantities. We propose to perform a (i) physico-chemical modeling of protein solutions, (ii) extensive numerical work probing relevant experimental situations, and (iii) comparison with experiments including those performed in our own Laboratory. Encouraged by recent results (as also by peer's response) we propose to investigate the models for protein solutions that can be treated via Wertheim's thermodynamic perturbation theory TPT1 and/or integral equation theories. We plan to study protein aggregation, liquid-liquid phase separations, 2nd virial coefficient, solution viscosity, water properties at protein surface, and some other measurable properties. Solvation is a major driving force in biological mechanisms of action, including folding, binding, molecular recognition, aggregation, and partitioning so, by treating water as separate species (and not as a continuum), we shall capture the solvation physics more accurately than other theoretical approaches. We will study both, dilute and concentrated systems, characterized by volume restrictions (mimicking cell conditions), which are currently intensively studied. Calculations will be, wherever possible, critically confronted by our own measurements as also by the data from literature.
Significance for science
Much of biology depends on proteins interacting with each other, pairwise or in form of oligomers, mediated by water and different ligands, such as salts, polymers, and excipients needed for drug formulation. The self-assembly of proteins into various structures plays a crucial role in biology and is of great importance for pharmaceutical industry. We wish to understand how protein molecules interact with water, ions and in-between them, to better understand the biological processes and to perform a quality drug design. Recently, many cellular functions have been associated with membrane-less organelles (protein droplets), formed by liquid-liquid separation, one of the main thermodynamic properties to be studied in this project. Water is critically important in biology, mediating folding, binding, aggregation, partitioning and molecular recognition. If we do not account for water accurately, the results of even the otherwise accurate physical models may not provide realistic results. For example, modeling water as dielectric continuum cannot explain the salt-specific effects. An important arena of industrial research, connected to hydration, is formulating and stabilizing protein drugs. For these and other reasons not mentioned here, we need better solvation modeling for complex situations, where proteins bind other proteins to form specific complexes, where they aggregate, precipitate, crystallize or form fibrils and for situations, where salts and other additives are modulators of protein-protein interactions. We also need to include the key components of formulations of protein drugs (monoclonal antibodies), such as stabilizing excipients (osmolytes and/or amino acids). In the present project proposal, by treating water on equal level of approximation as other species present (and not merely as a structure-less continuum), we shall capture the hydration physics more realistically than previous theoretical approaches. There is no doubt that understanding the physical and chemical properties of mixtures of proteins with electrolytes in water is necessary for better understanding of cellular functions. Considering the importance of the inter-protein interactions for vast areas of biological science we believe that even small advancement in understanding of protein solutions represents a valuable achievement.
Significance for the country
Much of biology depends on proteins interacting with each other, pairwise or in form of oligomers, mediated by water and different ligands, such as salts, polymers, and excipients needed for drug formulation. The self-assembly of proteins into various structures plays a crucial role in biology and is of great importance for pharmaceutical industry. We wish to understand how protein molecules interact with water, ions and in-between them, to better understand the biological processes and to perform a quality drug design. Recently, many cellular functions have been associated with membrane-less organelles (protein droplets), formed by liquid-liquid separation, one of the main thermodynamic properties to be studied in this project. Water is critically important in biology, mediating folding, binding, aggregation, partitioning and molecular recognition. If we do not account for water accurately, the results of even the otherwise accurate physical models may not provide realistic results. For example, modeling water as dielectric continuum cannot explain the salt-specific effects. An important arena of industrial research, connected to hydration, is formulating and stabilizing protein drugs. For these and other reasons not mentioned here, we need better solvation modeling for complex situations, where proteins bind other proteins to form specific complexes, where they aggregate, precipitate, crystallize or form fibrils and for situations, where salts and other additives are modulators of protein-protein interactions. We also need to include the key components of formulations of protein drugs (monoclonal antibodies), such as stabilizing excipients (osmolytes and/or amino acids). In the present project proposal, by treating water on equal level of approximation as other species present (and not merely as a structure-less continuum), we shall capture the hydration physics more realistically than previous theoretical approaches. There is no doubt that understanding the physical and chemical properties of mixtures of proteins with electrolytes in water is necessary for better understanding of cellular functions. Considering the importance of the inter-protein interactions for vast areas of biological science we believe that even small advancement in understanding of protein solutions represents a valuable achievement.
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