Viscoelasticity and its influence on conformation and aggregation of proteins
The influence of the solvent on the thermodynamics of protein interactions and their aggregation are relatively well studied. A unique kinetic factor contributing to the thermodynamics is the solvent resistance to molecular motion, quantified as viscosity, which is a macroscopic characteristic of a fluid that describes its resistance to deformation. Influence of viscosity on the kinetics of complex solution processes have not been proven with any degree of certainty. Recently the role of viscosity in protein aggregation, has been studied in the context of protein crystallization. The folding rate in most solvated proteins kf, based on the Kramer’s’ model, is inversely proportional to the solvent friction g0, which is dependent on the viscosity
kf = C/γο
This dependence has been confirmed by simulations using Markovian dynamics on model proteins as well as by experiments for few solvated proteins. The Kramer’s’ theory has been tested experimentally in most cases and has in general proved to be correct. However, all of these studies have explored viscosities equal to or higher than the viscosity of water. The reason for this is simple: in a test tube, viscosity can be increased relatively easily by using viscogenic agents, while decreasing it is difficult, if not impossible. In the Biophysics Lab., contradictions to the Kramer’s’ theory have been demonstrated from classic studies on solvent viscosity on ligand binding kinetics and conformational relaxations of myoglobin wherein the solvent medium strongly damps the conformational dynamics of the protein molecule. This has resulted in a modification of Kramer’s’ theory to describe the dependence of folding rates on the friction introduced by the solvent. Thus in order to get good fitting to experimental data, one uses the following formula:
kf = C/ (γο+x)
Here x an adjustable parameter that depends on the size of the protein in addition to the other parameters of pH and temperature. In most models that deal with protein-solvent interactions, wherever a deviation from Kramer’s’ theory has been observed, internal friction has been introduced which is nothing but the reorganization of the protein interior in addition to external friction ( movement of solvent mlecules)
As a consequent of the above deviation, work in the Biophysics Lab. is presently addressing the viscoelastic regime that arises in these complex protein solutions, in the presence of small molecular additives which result in dramatic changes in the local viscosity and , one phase occupies a much larger volume than the other. Presently new experimental tool using the quartz crystal microbalance with dissipation is being designed to identify the ‘viscoelastic’ phases in both globular and fibrous proteins.