Chain Interactions in Poor-Solvent Polymer Solutions: Equilibrium and Nonequilibrium Aspects

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation

In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of inter-molecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with "seeds". In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such as colloidal particles.

Chain aggregation in dilute solutions of poly(methyl methacrylate) below the phase-separation temperature

For dilute solutions of poly(methyl methacrylate) in isoamyl acetate with the molecular weight M(w)=4.4 x 10(6), the phase-separation process was studied by static light-scattering measurements. The dilute solutions in the concentration range from 1.4 x 10(-4) to 3.8 x 10(-4) g/cm(3) were quenched to about 16 K below the phase-separation temperature, and the aggregation processes of polymer chains were measured over a period of several hours. By analyzing the light-scattering data with the Guinier plot, the weight-averaged molecular weight <M>(w) and z-averaged square radius <R2>(1/2)(z) for clusters of polymer chains were determined as a function of time t(min) and concentration c (g/cm(3)). The growth of clusters was represented by the exponential forms <M>(w)/M(0)=e(gct) and <R2>(z)/R(2)(0)=e(hct) as a function of ct, where M(0) and R2(0) were the values at t=0, and the constants g and h were determined to be g=11.6 and h=7.5. A double-logarithmic plot of <M>(w) versus <R2>(1/2)(z) yielded a straight line with the slope D=3.06+/-0.02. These characteristic features of the chain aggregation process were compared with the Smoluchowski equation for cluster-cluster aggregation with the collision kernel (i+j) for i-mer and j-mer. The observed slow growth of clusters was attributed to the reaction- limited cluster aggregation. The chain density in a cluster was found to increase with an increase of the cluster size, resulting in the slope D exceeding 3.

Early stages of homopolymer collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this paper, a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the straight theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages, the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages scale as N0, N(1/5), and N(6/5), respectively, where N is the degree of polymerization of the chain.