Effects of confinement and crowding on folding of model proteins

arXiv:0811.4581v1 [q-bio.BM] 27 Nov 2008 Effects of confinement and crowding on folding of model proteins published in: Biosystems. 2008 Dec;94(3):248-52 M. Wojciechowski and Marek Cieplak Institute of Physics, Polish Academy of Sciences, Al. Lotnik´ow 32/46, 02-668 Warsaw, Poland We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are studied by placing several identical proteins within the sphere, denaturing them, and then by monitoring refolding. If the interactions between the proteins are dominated by the excluded volume effects, the net folding times are essentially like for a single protein. An introduction of inter-proteinic attractive contacts hinders folding when the strength of the attraction exceeds about a half of the value of the strength of the single protein contacts. The bigger the strength of the attraction, the more likely is the occurrence of aggregation and misfolding. I. INTRODUCTION There is a growing interest in studies of biomolecules enclosed within a limited space. One reason is that almost all life processes take place in compartments such as cells where concentrations of proteins, lipids, shugars, and nucleic acids are large (Ellis and Minton, 2006). Such conditions are also desired in artificial life systems such as the liposomes that allow for protein synthesis within their interior(Murtas et al. , 2007). Chaperonin cages (Hartl and Hayer-Hartl, 2002), that assist in folding and refolding processes of proteins, offer an example of compartmentalization at a still smaller length scale. Another reason for the interest in the confinement effects is provided by recent advances in nanotechnology and resulting novel encapsulation techniques. These involve, for instance, reverse micelles which are mimetic systems of biological membranes composed of amphiphilic molecules. These molecules self-organize so that the polar head-groups point inward and hydrocarbon chains face the organic solvent (Luisi et al. , 1988; Matzke et al. , 1992; Melo et al. , 2003). The amount of the entrapped water is controlled by experimental conditions and a typical radius of the corresponding sphere can be as small as ∼20 ˚A. The water molecules at the inner surface have a propensity to organize (Moilanen et al. , 2007) and the conditions within need not be uniform (Baruah et al., 2006). When it comes to larger confined systems, there are many microfluidic ways to deposit droplets on surfaces, e.g. in the context of the protein and DNA microarrays (Duroux et al., 2007). It is thus interesting to undertake theoretical studies of proteins that are confined. A simple way to introduce confinement is through a sphere (Baumketner et al., 2003; Rathore et al., 2006), or a cage (Takagi et al., 2003), which are repulsive to proteins located on the inside. A sphere which has attractive hydrophobic and repulsive hydrophilic patches on the inside has been also discussed (Jewett et al., 2004) to elucidate the workings of chaperonins. One can also generate cavities by using many spheres, repulsive on the outside, to immitate the effects of crowding (Cheung et al., 2005). Most of the studies carried out so far have been focused on thermodynamics. The confinement has been found to lead to a greater thermodynamic stability, broader and taller specific heat and more compact unfolded conformations (Rathore et al., 2006; Takagi et al., 2003). Crowding is expected to enhance these effects even further (Cheung et al., 2005). 2 In this paper, we consider the kinetics of folding of a protein. This problem has already been studied by, Baumketner et al. (Baumketner et al., 2003) and Jewett et al. (Jewett et al., 2004). In the case of the confining repulsive sphere (Baumketner et al., 2003), the wall potential was represented by Vwall,B(r) = 4εwall πRs 5r " σ r −Rs 10 −  σ r + Rs 10# , (1) where Rs is the radius of the sphere, r is the distance of a Cα atom from the center of the sphere, εwall is the strength of the potential, and σ is take to be equal to 3.8˚A, i.e. to the distance between two consecutive Cα atoms in a protein. The folding time, determined at various temperatures, has been found to depend on Rs in a complicated manner. For instance, at temperatures below the optimal temperature it decreases with increasing the Rs, but it increases above this temperature. In the case of the non-uniform sphere (Jewett et al., 2004) the physics involved depends on the strength of attraction to the hydrophobic patches in the model. If the attractive patches act as strongly as the hydrophobic interactions in the protein, the protein sticks to the wall and folding is arrested, i.e. it takes forever. A reduction in the strength of the attraction leads to a lowering of the folding time until a minim

…(Full text truncated)…

This content is AI-processed based on ArXiv data.