Protein folding in confined and crowded environments

Abstract

Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k B T but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.The complexity of the cellular environments in which proteins function is increasingly been appreciated [1]. Potential impacts of two related, but distinct factors, confinement and macromolecular crowding, on protein folding are receiving extensive attention [2][3][4][5]. Confinement arises from encapsulation of proteins in compartments with dimensions on the scales of 10's to 100's Å, which are only moderately larger than the sizes of the proteins themselves. Examples of such compartments include the Anfinsen cage of chaperonins and the exit tunnel of ribosomes. Crowding refers to the exclusion of volumes to proteins of interest by the presence of other macromolecules. The aims of this paper are to discuss potential impacts of confinement and crowding on protein folding and to review the progress made by recent studies on protein folding in confined and crowded conditions and in cellular environments.

Single-molecule spectroscopy of protein folding in a chaperonin cage

“…However, our observations call for a differentiated view of chaperone action: since the folding rates of the domains within a single protein can be affected differently by the chaperonin, it is improbable that there is one universal chaperonin mechanism at work. This notion is supported by the large variability of effects of chaperonins on the folding of different proteins reported in the literature (20) and by theoretical concepts that provide a quantitative framework for the competition between intra-and intermolecular interactions that determine the folding rate and mechanism of a substrate protein inside the GroEL/GroES cage (1,8,(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)66). Future experimental and theoretical investigations will have to address the potential synergies of the different mechanisms, whose subtle balance may be required to achieve the promiscuity of many molecular chaperones.…”

“…A considerable body of theoretical work suggests that, even though moderate confinement of a polypeptide in a cavity can accelerate folding entropically, reduced folding rates are expected from stronger confinement that restricts conformational fluctuations and leads to an increase in molecular friction (13)(14)(15)(16)(17)(18)(19). In view of the small size of the chaperonin cavity, resembling a sphere with a radius of ∼3 nm (assuming a cavity volume of 120 nm 3 (64)), compared to the radius of gyration of denatured rhodanese of ∼3.8 nm (calculated assuming the typical persistence length of 0.4 nm for unfolded protein chains under native conditions (65)), a significant effect of confinement on the folding dynamics of rhodanese may be expected.…”

“…Even the autonomous folding of chaperone substrate proteins has been difficult to investigate because of their strong aggregation tendency (10). Contributions from confinement and crowding have been addressed in numerous studies using molecular simulations and theory (11)(12)(13)(14)(15)(16)(17)(18)(19)(20), but many of these concepts have eluded experimental examination.Here, we take a step towards closing this gap by investigating the GroEL/GroES chaperonin (1-3, 9) with single-molecule fluorescence spectroscopy (21-24), a method that is starting to provide previously inaccessible information on chaperonemediated protein folding (25)(26)(27)(28)(29)(30). GroEL/GroES is a remarkable molecular machine that binds nonnative proteins and allows them to fold within a cavity formed by the heptameric rings of GroEL and GroES.…”

“…Even the autonomous folding of chaperone substrate proteins has been difficult to investigate because of their strong aggregation tendency (10). Contributions from confinement and crowding have been addressed in numerous studies using molecular simulations and theory (11)(12)(13)(14)(15)(16)(17)(18)(19)(20), but many of these concepts have eluded experimental examination.…”

RNA structure prediction: Progress and perspective

“…[8,93,[107][108][109][110][111][112][113][114][115][116] However, most of the current structure prediction models seldom consider the conditions departing from the room/body temperature and high salt (namely, 1M NaCl). It is a challenge to predict RNA 3D structures at arbitrary temperature/ion conditions.…”