Conformation and Folding of Proteins and RNA

A globular protein will spontaneously self-assemble its components into a highly organized three-dimensional structure under appropriate physiological conditions. Our principal goal is to elucidate the stereochemical code that governs this folding reaction in an approach involving simulation, modeling, and analysis.

The core thermodynamic question in protein folding is: how can a polypeptide chain overcome conformational entropy and fold to its native state? A familiar model depicts the unfolded state of the protein as populating a more-than-astronomical number of conformational possibilities. In contrast, we recently re-evaluated this popular model by exhaustive enumeration and found that the entropy price needed to adopt any specific conformation is much less than previously thought. This realization has prompted us to pursue a novel approach to predicting folding, one that seeks to maximize entropy at every step.

Along these lines, we have been developing a practical algorithm, LINUS, to predict the fold of a protein from its amino acid sequence alone. LINUS is based on the idea that proteins fold hierarchically, starting from the unfolded state. The procedure ascends the folding hierarchy in discrete stages, with further accretion of structure at each step. The chain is represented in full atomic detail and folds under the influence of a simple scoring function.

Consistent with our results from exhaustive enumeration, LINUS simulations also indicate that the chain must already exhibit considerable pre-organization in the unfolded state. Further, they provide a physical basis for understanding the early emergence of protein secondary structure (helix, strands, and turns).

We have also begun to model the folding of RNA. Here, the conspicuous question is: how can a highly charged helical stack interact favorably with other like-charged stacks? Our approach focuses on the cloud of "territorially" bound counterions around these charged helices (i.e., Manning theory). A favorable entropic gain accompanies the condensation of two such clouds.

This idea is an analog of the hydrophobic effect in protein folding. There, the hydrophobic effect acts to condense apolar groups, with an associated increase in solvent entropy. In RNA folding, this counterion effect results in condensation of the charged helices, with an associated increase in cation entropy that compensates for unfavorable Coulombic repulsion.