Book of Abstracts: Albany 2003
June 17-21 2003
Protein Folding and Unfolding
At present, the PDB holds ~20,000 examples of folded proteins, solved by X-ray crystallography and NMR spectroscopy. However, the unfolded form remains elusive. Based on simple computational experiments, Flory concluded that each φ,ψ-pair in the protein backbone adopts conformations that are independent of its neighbors. This conjecture, known as the isolated-pair hypothesis, derived strong support from experimental work by Tanford and coworkers in the 1960s, who demonstrated that in 6M GuCl, the unfolded ensemble is a statistical coil. These ideas conditioned the expectations of subsequent generations of protein chemists, who came to regard the equilibrium unfolded ensemble as a vast collection of rapidly interconverting conformers, including the native one, albeit at undetectable concentration.
From this perspective, the central thermodynamic question is: how can the population overcome conformational entropy (~30R ln (10) = 40 kcal/mol at room temperature from the backbone alone) in order to stabilize a single conformer uniquely? The central dynamic question is: as the population wends its way toward the native state, how can chains avoid getting stuck in adventitious, ~kT?sized traps?
Using both explicit counting and simple simulations, we find that the size of conformational space is smaller than previously thought. The number of accessible conformations is winnowed by sterics and conformation-dependent solvent interactions. As a consequence, the unfolded chain is already pre-organized and the entropic cost of folding is reduced correspondingly.
Jenkins Department of Biophysics