Conformation spaces of proteins

We report a simple method for measuring the accessible conformational space explored by an ensemble of protein structures. The method is useful for diverse ensembles derived from molecular dynamics trajectories, molecular modeling, and molecular structure determinations. It can be used to examine a wide range of time scales. The central tactic we use, which has been previously employed, is to replace the true mechanical degrees of freedom of a molecular system with the conformationally effective degrees of freedom as measured by the root‐mean squared cartesian distances among all pairs of conformations. Each protein conformation is treated as a point in a high dimensional euclidean space. In this article, we model this space in a novel way by representing it as an N ‐dimensional hypercube, describable with only two parameters: the number of dimensions and the edge length. To validate this approach, we provide a number of elementary test cases and then use the N ‐cube method for measuring the size and shape of conformational space covered by molecular dynamics trajectories spanning 10 orders of magnitude in time. These calculations were performed on a small protein, the villin headpiece subdomain, exploring both the native state and the misfolded/folding regime. Distinct features include single, vibrationally averaged, substate minima on the 0.1–1‐ps time scale, thermally averaged conformational states that persist for 1–100 ps and transitions between these local minima on nanosecond time scales. Large‐scale refolding modes appear to become uncorrelated on the microsecond time scale. Associated length scales for these events are 0.2 Å for the vibrational minima; 0.5 Å for the conformational minima; and 1–2 Å for the nanosecond events. We find that the conformational space that is dynamically accessible during folding of villin has enough volume for ∼10 9 minima of the variety that persist for picoseconds. Molecular dynamics trajectories of the native protein and experimentally derived solution ensembles suggest the native state to be composed of ∼10 2 of these thermally accessible minima. Thus, based on random exploration of accessible folding space alone, protein folding for a small protein is predicted to be a milliseconds time scale event. This time can be compared with the experimental folding time for villin of 10–100 μs. One possible explanation for the 10–100‐fold discrepancy is that the slope of the “folding funnel” increases the rate 1–2 orders of magnitude above random exploration of substates. Proteins 2001;42:495–511. © 2001 Wiley‐Liss, Inc.