Paircoil2: improved prediction of coiled coils from sequence.

We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.

An important goal in biology is to predict from sequence data the high-resolution structures of proteins and the interactions that occur between them. In this paper, we describe a computational approach that can make these types of predictions for a series of coiled-coil dimers. Our method comprises a dual strategy that augments extensive conformational sampling with molecular mechanics minimization. To test the performance of the method, we designed six heterodimeric coiled coils with a range of stabilities and solved x-ray crystal structures for three of them. The stabilities and structures predicted by the calculations agree very well with experimental data: the average error in unfolding free energies is <1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations <0.7 A. We have also tested the method on a series of homodimers derived from vitellogenin-binding protein. The predicted relative stabilities of the homodimers show excellent agreement with previously published experimental measurements. A critical step in our procedure is to use energy minimization to relax side-chain geometries initially selected from a rotamer library. Our results show that computational methods can predict interaction specificities that are in good agreement with experimental data.

Gating as a control element in constrictive binding and guest release by hemicarcerands.

Theoretical modeling of the dynamics of complexation and decomplexation of guest molecules by container molecules reveals that gating has a critical influence on the ease of formation and stability of host-guest complexes. Hosts equipped with gates can form very stable complexes with a variety of guests under readily achievable conditions. Gating involves conformational processes of the host molecule that alter the size of the portals through which guest molecules pass. "French door" and "sliding door" mechanisms of gate opening are identified.