Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints.

The structures of two species of potato carboxypeptidase inhibitor with nonnative disulfide bonds were determined by molecular dynamics simulations in explicit solvent using disulfide bond constraints that have been shown to work for the native species. Ten structures were determined; five for scrambled A (disulfide bonds between Cys8-Cys27, Cys12-Cys18, and Cys24-Cys34) and five for the scrambled C (disulfide bonds Cys8-Cys24, Cys12-Cys18, and Cys27-Cys34). The two scrambled species were both more solvent exposed than the native structure; the scrambled C species was more solvent exposed and less compact than the scrambled A species. Analysis of the loop regions indicates that certain loops in scrambled C are more nativelike than in scrambled A. These factors, combined with the fact that scrambled C has one native disulfide bond, may contribute to the observed faster conversion to the native structure from scrambled C than from scrambled A. Results from the PROCHECK program using the standard parameter database and a database specially constructed for small, disulfide-rich proteins indicate that the 10 scrambled structures have correct stereochemistry. Further, the results show that a characteristic feature of small, disulfide-rich proteins is that they score poorly using the standard PROCHECK parameter database. Proteins 2000;40:482-493.

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

The folding of the potato carboxypeptidase inhibitor (PCI) from partially unfolded conformations by the introduction of native disulfide bond constraints was studied by molecular dynamics simulations in explicit solvent. PCI consists of a globular core (Cys8 to Cys34), two flexible terminal regions (Glu1 to Ile7 and Glu35 to Gly39) and three loop regions characteristic of the family of proteins known as knottins. To generate unfolded conformations, two high temperature (600 K) simulations were performed; one with the native disulfide bonds intact (N600), and one with the disulfide bonds broken (ND600). For comparison purposes, two simulations at 300 K were done; one with the native disulfide bonds (N300), and one with the disulfide bonds broken (ND300). The N300 simulation reached an energetic equilibrium within a few picoseconds and maintained a stable structure during the 500 ps simulation. The three other simulations led to partial unfolding. The largest changes were observed in ND600 simulation with an rms deviation of over 5 A and radius of gyration 12.5% larger than the crystal structure value. Six structures from the ND600 simulation and one from the N600 simulation were used as starting structures for nine refolding simulations with somewhat different protocols for reforming the native disulfide bonds; in all cases the disulfides were reformed at 600 K and the temperature was decreased to 300 K for equilibration of the folded structures. Except for one structure that was significantly misfolded (final rms of 6.64 A with respect to N300), the other folding simulations recovered the native simulation structure (N300) to within rms differences ranging from 1.8 to 3.2 A for the main-chain of the core, relative to the N300, the X-ray and the NMR structures. Of particular interest is the internal and overall refolding behavior of the three loop regions. The more unfolded starting structures led to smaller rms values for the folded structures. Several energetic and solvation models were used to evaluate the X-ray, NMR, N300 and refolded structures. Although most models can distinguish the X-ray, NMR and N300 from the refolded structures, there is no correlation between the rms values of the latter and their estimated stability. Implications of the present results for protein folding by simulations and database search methods are discussed.

Characterization of flexible molecules in solution: the RGDW peptide.

Molecular dynamics simulations with adaptive umbrella sampling of the potential energy are used to study conformations of the adhesion peptide RGDW. The peptide is simulated in a box of explicit water. It results in a combination of room temperature (300 K) simulations, in which conformations dominating the average properties of the system are sampled, with high temperature ( approximately 1000 K) simulations in which free energy barriers separating different local minima are crossed efficiently. The simulations with explicit water are compared to simulations of the isolated peptide using different treatments of the electrostatics, and to published experimental data. There is good agreement for data related to the backbone conformation of the peptide. Some discrepancies are evident for data related to side-chain conformations. Together the simulations and experiments provide a description of the RGDW system that is more detailed and reliable than what can be obtained by either simulations or experiments alone.

Zinc binding in proteins and solution: a simple but accurate nonbonded representation.

Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.