Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine Dimer

Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation

The dynamics of protein folding are complicated because of the various types of amino acid interactions that create secondary, supersecondary, and tertiary interactions. Computational modeling can be used to simulate the biophysical and biochemical interactions that determine protein folding. Effective folding to a desired protein configuration requires a compromise between speed, stability, and specificity. If the primary sequence of amino acids emphasizes one of these characteristics, the others might suffer and the folding process may not be optimized. We provide an example of a model peptide whose primary sequence produces a highly stable supersecondary two-helix bundle structure, but at the expense of lower speed and specificity of the folding process. We show how computational simulations can be used to discover the configuration of the kinetic trap that causes the degradation in the speed and specificity of folding. We also show how amino acid sequences can be engineered by specific substitutions to optimize the folding to the desired supersecondary structure.

Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories

Thermodynamic parameters such as free energies and heat capacities are important quantities for understanding processes involving structural transitions in complex molecules such as proteins. Computational investigations provide simulated data that can be used for calculating thermodynamic parameters. However, calculations give accurate results only if the simulations sample all of configuration space with the appropriate temperature-dependent Boltzmann equilibrium probabilities. For many systems, truly comprehensive sampling of configuration space is not computationally feasible. We present an approximation technique for the calculations that will give accurate values for thermodynamic parameters when the data is incomplete. Our work is applicable to systems in which there are two distinct, important regions of configuration space that must be sampled. Importantly, the results are also valid when the system is more complex than two-state systems. Transition pathways that involve intermediate configurations between two stable regions are allowed in this treatment, and therefore the results are valid for multistate systems.