A structure-based method for derivation of all-atom potentials for protein folding
AUTOR(ES)
Kussell, Edo
FONTE
National Academy of Sciences
RESUMO
A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a Cα distance rms from the native structure of less than 2 Å. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=122771Documentos Relacionados
- All-atom protein-folding simulations in generalized-ensembles
- A Free-Energy Approach for All-Atom Protein Simulation
- Dual folding pathways of an α∕β protein from all-atom ab initio folding simulations
- Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials
- The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation