Molecular dynamics simulations of peptides and proteins with amplified collective motions.
We present a novel method that uses the collective modes obtained with a coarse-grained model/anisotropic network model to guide the atomic-level simulations. Based on this model, local collective modes can be calculated according to a single configuration in the conformational space of the protein. In the molecular dynamics simulations, the motions along the slowest few modes are coupled to a higher temperature by the weak coupling method to amplify the collective motions. This amplified-collective-motion (ACM) method is applied to two test systems. One is an S-peptide analog. We realized the refolding of the denatured peptide in eight simulations out of 10 using the method. The other system is bacteriophage T4 lysozyme. Much more extensive domain motions between the N-terminal and C-terminal domain of T4 lysozyme are observed in the ACM simulation compared to a conventional simulation. The ACM method allows for extensive sampling in conformational space while still restricting the sampled configurations within low energy areas. The method can be applied in both explicit and implicit solvent simulations, and may be further applied to important biological problems, such as long timescale functional motions, protein folding/unfolding, and structure prediction.
Zhang
Zhiyong
Z
Key Laboratory of Structural Biology, and School of Life Sciences, University of Science and Technology of China, Chinese Academy of Sciences, Hefei, Anhui 230027, China.
Shi
Yunyu
Y
Liu
Haiyan
H
D016880:Anisotropy; D017122:Bacteriophage T4 / Q000737:chemistry / Q000201:enzymology; D003198:Computer Simulation; D004795:Enzyme Stability; D005240:Feasibility Studies; D046911:Macromolecular Substances; D008958:Models, Molecular; D009038:Motion; D009113:Muramidase / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012259:Ribonuclease, Pancreatic / Q000737:chemistry*; D013696:Temperature
D046911:Macromolecular Substances; D010446:Peptide Fragments; D010455:Peptides; D011506:Proteins; C060871:ribonuclease A S-peptide; D012259:Ribonuclease, Pancreatic; D009113:Muramidase