Molecular dynamics characterisations of the Trp-cage folding mechanisms: in the absence and presence of water solvents

Abstract

Protein folding is an important and yet challenging topic in current molecular biology. In this work, the folding dynamics and mechanisms of the Trp-cage mini-protein were studied with molecular dynamics simulations, in the absence and presence of water solvents. The important intermediates during the Trp-cage folding were determined by gradually decreasing the simulation temperature. The folding transition temperature was identified to be approximately 400 K, and the folding pathway was decomposed into six steps: U ↔ I ₁ ↔ I ₂ ↔ I ₃ ↔ I ₄ ↔ F ₁ ↔ F ₂, where U, I and F represent the unfolded, intermediate and folded states, respectively. The finding that the two helical subunits are successively formed is consistent with the experimental observations, and the Asp9/Arg16 salt bridge forms at the final stage and does not play a significant role during folding kinetics. The presence of water solvents induces hydrophobic collapse as the whole cage comparatively closes. Within aqueous solutions, the Trp-cage folding begins to contract into the meta-stable state, and by traversing the transition state it arrives at the native-like structure, which resembles the experimental structure closely.

Keywords:

• Trp-cage
• protein folding
• mechanism
• temperature-controlled molecular dynamics
• explicit solvent molecular dynamics

Acknowledgements

This work was supported by grants from the Special Fund for Basic Scientific Research of Central Colleges (No. DL09EA04-2), the Major State Basic Research Development Program (No. 2004CB719902), the National Natural Science Foundation of China (No. 20903019), the Talented Funds of Northeast Forestry University (No. 220-602042) and the Cultivated Funds of Excellent Dissertation of Doctoral Degree Northeast Forestry University (No. 140-602051).