Abstract:

Using temperature controlled and normal temperature molecular dynamics methods, an in-depth study
was undertaken on the folding mechanismof the tubulin active peptide (Pep1-28). The total simulation time was 380.0 ns. We found a clear folding pathway by gradually decreasing the temperature using temperature controlled molecular dynamics simulations. Noticeable folding was observed at about 550 K and reversible folding and unfolding mechanisms were determined as U(>1200 K)←→←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2 (300 K), where U is an unfolded conformation and I1, I2, I3, and I4 are four important intermediates in the folding process. F1 and F2 are two folded conformations with similar structures. Conformational transformation and the folding process take place very quickly in normal temperature molecular dynamics, causing great difficulty in observing effective and stable intermediate conformations. The normal temperature molecular dynamics folds into a local energy minimum with the structure having severe discrepancies with that of the temperature controlled (300 K). The energy difference between these two folded structures was calculated to be as high as 297.53 kJ·mol-1. Therefore, the temperature controlled molecular dynamics method can provide direct and reliable proof for folding and unfolding by presenting the important intermediate conformations and can also induce folding towards the global lowest-energy conformation by crossing over high energy barriers.

Key words: Tubulin, Temperature-controlled molecular dynamics, Conformational analysis, Folding mechanism, Intermediates