Global Transitions or Proteins Explored by a Multiscale Hybrid Methodology: Application to Dopamine Transporter

Abstract

Efficient and accurate mapping of transition pathways is a challenging problem in allosteric proteins. We propose here a new methodology which facilitates the sampling of the conformational space by recruiting all modes of motions naturally encoded by the protein architecture, while evaluating the atomic interactions and energetics via full-atomic molecular dynamics (MD) simulation protocol. The basic approach is to deform the structure collectively along the modes of motion predicted by the anisotropic network model (ANM), similar to our adaptive ANM procedure,1 but with major difference of considering the complete pool of all accessible modes using a Monte Carlo/Metropolis algorithm. Once a low-resolution intermediate structure is constructed it is set as the target for all atom-simulations analogous to our folding study2. The new method takes advantage of the speed of low-resolution approach while maintaining the accuracy of MD. After benchmarking the methodology with adenylate kinase we examined the transition mechanism of dopamine transporter (DAT) between its inward- and outward-facing states. An intermediate state occluded to both the extra- and intracellular regions is identified. The transition from intermediate-to-outward state involves a global bending of the N-terminal half of the transmembrane helix TM10, which drives the disruption of the salt bridge R85-D476 on TM1b and TM10, which, in turn, prompts the opening of the external gate. The intermediate-to-inward transition is facilitated by the rotation of TM4 and TM9 relative to the rest of the protein, and a redistribution of interactions between the N-terminal segment and TM8.1. Yang Z, Majek P, Bahar I. Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol 2009;5(4):e1000360.2. Arkun Y, Gur M. Combining optimal control theory and molecular dynamics for protein folding. PLoS One 2012;7(1):e29628.