Molecular Dynamics Simulations of the Dimerization of Transmembrane α-Helices

摘要

Membrane proteins account for nearly anquarter of all genes, but their structurenand function remain incompletely understood.nMost membrane proteins have transmembranen(TM) domains made up of bundles of hydropho-nbic -helices. The lateral association of TM heli-nces within the lipid bilayer is a key stage in thenfolding of membrane proteins. It may also playna role in signaling across cell membranes.nDimerization of TM helices is a simple example of such lateral association.nMolecular dynamics (MD) simulations have been used for over a decade to study membrane proteins in a lipidnbilayer environment. However, direct atomistic (AT) MD simulation of self-assembly of a TM helix bundle remains chal-nlenging. AT-MD may be complemented by coarse-grained (CG) simulations, in which small numbers of atoms arengrouped together into particles. In this Account, we demonstrate how CG-MD may be used to simulate formation ofndimers of TM helices. We also show how a serial combination of CG and AT simulation provides a multiscale approachnfor generating and refining models of TM helix dimers.nThe glycophorin A (GpA) TM helix dimer represents a paradigm for helix helix packing, mediated by a GxxxGnsequence motif. It is well characterized experimentally and so is a good test case for evaluating computational meth-nods. CG-MD simulations in which two separate TM helices are inserted in a lipid bilayer result in spontaneous for-nmation of a right-handed GpA dimer, in agreement with NMR structures. CG-MD models were evaluated via comparisonnwith data on destabilizing mutants of GpA. Such mutants increased the conformational flexibility and the dissocia-ntion constants of helix dimers. GpA dimers have been used to evaluate a multiscale approach: A CG model is con-nverted to an AT model, which is used as the basis of an AT-MD simulation. Comparison of three AT-MD simulationsnof GpA, one starting from a CG model and two starting from NMR structures, leads to convergence to a common refinednstructure for the dimer.nCG-MD self-assembly has also been used to model dimerization of the TM domain of the syndecan-2 receptor pro-ntein. This TM helix contains a GxxxG motif, which mediates right-handed helix packing comparable to that of the GxxxGnmotif in GpA. The multiscale approach has been applied to a more complex system, the heterodimeric IIb/u00013 inte-ngrin TM helix dimer. In CG-MD, both right-handed and left-handed structures were formed. Subsequent AT-MD sim-nulations showed that the right-handed structure was more stable, yielding a dimer in which the GxxxG motif of thenIIb TM helix packed against a hydrophobic surface of the u00013 helix in a manner comparable to that observed in twonrecent NMR studies.nThis work demonstrates that the multiscale simulation approach can be used to model simple membrane pro-nteins. The method may be applied to more complex proteins, such as the influenza M2 channel protein. Future refine-nments, such as extending the multiscale approach to a wider range of scales (from CG through QM/MM simulations,nfor example), will expand the range of applications and the accuracy of the resultant models.