Domański Jan, Sansom Mark S P, Stansfeld Phillip J, Best Robert B
Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States.
J Chem Theory Comput. 2018 Mar 13;14(3):1706-1715. doi: 10.1021/acs.jctc.7b00983. Epub 2018 Feb 9.
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
原子模拟最近已被证明足够精确，能够使球状蛋白质可逆折叠，并且为折叠机制提供了见解。从膜蛋白折叠和缔合的模拟中获得类似的理解将具有极大的医学意义。跨膜蛋白结构域折叠和组装的全原子模拟更具挑战性，尤其是由于脂质双分子层膜内的扩散非常缓慢。在这里，我们专注于膜蛋白折叠和组装的一个简单且特征明确的原型，即血型糖蛋白A（一种单跨膜螺旋的同型二聚体）的二聚化。我们使用CHARMM36力场确定了二聚体缔合的自由能景观。我们发现天然结构是一个亚稳态，但并不像根据解离常数的实验估计以及在各种条件下获得的众多实验结构所预期的那样稳定。我们探索了两种直接的方法来解决这个问题，并证明它们能产生解离常数与实验数据一致的稳定二聚体。
