Griffin Mary A, Friedel Miriam, Shea Joan-Emma
Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
J Chem Phys. 2005 Nov 1;123(17):174707. doi: 10.1063/1.2101458.
We study the effects of confinement, sequence frustration, and surface interactions on the thermodynamics of dimerization of an off-lattice minimalist beta-barrel protein using replica exchange molecular dynamics. We vary the degree of frustration of the protein by tuning the specificity of the hydrophobic interactions and investigate dimerization in confining spheres of different radii. We also investigate surface effects by tethering the first residue of one of the proteins to a uniformly repulsive surface. We find that increasing the confinement and frustration stabilize the dimer, while adding a repulsive surface decreases its stability. Different ensembles of structures, including properly dimerized and various partially dimerized states, are observed at the association transition temperature T(a), depending on the amount of frustration and whether a surface is present. The presence of a surface is predicted to alter the morphology of larger aggregates formed from partially unfolded dimeric conformations.
我们使用复制交换分子动力学研究了限制、序列受挫和表面相互作用对非晶格简约β桶蛋白二聚化热力学的影响。我们通过调整疏水相互作用的特异性来改变蛋白的受挫程度，并研究不同半径限制球内的二聚化情况。我们还通过将其中一种蛋白的第一个残基连接到均匀排斥表面来研究表面效应。我们发现增加限制和受挫会使二聚体稳定，而添加排斥表面会降低其稳定性。在缔合转变温度T(a)下，根据受挫程度和是否存在表面，会观察到不同的结构集合，包括正确二聚化和各种部分二聚化状态。预计表面的存在会改变由部分未折叠二聚体构象形成的较大聚集体的形态。
