How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: 尾2-Adrenergic Receptor in the Spotlight

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• 作者：Moutusi Manna ; Waldemar Kulig ; Matti Javanainen ; Joona Tynkkynen ; Ulf Hensen ; Daniel J. M眉ller ; Tomasz Rog ; Ilpo Vattulainen
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：July 14, 2015
• 年：2015
• 卷：11
• 期：7
• 页码：3432-3445
• 全文大小：741K
• ISSN：1549-9626

文摘

Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however. Instead the crystallized proteins are commonly engineered, including structural modifications (mutations, replacement of protein sequences by antibodies, bound ligands, etc.) whose impact on protein structure and dynamics is largely unknown. Here we explore this issue through atomistic MD simulations (鈭? 渭s in total), focusing on the 尾₂-adrenergic receptor (尾₂AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure of 尾₂AR, we remove the many modifications in 尾₂AR systematically one at a time, in six consecutive steps. After each step, we equilibrate the system and simulate it quite extensively. The results of this step-by-step approach highlight that the structural modifications used in crystallization can affect ligand and G-protein binding sites, packing at the transmembrane-helix interface region, and the dynamics of connecting loops in 尾₂AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on 尾₂AR are removed instantaneously at the same time, it turns out that the step-by-step method provides results that are superior in terms of maintaining protein structural stability. The results provide compelling evidence that for membrane proteins whose 3D structure is based on structural engineering, the preparation of protein structure for atomistic MD simulations is a delicate and sensitive process. The results show that most valid results are found when the structural modifications are reverted slowly, one at a time.