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

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Details

Original languageEnglish
Pages (from-to)3432-3445
Number of pages14
JournalJournal of Chemical Theory and Computation
Volume11
Issue number7
DOIs
Publication statusPublished - Jul 2015
Publication typeA1 Journal article-refereed

Abstract

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 (,5 its in total), focusing on the beta(2)-adrenergic receptor (beta(2)AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure beta(2)AR, we remove the many modifications in beta(2)AR 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 beta(2)AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on beta(2)AR 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.

Keywords

  • BETA-ADRENERGIC-RECEPTOR, MOLECULAR-DYNAMICS SIMULATIONS, ATOM FORCE-FIELD, COUPLED RECEPTORS, DRUG DESIGN, IONIC LOCK, CHOLESTEROL, BINDING, ACTIVATION, HELIX

Publication forum classification

Field of science, Statistics Finland