کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2184293 1095822 2015 10 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants
ترجمه فارسی عنوان
استفاده از شبیه سازی های دینامیکی مولکولی به عنوان یک کمک در پیش بینی مبادله دامنه از گزینه های محاسباتی پروتئین
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی بیولوژی سلول
چکیده انگلیسی


• Computational protein design (CPD) calculations that do not consider competing states may lead to off-target folding.
• We developed an MD simulation protocol as a post-CPD screening tool.
• The MD protocol identifies mutations leading to undesired competing states.
• The MD protocol predicts mutations that favor the target fold.
• CPD combined with MD screening can greatly improve design success rates.

In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical with its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure and that, in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51-amino-acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased B-factors derived from MD simulation in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography.

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ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Molecular Biology - Volume 427, Issue 16, 14 August 2015, Pages 2697–2706
نویسندگان
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