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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion
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Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion

机译：通过可极化力田地精确预测蛋白质NMR旋转舒适。 应用于强烈各向异性的旋转扩散

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Among the various biophysical methods available to investigate protein dynamics, NMR presents the ability to scrutinize protein motions on a broad range of time scales. H-1-N-15 NMR spin relaxation experiments can reveal the extent of protein motions across the picosecond-nanosecond dynamics probed by the fundamental parameters N-15-R-1, N-15-R-2, and H-1-N-15 NOE that can be well sampled by molecular dynamics (MD) simulations. An accurate prediction of these parameters is subjected to a proper description of the rotational diffusion and anisotropy. Indeed, a strong rotational anisotropy has a profound effect on the various relaxation parameters and could be mistaken for conformational exchange. Although the principle of NMR spin relaxation predictions from MD is now well established, numerous NMR/MD comparisons have hitherto focused on proteins that show low to moderate anisotropy and make use of a scaling factor to remove artifacts arising from water model-dependence of the rotational diffusion. In the present work, we have used NMR to characterize the rotational diffusion of the alpha-helical STAM2-UIM domain by measuring the N-15-R-1, N-15-R-2, and H-1-N-15 NOE relaxation parameters. We therefore highlight the use of the polarizable AMOEBA force field (FF) and show that it improves the prediction of the rotational diffusion in the particular case of strong rotational anisotropy, which in turn enhances the prediction of the N-15-R-1, N-15-R-2, and H-1-N-15 NOE relaxation parameters without the requirement of a scaling factor. Our findings suggest that the use of polarizable FFs could potentially enrich our understanding of protein dynamics in situations where charge distribution or protein shape is remodeled over time like in the case of multidomain proteins or intrinsically disordered proteins.
机译：其中用于调查的蛋白质动力学的各种生物物理方法，NMR呈现在广泛的时间尺度的能力，审议蛋白质运动。 H-1-N-15核磁共振自旋松弛实验可以揭示蛋白质运动穿过由基本参数N-15-R-1，N-15-R-2和H-1-探测皮秒纳秒动力学的程度N-15 NOE可通过分子动力学（MD）模拟很好地采样。这些参数的精确预测进行旋转扩散和各向异性的正确描述。事实上，强大的旋转各向异性对各种休闲参数产生深远的影响，并可能会被误构象交换。虽然从MD NMR自旋弛豫预测的原理是现在非常成熟，众多NMR / MD比较迄今一直侧重于蛋白质呈低到中度各向异性和利用缩放因子，以消除从旋转的水模型依赖所产生的假象扩散。在目前的工作中，我们使用NMR通过测量N-15-R-1，N-15-R-2和H-1-N-15，以表征α-螺旋STAM2-UIM域的旋转扩散NOE松弛参数。因此，我们突出使用可极化变形虫力场（FF），并表明，它提高了旋转扩散的预测在强旋转各向异性的特定情况下，这反过来又提高了N-15-R-1的预测， N-15-R-2和H-1-N-15 NOE松弛参数，而不缩放因子的要求。我们的研究结果表明，使用极化FF的可能丰富我们的蛋白质动力学的理解，在电荷分布或蛋白质形状是多结构域蛋白或内在无序蛋白质的情况下改造随着时间的推移像的情况。

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