Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular Diffusion.,The Journal of Physical Chemistry B

当前位置： X-MOL 学术 › J. Phys. Chem. B › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular Diffusion.
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-03-14 , DOI: 10.1021/acs.jpcb.7b11846
Christopher J Fennell , Neda Ghousifam , Jennifer M Haseleu ₁ , Heather Gappa-Fahlenkamp

Affiliation

We present an atomistic level computational investigation of the dynamics of a signaling protein, monocyte chemoattractant protein-1 (MCP-1), that explores how simulation geometry and solution ionic strength affect the calculated diffusion coefficient. Using a simple extension of noncubic finite size diffusion correction expressions, it is possible to calculate experimentally comparable diffusion coefficients that are fully consistent with those determined from cubic box simulations. Additionally, increasing the concentration of salt in the solvent environment leads to changes in protein dynamics that are not explainable through changes in solvent viscosity alone. This work in accurate computational determination of protein diffusion coefficients led us to investigate molecular-weight-based predictors for biomolecular diffusion. By introducing protein volume- and protein surface-area-based extensions of traditional statistical relations connecting particle molecular weight to diffusion, we find that protein solvent-excluded surface area rather than volume works as a better geometric property for estimating biomolecule Stokes radii. This work highlights the considerations necessary for accurate computational determination of biomolecule diffusivity and presents insight into molecular weight relations for diffusion that could lead to new routes for estimating protein diffusion beyond the traditional approaches.

中文翻译：

生物分子扩散中的计算信号蛋白动力学和几何质量关系。

我们目前对信号蛋白单核细胞趋化蛋白-1（MCP-1）的动力学进行原子级的计算研究，探讨了模拟几何形状和溶液离子强度如何影响计算的扩散系数。使用非立方有限尺寸扩散校正表达式的简单扩展，可以计算与立方框模拟确定的扩散系数完全一致的实验可比较扩散系数。另外，增加溶剂环境中盐的浓度会导致蛋白质动力学的变化，这仅凭溶剂粘度的变化是无法解释的。这项对蛋白质扩散系数的精确计算确定的工作使我们研究了基于分子量的生物分子扩散预测因子。通过引入传统的统计关系中基于蛋白质体积和蛋白质表面积的扩展，将粒子的分子量连接到扩散，我们发现蛋白质溶剂排除的表面积而不是体积可以更好地估算生物分子斯托克斯半径。这项工作强调了精确计算确定生物分子扩散性所需的考虑因素，并提出了对扩散分子量关系的洞察力，这可能会导致新的估算蛋白质扩散的途径超越传统方法。我们发现蛋白质溶剂排除的表面积而不是体积可以更好地估算生物分子斯托克斯半径。这项工作强调了精确计算确定生物分子扩散性所需的考虑因素，并提出了对扩散分子量关系的洞察力，这可能会导致新的估算蛋白质扩散的途径超越传统方法。我们发现蛋白质溶剂排除的表面积而不是体积可以更好地估算生物分子斯托克斯半径。这项工作强调了精确计算确定生物分子扩散性所需的考虑因素，并提出了对扩散分子量关系的洞察力，这可能会导致新的估算蛋白质扩散的途径超越传统方法。

更新日期：2018-03-06

点击分享查看原文

点击收藏

公开下载

阅读更多本刊最新论文