An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation.
An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation.
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一个有效的阿尔法螺旋模型和模拟框架的静态静电相互作用力估计。
DOI：
10.1038/s41598-021-88369-3
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发表时间：
2021-04-27
影响因子：
4.6
通讯作者：
Jones CI
中科院分区：
文献类型：
--
作者：
Butcher GG;Harwin WS;Jones CI
talin棒域内的α -螺旋线圈通过其展开和再折叠动力学具有机械和信号功能。更好地了解talin展开事件和所涉及的力量，应该可以更好地预测talin信号。为了克服目前分子动力学模拟中力测量的局限性，开发了一种直接在力域内运行的新的模拟框架。结合相应的alpha-helix建模方法，建立了基于机器人运动学的仿真框架，以明确目标力的相互作用。利用坐标框架有效地划分模拟结构，并应用静力分析来确定力和扭矩在蛋白质结构中的传播。利用库仑定律的静电近似结果表明，在5-40 pN的生理相关范围内，talin棒子域的模拟力相互作用。这涵盖了talin操作的力范围，并且比比较的全原子和粗粒度分子动力学更接近实验测量值2-3个数量级。因此，这种有针对性的、基于力的仿真能够产生比以前的仿真方法更真实的力值。
The alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.
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DOI：
10.1007/978-1-61779-307-3_23
发表时间：
2012-01-01
期刊：
PLATELETS AND MEGAKARYOCYTES, VOL 3: ADDITIONAL PORTOCOLS AND PERSPECTIVES
影响因子：
--
作者：
Jones, Chris I.;Barrett, Natasha E.;Jackson, Denise E.
通讯作者：
Jackson, Denise E.
DOI：
10.1111/jth.13302
发表时间：
2016-05
期刊：
Journal of thrombosis and haemostasis : JTH
影响因子：
--
作者：
Bye AP;Unsworth AJ;Gibbins JM
通讯作者：
Gibbins JM
影响因子：
17.1
作者：
Haining, Alexander William M.;von Essen, Magdalena;Hernandez, Armando del Rio
通讯作者：
Hernandez, Armando del Rio
塔林张力传感器揭示了局灶性粘附力传递和机械敏感性的新特征。
DOI：
10.1083/jcb.201510012
发表时间：
2016-05-09
期刊：
The Journal of cell biology
影响因子：
--
作者：
Kumar A;Ouyang M;Van den Dries K;McGhee EJ;Tanaka K;Anderson MD;Groisman A;Goult BT;Anderson KI;Schwartz MA
通讯作者：
Schwartz MA
DOI：
10.1093/bioinformatics/btq662
发表时间：
2011-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Benkert P;Biasini M;Schwede T
通讯作者：
Schwede T