Single Molecule Dwell-time Distributions

Dwell-time distributions, waiting-time distributions, or distributions of pause durations are widely reported in single molecule biophysical experiments. Simplified models have enabled kinetic analyses of many systems, but they may misrepresent the data if reverse and branching kinetic pathways are present. We have developed a novel computational method that overcomes these limitations and can handle complex kinetic schemes. Furthermore this method can be used to globally fit data under different conditions with a single kinetic scheme. This method was originally developed for the analysis of single molecule dwell-time distributions of myosin V under different concentrations and optical trap forces.Reference:Liao, J.-C., Spudich, J.A., Parker, D., Delp, S.L. (2007) Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. Proceedings of the National Academy of Sciences, USA, 104, 3171-3716.http://www.pnas.org/cgi/content/abstract/104/9/3171 <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=83#pack_195">dwell code MATLAB </a> : MATLAB code for simulating single molecule dwell-time distributions. </li> <li> <a href="https://simtk.org/frs?group_id=83#pack_281">simdwell </a> : single molecule dwell-time simulation </li> </ul>

在单分子生物物理实验中，停留时间分布、等待时间分布或暂停持续时间分布被广泛报道。简化的模型已使许多系统的动力学分析成为可能，但若存在反向和分支动力学途径，则可能无法准确反映数据。本研究团队开发了一种新颖的计算机方法，克服了这些局限性，并能够处理复杂的动力学方案。此外，该方法可应用于在单一动力学方案下，对不同条件下的数据进行全局拟合。该方法最初是为分析肌球蛋白V在不同浓度和光学陷阱力下的单分子停留时间分布而开发的。参考文献：Liao, J.-C., Spudich, J.A., Parker, D., Delp, S.L. (2007) 将吸收边界法扩展至拟合具有复杂动力学途径的分子马达的停留时间分布。美国国家科学院院刊，104，3171-3716.http://www.pnas.org/cgi/content/abstract/104/9/3171。本项目中包含以下软件/数据包：
<ul>
<li><a href="https://simtk.org/frs?group_id=83#pack_195">dwell code MATLAB</a>：用于模拟单分子停留时间分布的MATLAB代码。</li>
<li><a href="https://simtk.org/frs?group_id=83#pack_281">simdwell</a>：单分子停留时间模拟。</li>
</ul>