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Grid-steered molecular dynamics
Grid-steered molecular dynamics (G-SMD) is a flexible method for applying forces that our group has implemented in NAMD. Much as in experiment, simulation studies often involve perturbing the system in some way and monitoring the result. As simulations have become bigger, longer, and more complex, the need for more sophisticated forcing techniques has increased. In the G-SMD method, an arbitrary external potential field, defined on a grid, is applied to desired target atoms with arbitrary coupling, making it a very flexible tool. Because it is coded natively in NAMD, the performance impact of G-SMD is minimal. G-SMD provides tremendous flexibility in the forces that can be applied. It was originally designed to apply anenhanced electrostatic fieldto DNA threaded through the membrane protein α-hemolysin in order to realistically increase the DNA translocation speed. It is the basis for a method of combining crystallographic structures and cryo-EM maps to obtain an all-atom model developed by Trabucoet al.and calledMolecular Dynamics Flexible Fitting (MDFF)。我们小组最近还使用了这种方法的一种变体mechanical properties of a complete microtubule。
David B. Wells, and Aleksei AksimentievBiophys J(2010)
Microtubules are ubiquitous biological filaments found in all eukaryotic cells. They are the largest type of cellular filament, and are essential in processes ranging from mitosis and meiosis to flaggelar motility. Due to their structural importance, the mechanical properties of microtubules have been extensively studied. However, because of the small size of microtubules and their high rigidity, experimental studies have determined the Young's modulus only indirectly. Molecular dynamics (MD) simulations allows the elastic properties of a biopolymer to be determined computationally. However, while the atomic structures of the building blocks of a microtubule (α- and β-tubulin) have been solved, the only published structures of a complete microtubule are cryo-electron microscopy maps far from atomic resolution. Using the cryo-EM map as a guide, we have produced the first all-atom structure of a complete microtubule. With this model, we applied tension, compression, and shear to determine the elastic moduli of an effectively infinite microtubule, yielding results in agreement with previous estimates. Thisworkis one of the first to combine cryo-EM and crystallographic structures for subsequent all-atom MD simulation. The successful performance of such a model opens the door to the simulation of many other systems whose constituent units are known in atomic detail but whose complete structure is known only at lower resolution.
