摘要
本文报道了我们使用分子动力学方法模拟胰凝乳蛋白酶原激活过程的研究.使用我们所提出的虚拟势法,通过对不加虚拟势和加大小不等的虚拟势的几种情形的模拟和比较,对于激活过程可能具有的时间尺度以及过程中势垒的位置及性质都给出了一定的信息,这是只用普通(?)分子动力学方法不易达到的.
A Molecular Dynamics (MD) study of the activation of chymotrypsinogen is carried out In a long MD simulation of chymotrypsinogen of Ins, the Ile 16,which should move to the place occupied by Met192 in the zymogen, did not move any further when it is still 10A away from its destination. We proposed a method for dealing with this kind of problems by introducing a pseudo-potential which is proportional to the square of the distance between the atom which is moved largest during the activation and its destination. By changing the strength of the pseudo - potential and carrying out the MD simulation with the pseudo - potential included, one get some results about the actuvation process which is not easily obtainable by the usual MD simulation. We have found that, as expected, when the pseudo-potential is large, the Ile16 moves to its destination very quickly and when it is small Ilel6 does not move to its destination in the simulation time of about 1ns. The most interested things happened when the strength of the pseudo - potential is between the above two limits. We have seen that the distance of between Ilel6 and its destination, after a long period of oscillating around 10A, decreased very sharply in a very short period of time, which is dearly a evidence of jumping through a potential barrier. The potential peak is found to be about 9A away from the destination Metl92 Since a pseudo-potential is included in the calculation, the above result is only a approximation. We also pointed out that this pseudo - potential method, since it used the information of the final state, should work better than the simulated - annealing method, which is a more familiar method for jumping through potential barrier.
出处
《生物物理学报》
CAS
CSCD
北大核心
1990年第2期217-220,共4页
Acta Biophysica Sinica
