Conference publications

Abstracts

XVIII conference

Exploration of mechanical properties of proteins using the method of molecular dynamics

Glyakina A.V., Galzitskaya O.V.¹, Balabaev N.K.

Institute of Mathematical problems of biology RAS, Russia, 142290, Pushchino, Institutskaya 4

¹Institute of protein research RAS, Russia, 142290, Pushchino, Institutskaya 4

1 pp. (accepted)

Proteins play an important role in different biological processes. At the same time they are very perspective structural and functional elements of future nanodevices. Functional facilities of macromolecules basically are determined by their mechanical properties.

The mechanical properties of two immunoglobulin-binding domains of proteins L and G, which have the same three-dimensional structures, but differ in amino acid sequences, were investigated using the method of molecular dynamics (force field AMBER-99 [1]). To do this the proteins were stretched by the termini with constant force and constant velocity. During the simulations the all-atom model of proteins and explicit model of water [2] were used.

It was found that under the high forces (F > 800 pN) and stretching velocities (v > 0.0625 Å/ps) average times and average maximal forces which required for unfolding of these proteins are similar. Within decreasing of force and stretching velocity, in average, more times and larger force are required for the unfolding of protein G in comparison with protein L. It can be supposed that protein G is mechanically more stable than protein L in the range of low stretching velocities and forces. But at the same time the value of force does not change pathways of mechanical unfolding of these proteins [3].

References

1. Wang J., Cieplak А., Kollman P.A. How Well a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? // J. Comp. Chem., 21, 2000, 1049-1074.

2. Lemak A.S., Balabaev N.K. A Comparison between Collisional Dynamics and Brownian Dynamics. // Mol. Simul., 15, 1995, 223-231.

3. Glyakina A.V., Balabaev N.K., Galzitskaya O.V. Mechanical unfolding of proteins L and G with constant force: similarities and differences. // J. Chem. Phys., 131, № 045102, 2009, 1–10.

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