Biomedical Engineering Reference
In-Depth Information
Introduction to Molecular Dynamics: Theory
and Applications in Biomolecular Modeling
Yi Wang and J. Andrew McCammon
1
Introduction
Since the first molecular dynamics (MD) simulation of a protein was performed over
30 years ago [
87
], MD has been used to study a variety of biomolecular systems,
including proteins, nucleotides, lipid bilayers, and carbohydrates [
16
,
64
,
88
,
101
].
Today, the problems tackled by MD range from large conformational changes
in proteins to free energy differences associated with subtle modifications in
ligands [
46
,
62
,
65
,
127
]. Since the high spatial and temporal resolution of MD is
rarely achieved in conventional experimental techniques, MD is increasingly used in
combination with various experimental methods to provide a multiscale description
of the structure, dynamics, and function of a biomolecule.
In a nutshell, MD is a method to integrate the classical (Newtonian) equations of
motion for a set of particles [
5
,
38
]. The result is a trajectory of the system over a
certain period of time, usually tens to hundreds of nanoseconds. Various structural
and dynamic properties of the system can then be calculated from the trajectory,
some of which may be directly compared with experimental results. In Fig.
1
,we
have shown a typical simulation system, consisting of a protein surrounded by
solvent water molecules. The system is used to study the enzyme neuraminidase
from the avian influenza virus H5N1 and was simulated for 100 ns [
78
]. At each
step of this 100-ns simulation, the force “felt” by every atom is calculated according
to a predefined potential energy function. It is then used to solve the equations of
Search WWH ::
Custom Search