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Dynamics of myoglobin

Prof. Dr. G. Kneller, Centre de Biophysique Moleculaire, F-45071 Orleans

Myoglobin is a protein which transports oxygen in muscles of mammals. It consists of about 150 amino acids and was the first protein whose 3d structure was resolved by X-ray crystallography. The following video sequences are an attempt to visualize the origin of diffusive motion in myoglogin. They are based on an 300 picosecond Molecular Dynamics simulation of a single molecule in an primitive 'effective medium' which mimics the surrounding water.

It has been seen by quasielastic neutron scattering that the diffusive motion in myoglobin starts at about 200 K. Below 200 K the motion is harmonic. This temperature seems to be 'universal' for the mechanical functioning of proteins in general. The hypothesis is that the diffusive motion is due to a 'liquid-like' motion of the protein side chains which can be considered as rigid molecules of a 'side chain liquid'. It has been confirmed by a detailed analysis of the trajectory generated by the simulation.

Backbone motion (FileTypequicktime, 68 MB)

2.a) This sequence show the motion of the backbone which folds into 8 so-called alpha-helicies. The backbone exhibits a perturbed low-amplitude harmonic motion and no pronounced diffusive motion.

Side-chain motion

(31 selected side-chains) (FileTypequicktime, 89 MB)

2.b) Here the motion of 31 selected side chains is shown. The stochastic (diffusive) characteristics of the dynamics is well seen.

Corresponding rigid side-chain motion (FileTypequicktime, 70 MB)

2.c) In the ANALYSIS the side chains in the actual trajectory have been replaced by rigid reference structures using optimal superposition in a least-squares sense. The result is a 'rigid side-chain trajectory' which exhibits exactly the type of dynamics as the original side chains in the simulation. This is the visual proof of the hypothesis mentioned above.

The movies were generated with molscript and raster3d.