Myoglobin fluctuations

Both attractive forces and repulsive forces are included in van der Waals interactions. The attractive forces are due primarily to instantaneous dipole-induced dipole interactions that arise because of fluctuations in the electron charge distributions of adjacent nonbonded atoms. Individual van der Waals interactions are weak ones (with stabilization energies of 4.0 to 1.2 kj/mol), but many such interactions occur in a typical protein, and, by sheer force of numbers, they can represent a significant contribution to the stability of a protein. Peter Privalov and George Makhatadze have shown that, for pancreatic ribonuclease A, hen egg white lysozyme, horse heart cytochrome c, and sperm whale myoglobin, van der Waals interactions between tightly packed groups in the interior of the protein are a major contribution to protein stability. 

Nienhaus, K., Ostermann, A., Nienhaus, U., Parak, R, and Schmidt M. 2005. Ligand migration and protein fluctuations in myoglobin mutant L29W. Biochemistry 44 5095-5105. 

Albani, J. and Alpert, B. (1987). Fluctuation domains in myoglobin. Fluorescence quenching studies. European Journal of Biochemistry, 162, 175-178. 

To provide an understanding of the importance of solvent mobility and the intrinsic protein energy surface, an MDS of proteins and surrounding solvent molecules at different temperatures has been performed. The simulation of myoglobin dynamics showed that solvent mobility is the dominant factor in determining protein atomic fluctuations above 180 K (Vitkup et ah, 2000). The drastic effects of water molecule dynamics on the intramolecular motion of RNase and xylase was demonstrated in recent computer simulation studies (Reat et al., 2000 Tarek et al, 2000). Extensive simulations were carried out to identify the time-scale of water attachment to lysozyme (Steprone et... 

The picosecond internal dynamics of myoglobin was explored by measuring inelastic neutron scattering by Smith et al. [25]. At low temperatures they found the dynamics to be harmonic while at higher temperatures a considerable quasielastic scattering was detected. Agreement between the experimentally observed spectra and that calculated from molecular dynamics simulations also showed evidence for restriction of the conformational space sampled at 80 K relative to 300 K. On the basis of these results it was concluded that the protein is trapped in local minima at low temperatures in accord with the multiple substate model suggested by low temperature flash photolysis experiments and previous molecular dynamics simulations. Comparison of atomic fluctuation data sets collected at both 325 K and 80 K confirms that the room temperature... 

To characterise the functionally Important motions in hydrated myoglobin, simulations on its hydrated CO complex have been performed by Steinbach and Brooks [35], In this study the temperature and hydration dependence of equilibrium dynamics was investigated. The authors performed two sets of MD simulations, torsionally restrained and unrestrained calculations on dehydrated carbonmonoxy myoglobin at different temperatures between 100 K and 400 K were compared to that on the hydrated protein. They found that the dehydrated protein exhibits almost exclusively harmonic fluctuations at all temperatures, while remarkable anharmonic motions have been detected in the hydrated protein at about 200 K independently whether the torsions were constrained. The... 

Of interest also are the results concerning deviations of the atomic fluctuations from simple isotropic and harmonic motion. As discussed in Chapt. XI, most X-ray refinements of proteins assume (out of necessity, because of the limited data set) that the motions are isotropic and harmonic. Simulations have shown that the fluctuations of protein atoms are highly anisotropic and for some atoms, strongly anharmonic. The anisotropy and anharmonicity of the atomic distribution functions in molecular dynamics simulations of proteins have been studied in considerable detail.193"197 To illustrate these aspects of the motions, we present some results for lysozyme196 and myoglobin.197 If Ux, Uy, and Uz are the fluctuations from the mean positions along the principal X, Y, and Z axes for the motion of a given atom and the mean-square fluctuations are... 

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