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Molecular simulation at the interface between experiment and theory – Theoretical Biophysics Group,

SOLEIL and the Molecular Biophysics Centre, CNRS Orleans
SOLEIL Company Contents > All the news > News 2008 > Molecular simulation

The figure shows lattice vibrations in a protein crystal. The unit cell of the crystal contains eight lysozyme molecules. Four unit cells are shown individually colored. The lattice vibrations have been calculated using an elastic network model that describes the interactions in protein systems by springs between pairs of carbon-alpha atoms that are near each other.

 

 

 

Internal dynamics of a lysozyme molecule in solution (water) for a few picoseconds (10-12 s). The solvent cannot be seen.

 

 

 

 

 

 

 

 

 

Network vibrations in a lysozyme crystal. The crystalline unit cell contains eight molecules of lysozyme. Four unit cells of different colour can be seen. The vibrations were calculated based on an elastic network model that describes the interactions in the protein systems as springs linking the nearby α-carbon atoms.

 

Molecular simulation can help in the prediction and analysis of experimental data and in developing theoretical models of the dynamics of proteins and protein crystals. 

 
Recent references: 
[1] V. Calandrini and G.R. Kneller. Influence of pressure on the fractional
relaxation dynamics in proteins: A simulation study. J. Chem. Phys. 128(6):065102, 2008.
 
[2] V. Calandrini, D. Abergel, and G.R. Kneller. Protein dynamics from a NMR perspective: Networks of coupled rotators and fractional brownian dynamics. J .Chem. Phys. 128(14):145102, 2008.
 
[3] V. Calandrini, V. Hamon, K. Hinsen, P. Calligari, M.-C. Bellissent-Funel, and
G.R. Kneller. Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering. Chem. Phys., 345:289–297, 2008.
 
[4] K. Hinsen and G.R. Kneller. Solvent effects in the slow dynamics of proteins. Proteins: Structure, Function, and Genetics, 70(4):1235–1242, 2008.
 
[5] G.R. Kneller. Eckart axis conditions, Gauss’ principle of least constraint, and
the optimal superposition of molecular structures. J. Chem. Phys., 128(194101), 2008
 
[6] K. Wood, S. Grudinin, B. Kessler, M. Weik, M. Johnson, G.R. Kneller, D. Oesterhelt, and G. Zaccai. Dynamical heterogeneity of specific amino acids in bacteriorhodopsin. J. Mol. Biol., 380(3):581–591, 2008.
 
[7] K. Hinsen, Structural flexibility in proteins: impact of the crystal environment, Bioinformatics 24:521-528 (2008)

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