Hydrogen atoms in proteins: Positions and dynamics

Niklas Engler *, Andreas Ostermann * , Nobuo Niimura  and Fritz G. Parak * 

*Physik Department E17, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany; and Advanced Science Research Centre, Japan Atomic Energy Research Institute, Tokai-mura, Ibaraki-ken 319-1195, Japan

Communicated by Robert H. Austin, Princeton University, Princeton, NJ, July 9, 2003 (received for review August 5, 2002)

Hydrogen atoms constitute about half of the atoms in proteins. Thus they contribute to the complex energy landscape of proteins [Frauenfelder, H., Sligar, S. G. & Wolynes, P. G. (1991) Science 254, 1598-1603]. Neutron crystal structure analysis was used to study the positions and mean-square displacements of hydrogen in myoglobin. A test of the reliability of calculated hydrogen atom coordinates by a comparison with our experimental results has been carried out. The result shows that >70% of the coordinates for hydrogen atoms that have a degree of freedom is predicted worse than 0.2 Å. It is shown that the mean-square displacements of the hydrogen atoms obtained from the Debye-Waller factor can be divided into three classes. A comparison with the dynamic mean-square displacements calculated from the elastic intensities obtained from incoherent neutron scattering [Doster, W., Cusack, S. & Petry, W. (1989) Nature 337, 754-756] shows that mainly the side-chain hydrogen atoms contribute to dynamic displacements on a time scale faster than 100 ps.

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