Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
Article first published online: 3 FEB 2004
Copyright © 1988 Alan R. Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 4, Issue 2, pages 148–156, 1988
How to Cite
Brünger, A. T. and Karplus, M. (1988), Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison. Proteins, 4: 148–156. doi: 10.1002/prot.340040208
- Issue published online: 3 FEB 2004
- Article first published online: 3 FEB 2004
- Manuscript Revised: 31 MAY 1988
- Manuscript Received: 4 AUG 1987
- Protein structure;
- empirical energy;
- energy minimization;
- molecular dynamics
A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.