Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison

A T Brünger, M Karplus


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.


Jun 16, 1977·Nature·J A McCammonM Karplus
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Jun 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·B R Gelin, M Karplus
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Aug 22, 2000·Biopolymers·C GuilbertJ C Smith
Mar 1, 1990·Biopolymers·M NilgesA M Gronenborn
Dec 24, 2002·Journal of Computational Chemistry·Robert J PetrellaMartin Karplus
Feb 1, 1994·Protein Science : a Publication of the Protein Society·Z S Hendsch, B Tidor
Feb 1, 1997·Protein Science : a Publication of the Protein Society·S T WlodekJ A McCammon
Jan 7, 1998·Protein Science : a Publication of the Protein Society·T LazaridisM Karplus
Mar 26, 1998·Protein Science : a Publication of the Protein Society·L T ChongB Tidor
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Jun 1, 1992·Journal of Molecular Graphics·X de la CruzI Fita
Nov 26, 2002·Journal of Molecular Biology·Olivier Michielin, Martin Karplus
May 5, 1998·Molecular Immunology·U LamminmäkiT Lövgren
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