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Neutron Protein CrystallographyHydrogen, Protons, and Hydration in Bio-macromolecules$
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Nobuo Niimura and Alberto Podjarny

Print publication date: 2011

Print ISBN-13: 9780199578863

Published to Oxford Scholarship Online: May 2011

DOI: 10.1093/acprof:oso/9780199578863.001.0001

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Hydrogen, protons, and hydration in bio-macromolecules

Hydrogen, protons, and hydration in bio-macromolecules

Chapter:
(p.124) Part III Hydrogen, protons, and hydration in bio-macromolecules
Source:
Neutron Protein Crystallography
Author(s):

Nobuo Niimura

Alberto Podjarny

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780199578863.003.0003

In this final part, as many as possible of the results from neutron protein crystallography (NPC) to date are introduced. To organize the results from NPC, an online database called the “Hydrogen and Hydration in Proteins Data Base” (HHDB) has been created. This database catalogs all of the hydrogen-atom positions in biological macromolecules and in hydration water molecules that have been determined thus far by NPC. The HHDB provides a graphic interface for visualizing all types of interactions involving hydrogen atoms, such as methyl-group configurations, the potential number of hydrogen bonds (H-bonds) of amino acid residues, bifurcated H-bonds, noncolinear H-bonds, frustrated H-bonds, and hydrogen-to-deuterium exchange. The significance and insight of these kinds of information are illustrated by using two proteins, RNase A and insulin, as examples. The physiological significances of the protonation/deprotonation of biologically important amino-acid residues are also illustrated by various proteins.

Keywords:   hydrogen bond, noncolinear HB, bifurcated HB, HHDB, methyl group configuration, hydration, histidine, carboxylate group

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