Neutron crystallography for the study of hydrogen bonds in macromolecules
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
- Authors:
-
[2];
- European Spallation Source (ESS), Lund (Sweden); Lund Univ. (Sweden). Dept. of Biochemistry and Structural Biology
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- European Spallation Source (ESS), Lund (Sweden); Lund Univ. (Sweden). Dept. of Biology
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC). Biological and Environmental Research (BER) (SC-23)
- OSTI Identifier:
- 1352431
- Report Number(s):
- LA-UR-17-22132
Journal ID: ISSN 1420-3049
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Molecules
- Additional Journal Information:
- Journal Volume: 22; Journal Issue: 4; Journal ID: ISSN 1420-3049
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biological Science; neutron crystallography, protein structure
Citation Formats
Oksanen, Esko, Chen, Julian C., and Fisher, Zoe. Neutron crystallography for the study of hydrogen bonds in macromolecules. United States: N. p., 2017.
Web. doi:10.3390/molecules22040596.
Oksanen, Esko, Chen, Julian C., & Fisher, Zoe. Neutron crystallography for the study of hydrogen bonds in macromolecules. United States. https://doi.org/10.3390/molecules22040596
Oksanen, Esko, Chen, Julian C., and Fisher, Zoe. Fri .
"Neutron crystallography for the study of hydrogen bonds in macromolecules". United States. https://doi.org/10.3390/molecules22040596. https://www.osti.gov/servlets/purl/1352431.
@article{osti_1352431,
title = {Neutron crystallography for the study of hydrogen bonds in macromolecules},
author = {Oksanen, Esko and Chen, Julian C. and Fisher, Zoe},
abstractNote = {The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.},
doi = {10.3390/molecules22040596},
journal = {Molecules},
number = 4,
volume = 22,
place = {United States},
year = {Fri Apr 07 00:00:00 EDT 2017},
month = {Fri Apr 07 00:00:00 EDT 2017}
}
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Accurate Hydrogen Positions in Organic Crystals: Assessing a Quantum-Chemical Aide
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Fluorescent Proteins: Shine on, You Crazy Diamond
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Combined High-Resolution Neutron and X-ray Analysis of Inhibited Elastase Confirms the Active-Site Oxyanion Hole but Rules against a Low-Barrier Hydrogen Bond
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- Journal of the American Chemical Society, Vol. 131, Issue 31
Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design
journal, June 2013
- Weber, Irene T.; Waltman, Mary Jo; Mustyakimov, Marat
- Journal of Medicinal Chemistry, Vol. 56, Issue 13
Analysis of the NMR Spin−Spin Coupling Mechanism Across a H−Bond: Nature of the H-Bond in Proteins
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Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution
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Direct detection of CH/π interactions in proteins
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Seeing the chemistry in biology with neutron crystallography
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Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement
journal, January 2009
- Blum, Marc-Michael; Mustyakimov, Marat; Rüterjans, Heinz
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Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography
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- Adachi, M.; Ohhara, T.; Kurihara, K.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 12
Low-barrier hydrogen bond in photoactive yellow protein
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- Proceedings of the National Academy of Sciences, Vol. 106, Issue 2
Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects
journal, August 2010
- Herve, C.; Rogowski, A.; Blake, A. W.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 34
Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography
journal, September 2012
- Chen, J. C. - H.; Hanson, B. L.; Fisher, S. Z.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases
journal, June 2014
- Kjaergaard, C. H.; Qayyum, M. F.; Wong, S. D.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 24
Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer
journal, April 2015
- Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John-Paul
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 18
X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.
journal, June 1989
- Carrell, H. L.; Glusker, J. P.; Burger, V.
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Structural basis for carbohydrate-binding specificity—A comparative assessment of two engineered carbohydrate-binding modules
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- Glycobiology, Vol. 22, Issue 7
Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds
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Neutron protein crystallography, beyond the folding structure of biological macromolecules
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- Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue a1
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)
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- Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 11
Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase)
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Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography
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Low-barrier hydrogen bonds and enzymic catalysis
journal, June 1994
- Cleland, W.; Kreevoy, M.
- Science, Vol. 264, Issue 5167
The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation
journal, January 2014
- Oksanen, Esko; Blakeley, Matthew P.; El-Hajji, Mohamed
- PLoS ONE, Vol. 9, Issue 1
Mechanism of Action of D-Xylose Isomerase
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