Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Neutron crystallography for the study of hydrogen bonds in macromolecules

Journal Article · · Molecules
 [1];  [2];  [3]
  1. European Spallation Source (ESS), Lund (Sweden); Lund Univ. (Sweden). Dept. of Biochemistry and Structural Biology
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. European Spallation Source (ESS), Lund (Sweden); Lund Univ. (Sweden). Dept. of Biology
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.
Research Organization:
Los Alamos National Laboratory (LANL)
Sponsoring Organization:
USDOE Office of Science (SC). Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1352431
Report Number(s):
LA-UR-17-22132
Journal Information:
Molecules, Journal Name: Molecules Journal Issue: 4 Vol. 22; ISSN 1420-3049
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English

References (75)

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase journal December 2016
Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values journal May 2011
Satisfying Hydrogen Bonding Potential in Proteins journal May 1994
Hydrogen bonding in globular proteins journal January 1984
Neutron protein crystallography: A complementary tool for locating hydrogens in proteins journal July 2016
Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability journal April 2005
Ultra-high Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor TMC114 journal October 2006
Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail journal May 2016
Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study journal June 2010
Cloning and sequence of a thermostable multidomain xylanase from the bacterium Rhodothermus marinus journal August 1997
Neutron Crystallographic Studies Reveal Hydrogen Bond and Water-Mediated Interactions between a Carbohydrate-Binding Module and Its Bound Carbohydrate Ligand journal October 2015
Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase journal September 2015
Solvent-Mediated Proton Transfer in Catalysis by Carbonic Anhydrase journal August 2007
Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different Ionization States in the Complex Formed with the Asymmetric Drug KNI-272 journal January 1996
The 0.78 Å Structure of a Serine Protease:  Bacillus lentus Subtilisin , journal September 1998
Accurate Hydrogen Positions in Organic Crystals: Assessing a Quantum-Chemical Aide journal January 2012
Binding of a Designed Substrate Analogue to Diisopropyl Fluorophosphatase:  Implications for the Phosphotriesterase Mechanism journal October 2006
Fluorescent Proteins: Shine on, You Crazy Diamond journal February 2013
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 journal August 2009
Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design journal June 2013
Analysis of the NMR Spin−Spin Coupling Mechanism Across a H−Bond:  Nature of the H-Bond in Proteins journal January 2004
Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution journal October 1992
Direct detection of CH/π interactions in proteins journal May 2010
Seeing the chemistry in biology with neutron crystallography journal January 2013
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement journal January 2009
Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography journal March 2009
Low-barrier hydrogen bond in photoactive yellow protein journal January 2009
Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects journal August 2010
Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography journal September 2012
Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases journal June 2014
Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer journal April 2015
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
Structural basis for carbohydrate-binding specificity—A comparative assessment of two engineered carbohydrate-binding modules journal March 2012
Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds journal May 2002
Neutron protein crystallography: beyond the folding structure of biological macromolecules journal December 2007
Neutron protein crystallography, beyond the folding structure of biological macromolecules journal August 2008
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP) journal October 2007
Neutron macromolecular crystallography with LADI-III journal October 2010
Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase) journal October 2010
Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography journal November 2014
Energy optimization of a regular macromolecular crystallography beamline for ultra-high-resolution crystallography journal January 2015
Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential journal June 2015
Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug journal July 2016
Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography journal January 2017
Low-barrier hydrogen bonds and enzymic catalysis journal June 1994
The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation journal January 2014
Mechanism of Action of D-Xylose Isomerase journal November 2000
Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values journal May 2011
Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus furiosus Rubredoxin: Implication of Hydronium Ions and Protonation State Equilibria in Redox Changes journal December 2012
Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus furiosus Rubredoxin: Implication of Hydronium Ions and Protonation State Equilibria in Redox Changes journal December 2012
Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase journal December 2016
Solvent-Mediated Proton Transfer in Catalysis by Carbonic Anhydrase journal November 2007
X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase journal April 2011
Automated 2D NOESY Assignment and Structure Calculation of Crambin(S22/I25) with the Self-Correcting Distance Geometry Based NOAH/DIAMOD Programs journal January 1999
C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability journal February 2014
Cloning and sequence of a thermostable multidomain xylanase from the bacterium Rhodothermus marinus journal August 1997
Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography journal December 2015
Neutron Structure of Human Carbonic Anhydrase II: A Hydrogen-Bonded Water Network “Switch” Is Observed between pH 7.8 and 10.0 journal November 2011
Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different Ionization States in the Complex Formed with the Asymmetric Drug KNI-272 journal January 1997
Neutron Diffraction of Acetazolamide-Bound Human Carbonic Anhydrase II Reveals Atomic Details of Drug Binding journal September 2012
Direct visualization of a Fe(IV)–OH intermediate in a heme enzyme journal November 2016
Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS journal August 2003
Neutron protein crystallography: beyond the folding structure of biological macromolecules journal December 2007
Short hydrogen bonds in photoactive yellow protein journal May 2004
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP) journal October 2007
Neutron macromolecular crystallography with LADI-III journal October 2010
Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase) journal October 2010
Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography journal November 2014
Energy optimization of a regular macromolecular crystallography beamline for ultra-high-resolution crystallography journal January 2015
Crystal structure of small protein crambin at 0.48 Å resolution journal March 2011
Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential journal June 2015
Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug journal July 2016
Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography journal January 2017
Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase journal July 2014
Hydrogen Atomic Positions of O–H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with 1H-NMR Chemical Shifts and X-ray Diffraction Methods journal March 2017

Cited By (11)

A shared vision for macromolecular crystallography over the next five years journal November 2019
Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds? journal August 2019
Neutron Macromolecular Crystallography book January 2020
Symmetry and 1 H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects journal January 2020
Unraveling the structural and chemical features of biological short hydrogen bonds journal January 2019
Neutron macromolecular crystallography journal February 2018
IMAGINE: neutrons reveal enzyme chemistry journal July 2018
Membrane-protein crystals for neutron diffraction journal November 2018
Membrane-protein crystals for neutron diffraction text January 2018
X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions journal November 2019
From Initial Hit to Crystal Optimization with Microseeding of Human Carbonic Anhydrase IX—A Case Study for Neutron Protein Crystallography journal November 2018

Similar Records

Powder Crystallography on Macromolecules
Journal Article · Mon Dec 31 23:00:00 EST 2007 · Acta Crystallographica Section A: Foundations of Crystallography · OSTI ID:959547

Neutron protein crystallography: Current status and a brighter future
Journal Article · Sat Dec 31 23:00:00 EST 2005 · Current Opinion in Structural Biology · OSTI ID:1003631

X-ray crystallography and biological metal centers: is seeing believing?
Journal Article · Sun Mar 07 23:00:00 EST 2010 · Inorg. Chem. · OSTI ID:1008483