Neutron macromolecular crystallography

2018 ◽  
Vol 2 (1) ◽  
pp. 39-55 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Alberto D. Podjarny
Keyword(s):  
Neutron Diffraction ◽  
Fluorescent Proteins ◽  
National Laboratory ◽  
Direct Determination ◽  
Drug Binding ◽  
Proton Accelerator ◽  
Biological Macromolecules ◽  
Macromolecular Crystallography ◽  
Neutron Sources ◽  
Oak Ridge

Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.

Designing and Validating Parallel Wire Suspension Bridge Wire Strands for Neutron Diffraction Stress Mapping

2017 ◽  
Vol 905 ◽  
pp. 123-130
Author(s):  
Adrian Brügger ◽  
Seung Yub Lee ◽  
İsmail Cevdet Noyan ◽  
Raimondo Betti
Keyword(s):  
Neutron Diffraction ◽  
Steel Wire ◽  
National Laboratory ◽  
Suspension Bridge ◽  
Galvanized Steel ◽  
Element Analysis ◽  
Parallel Wire ◽  
Oak Ridge ◽  
Contact Points ◽  
Suspension Bridge Cables

Suspension-bridge cables are constructed from strands of galvanized steel wire. They are failure-critical structural members, so a fundamental understanding of their mechanics is imminently important in quantifying suspension bridge safety. The load-carrying capabilities of such strands after local wire failures have been the subject of many theoretical studies utilizing analytical equations and finite-element analysis. Little experimental data, however, exists to validate these models.Over the past five years we have developed a methodology for measuring stress/strain transfer within parallel wire strands of suspension bridge cables using neutron diffraction [1,2]. In this paper we describe the design and verification of parallel cable strands used in our studies. We describe the neutron diffraction strain measurements performed on standard 7-wire and expanded 19-wire models in various configurations at both the Los Alamos National Laboratory Spectrometer for Materials Research at Temperature and Stress (LANL SMARTS) and at the Oak Ridge National Laboratory VULCAN Engineering Materials Diffractometer (ORNL VULCAN). Particular attention is placed on the challenges of aligning and measuring multibody systems with high strain gradients at body-to-body contact points.

scholarly journals Preface: Special Topic on Advances in Modern Neutron Diffraction at Oak Ridge National Laboratory

2018 ◽  
Vol 89 (9) ◽  
pp. 092601
Author(s):  
Katharine Page ◽  
Bianca Haberl ◽  
Leighton Coates ◽  
Matthew Tucker
Keyword(s):  
Neutron Diffraction ◽  
National Laboratory ◽  
Special Topic ◽  
Oak Ridge ◽  
Oak Ridge National Laboratory

Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase

2020 ◽  
Vol 76 (10) ◽  
pp. 946-953
Author(s):  
Takeshi Hiromoto ◽  
Koji Nishikawa ◽  
Seiya Inoue ◽  
Hiroaki Matsuura ◽  
Yu Hirano ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Active Site ◽  
National Laboratory ◽  
Reduced Form ◽  
Desulfovibrio Vulgaris ◽  
X Rays ◽  
Oak Ridge ◽  
Fe Complex ◽  
Cryogenic Conditions

A membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F is a metalloenzyme that contains a binuclear Ni–Fe complex in its active site and mainly catalyzes the oxidation of molecular hydrogen to generate a proton gradient in the bacterium. The active-site Ni–Fe complex of the aerobically purified enzyme shows its inactive oxidized form, which can be reactivated through reduction by hydrogen. Here, in order to understand how the oxidized form is reactivated by hydrogen and further to directly evaluate the bridging of a hydride ligand in the reduced form of the Ni–Fe complex, a neutron structure determination was undertaken on single crystals grown in a hydrogen atmosphere. Cryogenic crystallography is being introduced into the neutron diffraction research field as it enables the trapping of short-lived intermediates and the collection of diffraction data to higher resolution. To optimize the cooling of large crystals under anaerobic conditions, the effects on crystal quality were evaluated by X-rays using two typical methods, the use of a cold nitrogen-gas stream and plunge-cooling into liquid nitrogen, and the former was found to be more effective in cooling the crystals uniformly than the latter. Neutron diffraction data for the reactivated enzyme were collected at the Japan Photon Accelerator Research Complex under cryogenic conditions, where the crystal diffracted to a resolution of 2.0 Å. A neutron diffraction experiment on the reduced form was carried out at Oak Ridge National Laboratory under cryogenic conditions and showed diffraction peaks to a resolution of 2.4 Å.

scholarly journals Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals

2017 ◽  
Vol 73 (4) ◽  
pp. 235-240 ◽  
Author(s):  
Jahaun Azadmanesh ◽  
Scott R. Trickel ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Gloria E. O. Borgstahl
Keyword(s):  
Neutron Diffraction ◽  
Manganese Superoxide Dismutase ◽  
National Laboratory ◽  
Large Crystal ◽  
Neutron Data ◽  
Data Set ◽  
Cyclic Reduction ◽  
Oak Ridge ◽  
Manganese Superoxide ◽  
Enzymatic Mechanisms

Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å) from which data have been collectedvianeutron diffraction to sufficient resolution (2.30 Å) where hydrogen positions can be observed.

scholarly journals Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

IUCrJ ◽  
2017 ◽  
Vol 4 (1) ◽  
pp. 72-86 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Clifford J. Unkefer
Keyword(s):  
Coming Of Age ◽  
National Laboratory ◽  
Protein Crystallography ◽  
Enzyme Reaction ◽  
Department Of Energy ◽  
Environmental Research ◽  
Macromolecular Crystallography ◽  
Oak Ridge ◽  
The 1960S ◽  
Neutron Crystallography

The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

scholarly journals Neutron diffraction analysis ofPseudomonas aeruginosapeptidyl-tRNA hydrolase 1

2016 ◽  
Vol 72 (3) ◽  
pp. 220-223 ◽  
Author(s):  
Hana McFeeters ◽  
Venu Gopal Vandavasi ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Robert L. McFeeters
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Polyethylene Glycol ◽  
Neutron Diffraction ◽  
Room Temperature ◽  
Isopropyl Alcohol ◽  
National Laboratory ◽  
Neutron Diffraction Data ◽  
Batch Crystallization ◽  
Polyethylene Glycol 4000 ◽  
Oak Ridge

Perdeuterated peptidyl-tRNA hydrolase 1 fromPseudomonas aeruginosawas crystallized for structural analysis using neutron diffraction. Crystals of perdeuterated protein were grown to 0.15 mm3in size using batch crystallization in 22.5% polyethylene glycol 4000, 100 mMTris pH 7.5, 10%(v/v) isopropyl alcohol with a 20-molar excess of trilysine as an additive. Neutron diffraction data were collected from a crystal at room temperature using the MaNDi single-crystal diffractometer at Oak Ridge National Laboratory.

scholarly journals Extracting grain-orientation-dependent data fromin situtime-of-flight neutron diffraction. I. Inverse pole figures

2014 ◽  
Vol 47 (6) ◽  
pp. 2019-2029 ◽  
Author(s):  
G. M. Stoica ◽  
A. D. Stoica ◽  
K. An ◽  
D. Ma ◽  
S. C. Vogel ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
National Laboratory ◽  
Inverse Pole Figure ◽  
Face Centered Cubic ◽  
Oak Ridge ◽  
Weighting Factors ◽  
Quasi Monte Carlo ◽  
Grain Orientations ◽  
Engineering Materials

The problem of calculating the inverse pole figure (IPF) is analyzed from the perspective of the application of time-of flight neutron diffraction toin situmonitoring of the thermomechanical behavior of engineering materials. On the basis of a quasi-Monte Carlo (QMC) method, a consistent set of grain orientations is generated and used to compute the weighting factors for IPF normalization. The weighting factors are instrument dependent and were calculated for the engineering materials diffractometer VULCAN (Spallation Neutron Source, Oak Ridge National Laboratory). The QMC method is applied to face-centered cubic structures and can be easily extended to other crystallographic symmetries. Examples include 316LN stainless steelin situloaded in tension at room temperature and an Al–2%Mg alloy, substantially deformed by cold rolling andin situannealed up to 653 K.

scholarly journals The Neutron Macromolecular Crystallography Instruments at Oak Ridge National Laboratory: Advances, Challenges, and Opportunities

Crystals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 388 ◽  
Author(s):  
Flora Meilleur ◽  
Leighton Coates ◽  
Matthew Cuneo ◽  
Andrey Kovalevsky ◽  
Dean Myles
Keyword(s):  
National Laboratory ◽  
Unit Cell ◽  
Protein Crystals ◽  
Biological Macromolecules ◽  
Microbial Culture ◽  
Hydrogen Atoms ◽  
Oak Ridge ◽  
Oak Ridge National Laboratory ◽  
Challenges And Opportunities ◽  
Chemical States

The IMAGINE and MaNDi instruments, located at Oak Ridge National Laboratory High Flux Isotope Reactor and Spallation Neutron Source, respectively, are powerful tools for determining the positions of hydrogen atoms in biological macromolecules and their ligands, orienting water molecules, and for differentiating chemical states in macromolecular structures. The possibility to model hydrogen and deuterium atoms in neutron structures arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction studies at the 1.5–2.5 Å resolutions, which are typical for protein crystals. Neutrons have the additional benefit for structural biology of not inducing radiation damage to protein crystals, which can be critical in the study of metalloproteins. Here we review the specifications of the IMAGINE and MaNDi beamlines and illustrate their complementarity. IMAGINE is suitable for crystals with unit cell edges up to 150 Å using a quasi-Laue technique, whereas MaNDi provides neutron crystallography resources for large unit cell samples with unit cell edges up to 300 Å using the time of flight (TOF) Laue technique. The microbial culture and crystal growth facilities which support the IMAGINE and MaNDi user programs are also described.

Sign in / Sign up

Export Citation Format

Share Document