BrightnESS²: Enabling Further Collaboration Between Deuteration Partners

BrightnESS² is a three-year, EU-funded project within the European Commission’s Horizon 2020 Research and Innovation programme which focuses on the long-term sustainability of ESS and neutron scattering in Europe, and to further strengthen the network of facilities for research using neutrons. A total of 15 institutes and universities from Europe and South Africa are participants within the project.

As part of BrightnESS² the Deuteration Facility at the SFTC (UK) and the ESS Chemical Deuteration Laboratory (SE) are collaborating on the synthesis of structured deuterated phospholipids. At the moment, a limited number of deuterated, mixed acyl phospholipids (Figure 1) are available, and those that are available and prohibitively expensive for many neutron users and experiments.

 

general mixed acyl phospholipid.jpg
Mixed acyl phosphocholine lipids, where R1 and Rare different acyl tails.

The STFC Deuteration Laboratory has a wealth of experience in the synthesis of homo-acyl phospholipids and an active user community which continuously requests new phospholipid analogues for neutron experiments. The ESS Chemical Deuteration Laboratory is researching the application of enzymatic catalysis to the synthesis of deuterated molecules. Together, the facilities are working together to establish a new, modular method for the synthesis of tail-deuterated, mixed-acyl phospholipids, using enzymes to allow the regiospecific substitution of tails at the 1- and 2-positions. The modularity of the approach should mean that a large number of molecules can be accessed. The first target molecules are 1-palmitoyl-d31-2-oleoyl-d33-sn-3-phosphocholine (POPC-d64, Figure 2a) and 1-palmitoyl-d31-2-(9-oxononanoyl)-sn-3-phosphocholine (PoxnoPC-d31, Figure 2b).

POPC and PoxnoPC
2a) POPC-d64d31.

Now Open: First ESS Call for Deuteration and Crystallisation Support

Onyx Robot

The Deuteration and Macromolecular Crystallisation (DEMAX) Platform at ESS has opened its first call for proposals. DEMAX offers three pillars of support: biological deuteration (e.g. cell paste, soluble proteins, lipids, membranes), chemical deuteration (e.g. small organic molecules, surfactants, phospholipids) and crystallisation (biological macromolecules e.g. proteins).

At this time, DEMAX offers the following kinds of deuterated materials and services:

Total yeast-derived lipids
Tail-deuterated lipids
Saturated fatty acids/alcohols/halides/thiols
Oleic acid
Surfactants (e.g. sugar, amino acid)
Lactic acid
Bacterial cell pastes
Recombinant proteins
Support for large protein crystal growth (incl. sitting drop vapour diffusion, dialysis, batch, optimisation, targeted screening, testing with X-rays)

For this call, access is not limited to ESS member countries, and is free of charge. The deadline for proposal submissions is 5th April 2019. Find more information here: https://europeanspallationsource.se/node/244384

Questions? Contact the DEMAX team at demax@esss.se

 

Parr Reactor for Hydrothermal Deuteration Installed at ESS

The ESS DEULAB installed its first Parr reactor during the summer. The Parr reactor is capable of operating under conditions of high temperature (up to 350 °C) and high pressure (up to 131 bar) and is used in deuteration laboratories for hydrothermal, metal-catalysed H/D exchange reactions.

Parr reactor.jpg

The first reaction performed in the DEULAB using the Parr reactor was the deuteration of lauric acid:

lauric acid deuteration

Under these conditions, lauric acid with 89% deuteration of the non-exchangeable hydrogen atoms was obtained. The deuteration incorporation was determined by analysis of the isotopologue ratios in the mass spectrum:

lauric acid first cycle ms

This process can be repeated to produce very highly deuterated lauric acid (>98% deuteration of the non-exchangeable hydrogen atoms). It is applicable to other saturated fatty acids and will facilitate the synthesis of many classes of deuterated molecules with fatty acid synthons, such as lipids and surfactants, at the ESS DEULAB.

More for Less: Low-Cost, High-Yield Protein Deuteration for Neutron Crystallography

A team from Lund University, Karolinska Institute, and the European Spallation Source have published an optimized approach to high-yield protein deuteration at low cost, for neutron protein crystallography.

RELEVANCE

In general, neutron scattering experiments in life sciences require deuterated bio-reagents. In particular for neutron protein crystallography (NPX) studies there is a need for deuterated proteins in sufficient quantities to allow for crystallization and scale-up to obtain large (0.5 – 1.0 mm3) single crystals for neutron data collection (Figure 1). Our results demonstrate the progress in our abilities to produce deuterated proteins at an improved cost-to-yield ratio.

Figure1 copy
Figure 1. Photograph of a large, single crystal of human carbonic anhydrase.

BACKGROUND

Deuteration means to exchange Hydrogen (H) atoms with Deuterium (D) atoms. This is a crucial technique that allows us to benefit from the stronger neutron scattering power and lower background from D compared to H in NPX. For the production of recombinant proteins, deuteration is done in the production hosts, e.g. bacteria. While the benefits are clear, there are many drawbacks to deuteration, including high costs, toxic effects of D towards the production hosts resulting in low yield of biomass, and possibly changes in the biophysical properties of the recombinant protein, altogether, making it technically difficult to produce and crystallize deuterated proteins.

In our current study “Deuteration of human carbonic anhydrase for neutron crystallography: cell culture media, protein thermostability, and crystallization behavior” we address the challenges of expressing proteins in bacteria under deuterated conditions. Technical difficulties, such as cellular toxicity that results in reduced yields of recombinant protein and the high cost of deuterated growth media for the production, makes it challenging to produce enough deuterated protein for NPX studies. Furthermore, there are effects of full deuteration on protein stability and solubility. In almost all reported cases deuteration causes a reduction in thermal stability and solubility and consistently leads to smaller crystal sizes, compared to what is possible with the hydrogenous versions.

Our study was designed to address some of the technical difficulties of protein deuteration in vivo in bacteria and to study the biophysical effects with regards to thermal stability and crystallization behaviour of the products. We started with a survey of the literature and the global protein structure database (https://www.rcsb.org/) to reveal the most common approaches used for deuteration of proteins in NPX. Our goal was to prepare partially deuterated samples, in a short time with the best possible yield for the cost.

We combined further optimized approaches that still gave very good deuterium incorporation with optimal protein yields, but also significantly reduced the time and cost for producing the proteins compared to established protocols. After producing and isolating the deuterated proteins, we measured the D incorporation with mass spectrometry and tested thermal unfolding as a function of pH to characterize protein stability and solubility. Finally we tried to grow crystals of deuterated and non-deuterated proteins side-by-side to assess the impact of deuteration on crystallization behavior.

RESULTS

In this study we optimized the deuterated production of 3 different versions of human carbonic anhydrases.  Resulting from this are a cost effective cell culture medium and optimization of the cell culturing and expression protocols. Our analysis showed that the deuterated proteins were on average 1 – 4 °C less stable than the hydrogenous versions and this effect was strongly pH-dependent. Interestingly, deuterated proteins dissolved in D2O were more stable than deuterated proteins in H2O. However our partial deuteration strategy did not seem to affect protein solubility in the concentrations necessary for crystallization. Comparing crystallization trials of deuterated and non-deuterated proteins at the same pH indicated that deuteration had significant effects on crystallizability (Figure 2).

Figure2 copy.jpg
Figure 2. Side-by-side comparison of non-deuterated and deuterated protein crystallization behavior. Some proteins did not produce any crystals in the deuterated form.

In summary, our protein yield was ~2-fold lower than in non-deuterated conditions, but still producing tens of milligrams of pure protein, yields sufficient for NPX. We managed to get ~65-80% D incorporation, also sufficient for NPX applications, at a cost that was reduced by ~4 fold compared to previously reported protocols. We will adopt these methods to prepare deuterated samples for future neutron experiments.

FUTURE

These results are exciting and will help us be more efficient in deuterated protein production. However, there is still some work to be done. In particular, production of deuterated  protein is still ~120 fold more expensive as non-deuterated. So can we further optimize costs?

Also, as our studies indicate, there is a pH-dependent effect of deuteration on crystallization behavior and we will aim to optimize and find ways to adapt our conditions to maximize our chances of growing large crystals of deuterated proteins.

WHO?

The experimental team involved several scientists from Lund University, Karolinska Institute, and the European Spallation Source (DEMAX platform): Katarina Koruza, Benedicte Lafumat, Ákos Végvári, Wolfgang Knecht, and Zoe Fisher. The work was done as a collaboration between Lund University (Lund Protein Production Platform, LP3 www.lu.se/lp3) and the European Spallation Source (ESS) DEMAX platform.

Figure3 copy.jpg
Figure 3. Katarina Koruza inspecting crystallization plates under the microscope.

Funding for this work was received by the Royal Physiographic Society of Lund, Interreg/MAX4ESSFUN, The Crafoord Foundation, BioCARE and EU’s Horizon 2020 research and innovation program (SINE2020).

REFERENCE: Koruza K, Lafumat B, Végvári Á, Knecht W, Fisher SZ (2018) “Deuteration of human carbonic anhydrase for neutron crystallography: Cell culture media, protein thermostability, and crystallization behavior”, Arch Biochem Biophys. 645, p.26-33.

https://www.sciencedirect.com/science/article/pii/S0003986118300535?via%3Dihub

cover_ABB_deuteration2018

Enzyme Catalysis Extended: Lipase-Catalysed Synthesis at ESS

After applying lactate dehydrogenase catalysis to the synthesis of perdeuterated enantiopure lactic acid, the ESS deuteration lab is now extending its use of enzyme catalysis to the lipase class of enzymes. The natural function of these enzymes is to hydrolyse ester bonds of triglycerides, releasing free fatty acids, under aqueous conditions. Lipases are also remarkably stable in organic solvents, and so can be encouraged to perform the reverse esterification reaction under water-free or water-limited conditions (Scheme 1).

lipase equilibrium reaction
Scheme 1. Lipase-catalysed hydrolysis/formation of esters.

Lipases are already used extensively in synthetic chemistry, so much so that many of them are commercially available in immobilised form. The ESS lab has recently procured a rotating bed reactor (RBR – Figure 1), and some lipases immobilised on various solid supports, contained within cartridges designed to be used in combination with the RBR. This equipment should allow the use of lipases to perform efficient synthetic transformations of deuterated molecules using immobilised enzymes.

RBR
Figure 1. The SpinChem® rotating bed reactor (RBR) system used for immobilised lipase reaction in the ESS deuteration laboratory.

Initial work has begun with a simple, unlabelled esterification system (Scheme 2). The reaction can easily be monitored by GC-FID, allowing for analysis of reaction progress and kinetics (Figure 2).

lauric acid esterification
Scheme 2. Lauric acid esterification catalysed by immobilised CalB lipase.
GC trace lauric acid est
Figure 2. Lauric acid esterification can be monitored by GC-FID, comparing the peak areas of the acid and ester in hexane.

Work will soon continue with more complex, deuterium-labelled systems to produce deuterated materials of use in neutron scattering experiments.

J-PARC Deuterated Materials Workshop

J-PARC (Japan Proton Accelerator Research Complex) last month held a workshop entitled “Deuterated Materials Enhancing Neutron Science for Structure Function Applications”, at the Ibaraki Quantum Beam Research Centre, Tokai, Japan. There were over 60 participants in the workshop, which was held over two days. J‑PARC have recently established on-site laboratories dedicated to chemical and biological deuteration and the aim of the workshop was to discuss how to activate deuteration science at J‑PARC.

JPARC workshop
The delegates of the “Deuterated Materials Enhancing Neutron Science for Structure Function Applications” workshop held at J-PARC in October 2017.

Three plenary speakers outlined the current status of other deuteration laboratories around the world. Dr Tamim Darwish and Dr Anthony Duff from ANSTO described the chemical and biological deuteration laboratories at the National Deuteration Facility, ANSTO, which have been functioning well as user laboratories for several years. Dr Anna Leung presented the research at the newly-established DEULAB at ESS, and also acted as a representative for the other members of the DEUNET (the laboratories at ISIS, ILL and FZJ). Professor Sajiki from Gifu Pharmaceutical University provided the fourth plenary session. Professor Sajiki has worked in the field of deuteration science for many years, and presented some of his recent results in the field.

Ten invited talks provided an excellent overview of the current research involving deuterated materials in Japan, and initiated excellent discussion about the future of deuterated materials research, and where more effort should be focussed to produce high-impact research. The meeting concluded that a deuteration community ought to be organised in Japan to leverage the advantages of collaborative research. Furthermore, this community ought to continue to interact with deuteration laboratories across the world. In addition to the existing collaboration between J‑PARC and the chemical deuteration laboratory at ANSTO, J‑PARC has joined the European chemical deuteration network (DEUNET) as an observer member, a development which is certain to benefit both deuteration communities and their users.