Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme.

This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications. © Ramos et al. 2021.

Introduction

Biomolecular deuteration is widely used in structural biology, where it plays a crucial role in techniques such as neutron macromolecular crystallography (NMX), small-angle neutron scattering (SANS), neutron reflectometry (NR), neutron spectroscopy and nuclear magnetic resonance (NMR) (Haert­lein et al., 2016 ▸; Varga et al., 2007 ▸). For neutron studies, the fact that <span class="Chemical">deuterium (D), an isotope of <span class="Chemical">hydrogen (H), possesses a positive coherent neutron scattering length and a small incoherent neutron scattering cross section, and also an integer nuclear spin, is of central importance. In NMX, perdeuteration may be used to eliminate the incoherent scattering arising from the two spin states of the H atom (incoherent scattering cross section of 80.27 barns; Sears, 1992 ▸); this allows the use of samples that are approximately one order of magnitude smaller by volume (Hazemann et al., 2005 ▸) and may result in improved resolution (Blakeley, 2009 ▸). Perdeuteration enhances the visibility of the coherent signal (Bragg reflections), fully exploiting the higher coherent scattering length of deuterium (6.67 fm) in comparison with that of hydrogen (∼3.74 fm). Furthermore, perdeuteration helps to avoid cancellation effects (arising from the negative scattering length of hydrogen) that may occur for neutron Fourier maps based on data with intermediate resolution (for example d > 1.6 Å). In SANS, the use of deuterated samples allows contrast-matching techniques (Dunne et al., 2017 ▸; Laux et al., 2008 ▸; Haertlein et al., 2016 ▸) to provide unique information on protein–protein (Vijayakrishnan et al., 2010 ▸), protein–nucleic acid (Cuypers, Trubitsyna et al., 2013 ▸) or protein–lipid (Breyton et al., 2013 ▸) interactions. Sophisticated technologies have also been developed to allow the production of stealth-deuterated nanodiscs (Maric et al., 2014 ▸, 2015 ▸) for the study of membrane proteins (Josts et al., 2018 ▸; Nitsche et al., 2018 ▸; Kehlenbeck et al., 2019 ▸). In the case of NR, a wide range of research now routinely exploits the contrast enabled through the use of selective deuteration (Grage et al., 2011 ▸; Moulin et al., 2018 ▸; Waldie et al., 2018 ▸, 2019 ▸, 2020 ▸). Deuterium labelling and reverse labelling have also been used for neutron scattering studies of the dynamics of biological macromolecules (Foglia et al., 2016 ▸), in particular when coupled with hydration water dynamics (Wood et al., 2013 ▸). In the case of solution-state NMR, deuterium labelling is essential for multidimensional heteronuclear NMR studies of proteins, especially high-molecular-weight proteins and macromolecular complexes. Partial deuteration simplifies the NMR spectra from the remaining 1H nuclei and also contributes to spectra with a higher signal-to-noise ratio owing to the effects on the relaxation of bonded or adjacent 1H, 13C and 15N atoms (Sattler & Fesik, 1996 ▸). While major developments in in vivo deuteration technologies have occurred in the last 15 years, the expression of deuterated protein is often complex and expensive and may be associated with low yields. The way in which it is carried out depends on the downstream application and on the labelling regime needed to answer the scientific questions posed (Haertlein et al., 2016 ▸). In the case of neutron crystallographic applications, the goal is invariably to perdeuterate the sample so that the incoherent scattering from hydrogen is removed from the recorded data to the maximum possible extent.

Hen egg-white lysozyme (HEWL) was the first enzyme structure to be solved by X-ray crystallography (Blake et al., 1965 ▸), and has subsequently become a widely used model in structural biology in a variety of contexts including protein-folding studies (Miranker et al., 1991 ▸, 1993 ▸; Radford et al., 1992 ▸; Wildegger & Kiefhaber, 1997 ▸) and crystallization (Durbin & Feher, 1986 ▸; McPherson & DeLucas, 2015 ▸; <span class="Chemical">Darmanin et al., 2016 ▸). It is a small (129 residues, 14.3 k<span class="Chemical">Da) and stable protein that in its hydrogenated form can be acquired at low cost and crystallized in numerous space groups under well known conditions. HEWL is a hydrolase from Gallus gallus that cleaves the 1,4-β-linkages between N-acetylmuramic acid and N-acetyl-d-glucosamine residues in peptido­glycan. The recombinant production of HEWL in Escherichia coli is challenged by the reductive environment of the bacterial cytosol, which prevents the correct formation of its four disulfide bridges, resulting in the formation of inclusion bodies. The use of the yeast Pichia pastoris has been investigated as an expression system for the production of recombinant HEWL (Liu et al., 2003 ▸; Li et al., 2012 ▸; Mine et al., 1999 ▸; Campbell et al., 2018 ▸). While this approach results in the production of high-quality protein, the low yield is problem­atic for neutron crystallographic and spectroscopic applications. For this reason, we developed an approach whereby large quantities of insoluble protein were produced as inclusion bodies in E. coli, followed by an optimized refolding process, significantly improving the yield.

Using this strategy, large amounts of correctly folded <span class="Chemical">perdeuterated HEWL (<span class="Chemical">D-HEWL) can be obtained at a financially viable level. Of particular interest is the fact that the refolded perdeuterated lysozyme from E. coli (D-HEWLEC) provides important insights into the structural and biophysical properties of HEWL when compared with those of the perdeuterated analogue produced in P. pastoris (D-HEWLPP) and those of the commercially available non­recombinant hydrogenated protein (H-HEWL). These variants are identical in primary structure, with the exception of an additional glycine at the N-terminus of D-HEWLEC.

Atomic resolution X-ray structures have been determined for all three variants using triclinic crystals obtained in closely comparable conditions. The effect of deuteration on reduced thermal stability and activity is noted. The structural analyses highlight subtle but important differences that are related to the decrease in the thermal stability of <span class="Chemical">D-HEWLEC; these differences are of significance for protein folding (Biter et al., 2016 ▸), enzymatic activity (Lea & Simeonov, 2012 ▸), crystallization (Geders et al., 2012 ▸; Reinhard et al., 2013 ▸) and protein–ligand interactions (Bai et al., 2019 ▸; Forneris et al., 2009 ▸; Holdgate et al., 2010 ▸; Ramos et al., 2019 ▸). The improved yield (by a factor of more than three compared with that found using <span class="Species">P. pastoris) paves the way for a wide range of studies that can exploit H/D isotopic substitution in this protein.

Methods

Expression of D-HEWLEC

Recombinant <span class="Chemical">D-HEWL was overexpressed in <span class="Species">E. coli BL21 (DE3) cells grown in a Labfors 2.3 l computer-controlled fermenter (Infors, France) using a high cell-density culture (HCDC) strategy. Transformation of chemically competent cells with the vector pET-28a(+) (GenScript) containing codon-optimized cDNA for HEWL expression (Supplementary Fig. S1) was performed by heat shock. Using a lysogeny broth (LB) solid medium supplemented with 40 µg ml−1 kanamycin (catalogue No. 60615; Sigma–Aldrich), transformed cells were selected. The cells containing the vector were then adapted to hydrogenated Enfors minimal medium containing hydrogenated glycerol and kanamycin. The cells were further adapted to fully deuterated Enfors medium supplemented with d8-glycerol (catalogue no. DLM-558-PK; Eurisotop) and antibiotic. 100 ml precultures were prepared to inoculate 1.4 l minimal medium in the fermenter. During batch and fed-batch phases, the pD (pD = pHmeasured + 0.4; Glasoe & Long, 1960 ▸) was maintained at 6.4 by adding NaOD. The gas-flow rate of sterile-filtered air was 0.5 l min−1. Stirring was adjusted to ensure a dissolved oxygen level of 30%. The initial glycerol supply was consumed during the batch phase. The cells were then fed continuously with fresh feeding solution containing 12% d8-glycerol in an exponential manner (fed-batch phase). When the cell density reached an OD of 10, recombinant protein expression was induced by adding IPTG to a final concentration of 1 mM. The cells were harvested after 24 h of induction. The final volume of cell culture extracted from the fermenter was approximately 1.8 l.

Inclusion-body separation of D-HEWLEC

The inclusion bodies were purified in a centrifugation-based approach, with several washing steps to remove nucleic acids, <span class="Chemical">lipids and other contaminants. After pelleting the <span class="Species">E. coli cells, lysis was promoted by sonication with a Vibra-Cell ultrasonic liquid processor (VCX-750-220, Sonics & Materials), performing three cycles of 30 s at amplitude 0.8 in a buffer consisting of 0.1 M Tris–HCl pH 8.45, 150 mM NaCl, 25 mM EDTA, 25 mM DTT, 0.5% Triton X-100. The suspension was centrifuged at 10 080g for 1 h at 4°C to separate the soluble and insoluble fractions. The supernatant was discarded and the pellet was solubilized in 0.1 M Tris–HCl pH 8.45, 150 mM NaCl, 25 mM EDTA, 25 mM DTT, 1 M guanidine–HCl, 1% Triton X-100 using a homogenizer (D1000, Benchmark). The suspension was sonicated three times for 10 s at amplitude 0.4 and was then centrifuged at 22 680g for 30 min at 4°C. This washing step was performed six times, with Triton X-100 excluded from the buffer in the last two cycles.

Purification of D-HEWLEC

The inclusion bodies were solubilized in 0.1 M <span class="Chemical">Tris–<span class="Chemical">HCl pH 8.45, 150 mM NaCl, 25 mM EDTA, 25 mM DTT, 6 M guanidine–HCl using a homogenizer. The suspension was sonicated three times for 10 s at amplitude 0.4 and then centrifuged at 22 680g for 1 h at 4°C. The soluble fraction was collected and filtered through 0.4 µm filters. Purification of unfolded protein was performed by gel filtration on a HiLoad 16/600 Superdex 200 pg column (GE Healthcare) equilibrated in the same buffer. Protein fractions of 5 ml were diluted to avoid saturation of the UV detector of the HPLC and were injected into the column, running an isocratic flow at 1.0 ml min−1. Pure protein eluted at 0.6–0.7 column volumes (CV). The fractions of pure protein collected were frozen at −80°C until the refolding procedure.

Refolding of D-HEWLEC

Denatured protein was refolded at room temperature in a size-exclusion chromatography (SEC) setup using a HiLoad 16/600 Superdex 200 pg column equilibrated with 0.1 M <span class="Chemical">Tris–<span class="Chemical">HCl pH 8.45, 2 M urea, 1 mM EDTA, 3 mM reduced glutathione, 0.3 mM oxidized glutathione as described by Batas & Chaudhuri (1996 ▸). 5 ml injections of pure unfolded HEWL at concentrations of 1–2 mg ml−1 were performed in each run; the isocratic flow was set to 0.1 ml min−1, resulting in monomeric HEWL fractions being collected at 0.9 CV.

The protein buffer was exchanged to 50 mM <span class="Chemical">sodium acetate <span class="Chemical">pD 4.5 in D2O by desalting using two coupled HiTrap 5 ml desalting columns (GE Healthcare). Injections of 2.5 ml of protein at 0.6 mg ml−1 were performed. The protein was subsequently concentrated to 20 mg ml−1 for crystallization experiments.

Expression and purification of D-HEWLPP

The expression of <span class="Chemical">D-HEWLPP was achieved as <span class="Chemical">described by Campbell et al. (2018 ▸). Since the protein was secreted into the extracellular medium, the supernatant was recovered upon cell pelleting. The supernatant was diluted by the addition of 50 mM Tris–HCl pH 7.8 buffer to achieve a solution conductivity of below 10 mS cm−1. Pure protein was obtained by ion-exchange chromatography (IEC) using an SP-Sepharose column (GE Healthcare) and elution with a 30 ml NaCl gradient from 0 to 1 M in 50 mM Tris–HCl pH 7.8 buffer. Following the same approach as the final buffer exchange of D-HEWLEC, the D-HEWLPP buffer was exchanged to 50 mM sodium acetate pD 4.5 in D2O by desalting. The protein was concentrated to 30 mg ml−1 for crystallization experiments.

Mass spectrometry (MS)

MS under denaturing conditions was utilized to assess the mass of the intact <span class="Chemical">deuterated proteins and their degree of labelling. Specifically, liquid-chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) on a 6210 TOF mass spectrometer coupled to an HPLC system (1100 series, Agilent Technologies) was performed. <span class="Chemical">Data acquisition was carried out in positive-ion mode, and mass spectra were recorded in the 300–3200 m/z range. The following experimental settings were utilized: the ESI source temperature was set to 300°C, N2 was used as a drying gas (with a flow rate of 7 l min−1) and as a nebulizer gas (using a pressure of 69 kPa) and the capillary needle voltage was 4 kV. Voltages in the first part of the instrument were set as follows: the voltage of the fragmentor was 250 V and that of the skimmer was 60 V. The acquisition rate was one spectrum per second. Instrument pressure values were typically 2.33 Torr (rough vacuum) and 4.6 × 10−7 Torr (TOF vacuum). The mass spectrometer was calibrated with tuning mix (ESI-L, Agilent Technologies). The HPLC mobile phases were prepared with HPLC-grade solvents. The mobile phase A composition was 95% H2O, 5% acetonitrile (ACN), 0.03% trifluoroacetic acid (TFA). The mobile phase B composition was 95% ACN, 5% H2O, 0.03% TFA.

As partial D-to-H back-exchange would be possible during the experiment, both samples were dialyzed against 50 mM <span class="Chemical">sodium acetate pH 4.5 buffer in <span class="Chemical">H2O prior to the MS experiment to ensure full back-exchange and thus allow the evaluation of the number of D atoms in all non-exchangeable positions.

Just before the analysis, the samples were diluted in 0.03% <span class="Chemical">TFA to obtain a concentration of 5 µM and a volume of 20 µl. The samples were loaded into glass vials, which were placed on a sample loader refrigerated at 10°C. 4 µl of each sample (i.e. ∼20 pmol of protein) was injected into the HPLC system directly connected to the mass spectrometer. The injected sample was first trapped and de<span class="Chemical">salted on an RP-C8 cartridge for 3 min at a flow rate of 50 µl min−1 using 100% mobile phase A. Afterwards, the proteins were separated on an RP-C8 column using a linear gradient from 5 to 95% mobile phase B for 15 min and subjected to ESI prior to the TOF detection of their m/z signals. The software MassHunter BioConfirm (version B.07.00; Agilent Technologies) was used to calculate masses from m/z values obtained during the MS experiments.

Differential scanning fluorimetry (DSF)

DSF measurements were performed using a Prometheus instrument (NanoTemper). The setup included a temperature ramp from 20 to 95°C with increments of 1.0°C min−1, following unfolding by the intrinsic fluorescent signal from the <span class="Chemical">tryptophan residues (six <span class="Chemical">tryptophans in HEWL). Lyophilized H-HEWL powder was dissolved in 50 mM sodium acetate pD 4.5 in D2O to match the conditions of D-HEWLEC and D-HEWLPP. The experiment was repeated in the hydrogenated buffer of the activity assay, where the samples were diluted in 0.1 M sodium phosphate pH 7.5, 0.1 M NaCl, 2 mM NaN3 in H2O in a ratio of at least 1:50. The results presented correspond to samples at concentrations of 0.3 mg ml−1 with a 40% excitation power and were obtained for at least two HEWL preparations as duplicate or triplicate measurements for every condition.

HEWL activity assays

The activity assays were performed based on the work of Shugar (1952 ▸). The activity is followed by the absorbance at 450 nm at 25°C, with measurements every minute for 20 min. Nunc 96-well flat-bottom plates (Thermo Fisher Scientific) were used with each sample in triplicate, including negative controls without protein. The 100 µl samples used for these experiments comprised 50 µl protein sample at 0.2 mg ml−1 and 50 µl <span class="Species">Micrococcus lysodeikticus cell suspn>ension in <span class="Chemical">H2O with 0.1 M sodium phosphate pH 7.5, 0.1 M NaCl, 2 mM NaN3. After averaging triplicates of each experiment, the activity curves were plotted against time, and the linear phase (R 2 > 0.91) corresponding to the first 8 min of reaction was considered to retrieve the initial velocities. Standard deviations were derived from three separate experiments and a t-test was performed for each pair of results to assess the significance of the homoscedastic hypothesis, meaning the probability of the pairs of measured values being equal.

Protein crystallization

H-HEWL (catalogue No. L6876; Sigma–Aldrich) was crystallized in the triclinic form in batch-like conditions using a precipitation step as <span class="Chemical">described by Vi<span class="Chemical">dal et al. (1999 ▸). 5 µl drops were prepared consisting of 2.5 µl H-HEWL at 20 mg ml−1 dissolved in deionized water and 2.5 µl 0.4 M NaNO3, 50 mM sodium acetate pH 4.5. Under these conditions, monoclinic crystals readily formed at room temperature. To obtain the triclinic crystal form, the crystallization plate was stored at 4°C overnight and then subsequently kept at 18°C. During the cold storage, crystals of both the triclinic and monoclinic forms nucleate. When the temperature is raised, the less stable monoclinic form dissolves, leaving almost exclusively nuclei of the triclinic form (Legrand et al., 2002 ▸). Triclinic crystals appeared after three days.

Triclinic crystals of <span class="Chemical">D-HEWL were obtained by initial microseeding using triclinic <span class="Chemical">H-HEWL seeds from a crystal in 100% D2O buffer. The seed solution was made by crushing the crystal in 0.3 M NaNO3, 50 mM sodium acetate pD 4.5. Subsequently, the solution was transferred to an Eppendorf tube containing a zirconium silicate ceramic seed bead (Hampton Research) and vortexed to produce microseeds. Seed stocks of 1:100 and 1:1000 dilutions were used in the crystallization experiments. Sitting drops of 5.5 µl were prepared by microbatch under oil and stored at 18°C. The drops consisted of 2.5 µl D-HEWLEC at 20 mg ml−1 or D-HEWLPP at 30 mg ml−1, 2.5 µl 0.3 M NaNO3, 50 mM sodium acetate pD 4.5 and 0.5 µl of the H-HEWL seed solution. Triclinic crystals of D-HEWL of up to 0.1 mm3 were obtained within one week.

X-ray data collection, processing and model refinement

Synchrotron X-ray diffraction data were collected at 100 K from crystals of H-HEWL, <span class="Chemical">D-HEWLEC and D-HEWLPP. The data collections were performed on beamline I03 at Diamond Light Source (DLS), UK and on BioMAX at MAX IV, Sweden (Table 1 ▸). Crystals of approximately 0.1 mm3 were cooled in cryoprotectant solutions of 25–35%(v/v) glycerol or d8-glycerol with 0.3 M NaNO3 and 50 mM sodium acetate pH/pD 4.5 in H2O for H-HEWL or D2O for both D-HEWL forms. Due to the low triclinic crystal symmetry, the data sets were measured in two different κ orientations to improve the completeness of the data. The data were reduced, merged and scaled using XDS (Kabsch, 2010 ▸). Initial phases were estimated by molecular replacement in Phenix (Liebschner et al., 2019 ▸), using the structure deposited in the Protein Data Bank (PDB; Berman et al., 2000 ▸) as entry 4yeo (Shabalin et al., 2015 ▸), stripped of ligands and water molecules, as a starting model. Model refinement was performed using Phenix (Liebschner et al., 2019 ▸), with the same set of reflections flagged for the R free calculation. Model building was achieved using Coot (Emsley et al., 2010 ▸). The D-HEWLEC model from a late stage of refinement was used for the initial refinement of D-HEWLPP and H-HEWL to maintain the labelling of residue disorder as well as of water molecules and ions. H/D atoms were added to the models as riding atoms in ideal positions. The occupancy of water molecules and ions was refined for atoms with B factors above 20 Å2 and was otherwise fixed to 1. Water molecules which displayed a density lower than 1.5 σ in the 2F o − F c electron-density map were removed from the models.

Table 1

X-ray diffraction data-collection and model-refinement statistics for H-HEWL, D-HEWLEC and D-HEWLPP

Values in parentheses are for the outer resolution shell.

	H-HEWL	D-HEWLEC	D-HEWLPP
Cryoprotectant	25%(v/v) glycerol	35%(v/v) d8-glycerol	30%(v/v) d8-glycerol
Strategy	2 κ orientations, 180° scans	2 κ orientations, 180° scans	2 κ orientations, 360° scans
Beamline and source	I03, DLS	I03, DLS	BioMAX, MAX IV
Detector	EIGER2 XE 16M	EIGER2 XE 16M	EIGER hybrid-pixel 16M
Wavelength (Å)	0.7293	0.7293	0.7999
Resolution range (Å)	31.99–1.00 (1.036–1.000)	32.01–0.98 (1.015–0.980)	32.01–1.00 (1.036–1.000)
Space group	P1	P1	P1
a, b, c (Å)	26.76, 31.07, 33.77	26.67, 30.97, 33.74	26.67, 30.97, 33.74
α, β, γ (°)	89.211, 72.459, 67.863	89.439, 72.818, 67.503	89.439, 72.818, 67.503
Total reflections	178195 (17670)	278571 (24674)	337122 (32144)
Unique reflections	50297 (4908)	52966 (5018)	49991 (4880)
Multiplicity	3.5 (3.6)	5.3 (4.9)	6.7 (6.6)
Completeness (%)	97.47 (94.95)	97.44 (92.67)	97.71 (95.50)
Mean I/σ(I)	9.25 (2.81)	18.09 (4.21)	15.07 (6.92)
Wilson B factor (Å2)	8.43	7.12	8.81
R merge	0.0727 (0.386)	0.0424 (0.273)	0.0803 (0.262)
R meas	0.0856 (0.453)	0.0470 (0.306)	0.0876 (0.284)
R p.i.m.	0.0449 (0.236)	0.0201 (0.136)	0.0344 (0.109)
CC1/2	0.996 (0.884)	0.999 (0.935)	0.992 (0.979)
CC*	0.999 (0.969)	1.00 (0.983)	0.998 (0.995)
Reflections used in refinement	50286 (4906)	52964 (5018)	49982 (4878)
Reflections used for R free	2398 (218)	2510 (223)	2400 (222)
R work	0.1172 (0.1577)	0.1049 (0.1323)	0.1205 (0.1206)
R free	0.1319 (0.1740)	0.1145 (0.1423)	0.1341 (0.1326)
CCwork	0.976 (0.956)	0.977 (0.969)	0.965 (0.977)
CCfree	0.976 (0.945)	0.972 (0.963)	0.941 (0.970)
No. of non-H/D atoms
Total	1502	1467	1474
Macromolecule	1308	1291	1299
Ligands	40	40	40
Solvent	154	136	135
Protein residues	129	130	129
R.m.s.d., bond lengths (Å)	0.011	0.008	0.013
R.m.s.d., angles (°)	1.46	1.42	1.62
Ramachandran favoured (%)	96.85	97.66	97.64
Ramachandran allowed (%)	3.15	2.34	2.36
Ramachandran outliers (%)	0	0	0
Rotamer outliers (%)	0.7	1.44	0.71
Clashscore	4.18	2.32	4.6
Average B factor (Å2)
Overall	11.06	9.96	11.84
Macromolecule	10.27	9.19	11.33
Ligands	16.50	16.71	16.55
Solvent	16.37	15.25	15.35

X-ray structure analysis and comparison

Structural alignment of the entire protein chains was achieved with the CEALIGN plugin (Shindyalov & Bourne, 1998 ▸) using the Cα atoms from 128 residues, while alignment of the Lys97–<span class="Chemical">Gly104 region (using all atoms) was performed with the SUPER function of PyMOL (version 2.0; Schrödinger). EDSTATS (Tickle, 2012 ▸) from the CCP4 suite (Winn et al., 2011 ▸) was employed to evaluate the quality of the models according to the data, allowing the identification of residues that may not have been reliably modelled for further analysis. The combination of cutoffs considered was 90% for the RSCC, 1σ for the sample RSZO and −3σ and +3σ for RSZO− and RSZO+, respectively. Hydrogen-bond analysis was performed using HBPLUS (McDonald & Thornton, 1994 ▸). Results that included intra-residue interactions and residues that were not reliably modelled according to the metrics from EDSTATS (Tickle, 2012 ▸) were not considered for the comparison between models, with the exception of Thr89 from D-HEWLPP, which participates in an extensive hydrogen-bond network involving His15, Asp87 and Asn93. The graphical representations presented here were made in PyMOL.

Results

Increased yield by refolding from inclusion bodies

Inclusion bodies from <span class="Chemical">D-HEWLEC expression were separated from insoluble contaminants, as shown by <span class="Chemical">SDS–PAGE of the supernatants from the washing steps (Supplementary Fig. S2). The untagged D-HEWLEC was further purified by gel filtration, eluting as a single peak around 0.6–0.7 CV, with fractions F5–F7 being collected for the refolding step [Figs. 1 ▸(a) and 1 ▸(b)].

Figure 1

The expression of insoluble D-HEWL in E. coli followed by refolding increases the yield of protein production by more than threefold. (a) Chromatogram from the denaturing SEC, yielding pure unfolded D-HEWLEC, which eluted at 0.6–0.7 CV. (b) Fractions from the denaturing SEC on a 12% SDS–PAGE gel. Lane S, Precision Plus Protein Dual Xtra Standards (Bio-Rad); lane I, injected sample of unpurified D-HEWLEC from the inclusion-body washing steps; lanes F1–F9, collected fractions from the denaturing SEC as indicated at the top of (a). Fractions F5–F7 were used in subsequent refolding experiments. (c) Refolding SEC chromatogram, where monomeric D-HEWL elutes at 0.9 CV. The fractions eluting before and after the monomeric refolded D-HEWLEC are likely to be misfolded or oligomeric and partially unfolded forms of D-HEWLEC, respectively. This is followed by the elution of the guanidine–HCl and the DTT from the denaturing buffer, as shown by the increase in conductivity. (d) Comparison of the D-HEWL expression yields between the two systems, E. coli and P. pastoris. *Considering an average refolding yield of 20%, the final yield of D-­HEWLEC production is 37 mg l−1 without further denaturing and refolding of the misfolded, oligomeric and partially unfolded fractions.

D-HEWLEC was refolded in-column using a low flow rate of 0.1 ml min−1, which allowed de<span class="Chemical">salting of the unfolded protein and separation of the monomeric and oligomeric, misfolded and partially unfolded fractions [Fig. 1 ▸(c)]. The fractions of refolded D-HEWL in refolding buffer and in deuterated protein buffer are shown on a 12% SDS–PAGE gel in Supplementary Fig. S3. The refolding yields were impacted by the fact that the molecular weight of HEWL is close to the lower exclusion limit of the gel-filtration column (M r = 10 kDa), which hindered optimal separation of the monomeric protein fraction from the denaturing buffer. Injections of 6.5 mg unfolded protein resulted in average refolding yields of 20%. The expression, purification and refolding strategy yielded 186 mg of pure protein per litre of culture on average, from which, considering a consistent refolding yield of 20%, 37 mg was recovered in a native-like state. These results represent more than a threefold increase in D-HEWL production compared with the P. pastoris system [Fig. 1 ▸(d)].

All non-exchangeable H positions are fully deuterated in both D-HEWLEC and D-HEWLPP

The deuteration level of <span class="Chemical">D-HEWLEC and <span class="Chemical">D-HEWLPP was assessed by LC/ESI-MS. Prior to the MS experiments, both samples were dialyzed against 50 mM sodium acetate pH 4.5 buffer in H2O to avoid partial back-exchange during the experiment. Therefore, the expected masses included D in all non-exchangeable positions (i.e. bound to C) and, with full back-exchange, H in all labile positions (Table 2 ▸).

Table 2

Expected and observed masses for D-HEWLEC and D-HEWLPP in the MS experiments

Sample	MW of hydrogenated oxidized form (Da)	No. of non-exchangeable H positions	No. of exchangeable H positions	Expected mass of perdeuterated variant in H2O (Da)	Observed mass in H2O (Da)
D-HEWLEC	14362	698	256	15064	15060
D-HEWLPP	14305	696	255	15005	15005

<span class="Chemical">D-HEWLEC has 130 residues, with one additional <span class="Chemical">glycine at the N-terminus compared with the other HEWL variants studied (Supplementary Fig. S1), resulting in differences in the expected masses. The masses observed by MS of 15 060 and 15 005 Da (Supplementary Fig. S4) for D-HEWLEC and D-HEWLPP, respectively, closely match the expected values (Table 2 ▸) and verify the successful replacement of H atoms by D atoms in non-exchangeable positions. D-HEWLEC shows a minor difference of 4 Da between the expected and the observed masses, which shows that 99.4% of all non-exchangeable positions are occupied by D. The D-HEWLPP observed mass exactly matched the expected value of the fully deuterated form.

Perdeuterated variants of lysozyme are stable and active

DSF assays were performed to retrieve information on the folding and stability of <span class="Chemical">D-HEWLEC and <span class="Chemical">D-HEWLPP using H-HEWL as a reference. Results were obtained using the same deuterated buffer (50 mM sodium acetate pD 4.5 in D2O) and showed that both variants of D-HEWL are thermally less stable than H-HEWL [Figs. 2 ▸(a) and 2 ▸(b)]. The refolded D-HEWLEC is less thermally stable than D-HEWLPP, with a difference in melting temperature of 4.9°C. Moreover, compared with H-HEWL, the refolded D-HEWLEC shows a decrease in thermal stability of 6.8°C. If the D-HEWLEC was not completely separated from denaturing salts upon refolding, a small population of misfolded protein could potentially be present in the sample. To test this, D-HEWLEC crystals were washed and dissolved in protein buffer (from now on referred to as D-HEWLEC after crystallization) and analyzed by DSF [Figs. 2 ▸(a) and 2 ▸(b)]. With differences of less than 1°C observed between D-HEWLEC before and after crystallization, it was concluded that the lower thermal stabil­ity was not attributable to the presence of misfolded protein in the D-HEWLEC sample.

Figure 2

Stability and activity of the HEWL variants. (a) T m values for H-HEWL, D-HEWLEC (before and after crystallization) and D-HEWLPP in deuterated protein buffer (50 mM sodium acetate pD 4.5) and in hydrogenated activity-assay buffer (0.1 M sodium phosphate pH 7.5, 0.1 M sodium chloride, 2 mM sodium azide). (b) Thermal unfolding curves (first derivative against temperature) of H-HEWL (green), D-­HEWLEC before crystallization (continuous dark blue line) and after crystallization (dashed light blue line) and D-HEWLPP (red) in deuterated protein buffer. (c) Enzymatic activity of H-HEWL (green), D-HEWLEC (dark blue, before crystallization; light blue, after crystallization) and D-HEWLPP (red) in the hydrogenated activity-assay buffer. The p-values represent the significance of the homoscedastic hypothesis, meaning the probability of the pairs of measured values being equal.

The enzymatic activities of the <span class="Chemical">D-HEWL variants were also assessed. As part of this, DSF measurements were performed in activity-assay buffer (0.1 M <span class="Chemical">sodium phosphate buffer pH 7.5 in H2O with 0.1 M NaCl and 2 mM NaN3). A systematic decrease in stability of all of the samples was observed in this buffer [Fig. 2 ▸(a)]. The D-HEWL variants are less active than H-HEWL (D-HEWLEC and D-HEWLPP exhibited 51% and 67% of the activity of H-HEWL, respectively; both were significantly different, with t-test p values of <0.05) [Fig. 2 ▸(c)]. Conversely, the activity difference between D-HEWLEC and D-HEWLPP is not significant (p = 0.19). As for the thermal stability, no significant differences were observed between D-HEWLEC before and after crystallization.

Structural similarities and differences

Atomic resolution X-ray diffraction data were collected for all three variants: H-HEWL, <span class="Chemical">D-HEWLEC and D-HEWLPP. The data sets all extended to at least 1.00 Å resolution, although, as evident from the merging statistics (Table 1 ▸), the resolution cutoff was limited by the experimental geometry (detector distance and coverage) and not by the diffraction power of the crystals. Given the low symmetry of the P1 space group, a data-collection strategy with sweeps collected in two distinct crystal orientations (different κ angles) was implemented. An overall completeness of greater than 90% was obtained to a resolution of 1.00 Å. Refinement of the three variants of lysozyme provided the basis for comparison of the features and differences between the structures. The quality and resolution of the diffraction data allowed the visualization of elusive structural detail, including side-chain and main-chain disorder, and the interpretation of complex hydrogen-bonding patterns and their underlying structural dynamics.

Secondary and tertiary structures are retained

Numerous structures of HEWL are available in the PDB, <span class="Gene">representing a multitude of crystallization conditions, different space groups, ligands, humidity levels, mutations etc., but a benchmark in this large pool of structures is the P1 structure refined to 0.65 Å reesolution by Wang et al. (2007 ▸) (PDB entry 2vb1). With a r.m.s.d. of 0.23 Å between the Cα atoms, the three-dimensional structure of H-HEWL obtained in our study closely matches this model. There are some differences between the disorder modelled in the two structures, which may reflect the difference in resolution of the corresponding data sets.

In order to perform a comparison of the structure of H-HEWL with the structures of the two <span class="Chemical">D-HEWL variants, the model of H-HEWL was obtained from similar crystallization conditions, <span class="Chemical">data-collection and refinement parameters and resolution limits to those for the D-HEWL structures.

The structural alignment based on Cα atoms between the three HEWL variants showed a high degree of similarity, with an r.m.s.d. of 0.11 Å for both <span class="Chemical">D-HEWLEC and <span class="Chemical">D-HEWLPP in comparison with H-HEWL [Fig. 3 ▸(a)]. The conserved tertiary and secondary structures indicate that perdeuteration did not have a significant impact on the overall protein fold, as has been demonstrated in many neutron crystallographic studies of other proteins (Artero et al., 2005 ▸; Haupt et al., 2014 ▸; Langan et al., 2014 ▸; Cuypers, Mason et al., 2013 ▸; Yee et al., 2019 ▸; Liu et al., 2007 ▸; Koruza et al., 2019 ▸). The r.m.s.d. between the two D-HEWL variants was 0.13 Å, suggesting that the refolding process had little effect on the global protein fold.

Figure 3

The overall structures and normalized B factors of the three HEWL variants. (a) Ribbon representation of the structurally aligned models of H-HEWL (green), D-HEWLEC (blue) and D-HEWLPP (red). (b) The active site and the polysaccharide-binding cleft shown for all three molecules: H-HEWL (green), D-HEWLEC (blue) and D-HEWLPP (red). (c) Plot of the normalized residue-averaged B factors from the H-HEWL (green), D-HEWLEC (blue) and D-HEWLPP (red) models.

Alternate conformations and hydrogen-bond patterns

The atomic resolution X-ray data enabled a detailed <span class="Chemical">description of backbone and side-chain disorder. Alternate conformations were modelled for approximately 30% of the protein residues. Overall, the structures exhibited similar disorder patterns; the only exceptions were residues Glu7, Asn19, Ser24, Gln41, Thr89 and Gln121 (Supplementary Fig. S5). Given the high resolution of the X-ray data, the structural analysis includes a comparison of hydrogen bonds in the three structures, as this is of central interest for an understanding of differences in thermal stability.

Even at this high resolution, the electron-density maps in specific regions do not allow unambiguous modelling. Thus, the results from HBPLUS (McDonald & Thornton, 1994 ▸) were filtered considering the RSCC and RSZO metrics from EDSTATS (Tickle, 2012 ▸; details are shown in Supplementary Figs. S6–S8) to ensure the reliability of the subsequent analysis. The following residues did not comply with the applied cutoffs in one or more of the structures: <span class="Chemical">Gly0, <span class="Chemical">Ala9, Gly26, Asn27, Ala32, Phe38, Tyr53, Leu56, Ile58, Trp62, Cys64, Thr89, Ser91, Val92, Asp101, Gly102, Asn103, Gly104, Met105, Asn106, Ala107, Cys127 and Leu129. Discrepancies in hydrogen-bond lengths larger than 0.1 Å between all three structures were considered and inspected individually.

A comparison of the active site, with the catalytic residues <span class="Chemical">Asp35 and <span class="Chemical">Glu52, and the polysaccharide-binding cleft (Phillips, 1967 ▸) initially showed only minor differences in residue positions and conformations [Fig. 3 ▸(b)]. However, the residues Lys97–Gly104 display a high level of disorder, reflected by increased B values, most noticeably in the structure of D-HEWLEC [Fig. 3 ▸(c)]. As also reported by Wang et al. (2007 ▸), this region contains main-chain disorder due to a partial peptide-plane flip of Asn103, which causes strain on the backbone of residues Lys97–Gly104 (Fig. 4 ▸), propagating through hydrogen-bond interactions. The occupancy of the loop conformation associated with the flipped Asn103 (conformation B) was 46% in D-HEWLEC, 38% in D-HEWLPP and 33% in H-HEWL. Structural alignment of this region (Lys97–Gly104, using all atoms) showed that in comparison with H-HEWL, D-HEWLEC and D-HEWLPP deviate by 0.27 and 0.16 Å, respectively. Meanwhile, the r.m.s.d. between D-HEWLEC and D-HEWLPP was 0.21 Å.

Figure 4

Increased disorder in the Lys97–Gly104 region of D-HEWLEC compared with both D-HEWLPP and H-HEWL. Representation of the backbone disorder resulting from the strain induced by the Asn103 partial peptide flip in D-HEWLEC (a), D-HEWLPP (b) and H-HEWL (c). The 2F o − F c electron-density maps represented are contoured at 1σ.

Main-chain disorder was also observed in the <span class="Chemical">Lys13–<span class="Chemical">Gly16 region, which is part of the first α-helix, with variations in the Gly16 N–Lys13 O hydrogen bond (Supplementary Fig. S9). However, this relates to the disorder of the His15 side chain, together with the interaction of Lys13 with the C-terminal residue Leu129 and of Gly16 with the disordered Arg114 via crystal contacts. The alternate conformations of His15, A and B, appear to be stabilized by water-mediated hydrogen bonds to Asn93 and by a hydrogen-bond to nitrate ion 9, respectively (Fig. 5 ▸).

Figure 5

Disorder and hydrogen-bond patterns surrounding the His15 side chain. A representation is shown of the overall environment around His15 in D-­HEWLEC (a), D-HEWLPP (b) and H-HEWL (c). The 2F o − F c electron-density maps represented are contoured at 1σ. Highlighted hydrogen-bond interactions correlated with His15 side-chain disorder are shown for conformation A of D-HEWLEC (d), D-HEWLPP (e) and H-HEWL (f) and for conformation B of D-HEWLEC (g), D-HEWLPP (h) and H-HEWL (i).

The most evident differences between the structures in this region are the disorder of <span class="Chemical">Thr89 in H-HEWL, and more profoundly in <span class="Chemical">D-HEWLPP, and the absence of water 81 in D-HEWLPP. For His15A, water 81 seems to be important in restraining Thr89 in H-HEWL and D-HEWLEC, contrary to the observation in D-HEWLPP. In the absence of water 81 in D-HEWLPP, a significant displacement of Thr89 occurs, stabilizing the His15 side chain. Furthermore, a steric clash with Thr89 appears to force flipping of the Asp87 side chain. The visualization of this extended hydrogen-bond network is supported by the similar refined occupancies of His15A, water 57, Thr89B and Asp87B of 47%, 34%, 39% and 41%, respectively. Meanwhile, in the H-HEWL and D-HEWLEC structures, His15A interacts with Asn93 and Asp87 through hydrogen bonds mediated by waters 57 and 81, as shown by their refined occupancies (51% for His15A, 65% for water 57 and 55% for water 81 in H-HEWL; 58% for His15A, 70% for water 57 and 55% for water 81 in D-HEWLEC).

On the other hand, <span class="Chemical">His15B in all three HEWL structures forms a <span class="Chemical">hydrogen bond to nitrate ion 9, which is further stabilized by hydrogen bonds to Ile88 N and water 72. This interaction network is supported by the refined occupancies of His15B and nitrate ion 9 (42% and 49% in H-HEWL, 49% and 56% in D-HEWLEC and 66% and 47% in D-HEWLPP, respectively). The low B factor refined for the O2 atom of this nitrate ion revealed the presence of a water molecule when the nitrate is not occupying the space (the occupancy of nitrate 9 O2 is 1, while the nitrate occupancy is refined based on N, O1 and O3). Additionally, in D-HEWLPP the His15B side chain forms a hydrogen bond to the nitrate ion, which replaces its interaction with Thr89 and promotes the interaction of Thr89A with Asp87A, as shown by their matching occupancies of 61% and 59%, respectively.

The presence of <span class="Chemical">Gly0 at the N-terminus of <span class="Chemical">D-HEWLEC influences the hydrogen-bond pattern in this region. Specifically, Gly0 cancels the Lys1 N–Thr40 OG1 interaction, instead favouring a Thr40 OG1–Lys1 O hydrogen bond (Fig. 6 ▸). Additionally, Gly0 does not interact with other protein residues and increases the disorder of the N-terminus of D-HEWLEC. In H-HEWL and D-HEWLPP, water molecule 138 occupies the position of Gly0 and enables water-mediated hydrogen bonds between Lys1 N and Ser86B OG.

Figure 6

Representation of the differences in the hydrogen-bond patterns involving Lys1 and Thr40 in D-HEWLEC with the additional Gly0 residue (a), D-­HEWLPP (b) and H-HEWL (c). The 2F o − F c electron-density maps represented are contoured at 1σ.

In addition, several minor differences between the three structures were noted, where <span class="Chemical">D-HEWLEC in particular stands out. In <span class="Chemical">D-HEWLEC Asn19 was observed in a single conformation, allowing a stable Gly22 N–Asn19 O hydrogen bond of 2.96 Å, while in D-HEWLPP and H-HEWL disorder was observed, with the major conformation (occupancies of 60% and 69%, respectively) resulting in a significantly longer Gly22 N–Asn19 O hydrogen bond (Supplementary Fig. S10). This variation is correlated with the alternate conformations of the Asn19 side chain in H-HEWL and D-HEWLPP, where the minor conformation of Asn19 participates in crystal contacts with Ser81 O, while the major conformation is involved in crystal contacts with the disordered Gln41 OE1. In D-HEWLEC only the latter conformation is present, as Gln41 is ordered, resulting in a single conformation of Asn19 with the shorter intramolecular Gly22 N–Asn19 O hydrogen bond. This shorter interaction suggests a more stable 310-helix between Tyr20 and Gly22 in D-HEWLEC, although this may be a consequence of the stable crystal contact between the side chains of Asn19 and Gln41, thus not influencing stability in solution.

In all three structures <span class="Chemical">Ser81 adopts two distinct conformations, giving rise to different <span class="Chemical">Leu84 N–Ser81 O hydrogen-bond lengths (Supplementary Fig. S11), where the major conformation corresponds to the shorter of the two inter­actions. However, the lower occupancy of this major conformation in D-HEWLEC (66% compared with 82% in both D-HEWLPP and H-HEWL), together with the larger difference in the hydrogen-bond lengths of the two conformations, indicates that the Leu84 N–Ser81 O interaction is potentially weaker in D-HEWLEC, destabilizing its 310-helix.

Furthermore, in another 310-helix (Val120–<span class="Chemical">Arg125), minor variations were observed in the Arg125 NH2–Asp119 OD2 and Arg125 NH2–Gln121B OE1 hydrogen bonds, with the shorter Arg125 NH2–Asp119 OD2 interactions found in H-HEWL (Supplementary Fig. S12). Additionally, in D-HEWLEC Arg5 forms longer side chain–main chain hydrogen bonds to Trp123 O and Arg125 O, respectively, representing a minor destabilization of the tertiary structure in comparison to D-HEWLPP and H-HEWL.

Discussion

By using an <span class="Species">E. coli expression system in parallel with in-column protein refolding, it is possible to obtain a more than threefold gain in the production of <span class="Chemical">D-HEWL in comparison with yields for the P. pastoris system. The increase in yield is proportional to the financial cost reduction of protein production, since the approximate cost per litre of E. coli and P. pastoris cultures is similar. The cost is dominated by the deuterated materials, which for D-HEWL production using the E. coli system is roughly 140 euros per milligram of protein, in comparison to approximately 450 euros per milligram using P. pastoris. Although non-optimal in separating monomeric lysozyme from denaturing salts, the SEC column used in refolding provided the highest yields when compared with analytical columns. This observation is related to difficulties in removing such high concentrations of salt and the need to separate oligomeric from monomeric fractions while injecting milligram amounts of sample. Furthermore, the yield of the protocol can be further increased by dialyzing the oligomeric, misfolded and partially unfolded fractions of D-HEWLEC from refolding against denaturing buffer and reinjecting them into a refolding SEC. Complete perdeuteration of non-exchangeable sites in both D-HEWL variants was demonstrated by mass spectrometry. A similar refolding approach has been applied for the production of a perdeuterated antifreeze protein (Petit-Haertlein et al., 2009 ▸), with the difference that refolding was carried out in a deuterated buffer. The refolding of perdeuterated lysozyme reported here is, to our knowledge, the first example of a perdeuterated protein exceeding 7 kDa and with multiple disulfide bonds. Refolding in D2O was also attempted; however, it led to a decrease in the refolding yield (data not shown) owing to reduced separation of the monomeric protein fraction and denaturing salts. This observation is likely to be due to the slower dynamics in heavy water, resulting in a delay in the elution of the folded monomeric lysozyme fraction. Additionally, using D2O would not be cost-effective, given the numerous refolding SEC runs that are required to obtain several milligrams of refolded protein. As the refolding of D-HEWLEC was performed in H2O buffer, it may result in the caging of H atoms in exchangeable positions, i.e. exchanged during the unfolded state and then trapped upon refolding. The protein fold may keep specific regions protected from any interaction with solvent molecules; hence, to exchange these H atoms to D atoms the protein must be at least partially unfolded in D2O buffer. To unambiguously identify the positions occupied by caged H atoms in the protein structure, neutron crystallography or NMR experiments are required. An indication of relevant positions is found in a reverse setup, where 20 H atoms were exchanged to D using unfolding and refolding processes of H-HEWL in D2O (Kita & Morimoto, 2016 ▸), as observed in the neutron structure deposited in the PDB (PDB entry 6k8g; Kita & Morimoto, 2020 ▸).

Biophysical characterization of both <span class="Chemical">D-HEWL variants and commercially available unlabelled HEWL shows that both <span class="Chemical">D-HEWL molecules are stable and active. The perdeuterated variants showed lower thermal stability relative to the hydrogenated protein both in D2O and H2O buffers, in line with what has been reported in several biophysical studies on protein deuteration (Berns, 1963 ▸; Hattori et al., 1965 ▸; Brockwell et al., 2001 ▸; Meilleur et al., 2004 ▸; Koruza et al., 2018 ▸; Nichols et al., 2020 ▸). Additionally, it seems that both hydrogenated and perdeuterated forms of HEWL have an increased transition temperature in D2O compared with H2O, as described in previous studies (Makhatadze et al., 1995 ▸; Efimova et al., 2007 ▸). However, the data presented here are not sufficient to draw definitive conclusions on this solvent-isotope effect, since the D2O and H2O buffers used have significantly different compositions (aimed at crystallization and activity measurements, respectively). Additionally, the presence of residual H atoms in H-HEWL, due to the limited time for H/D exchange and the limited solvent accessibility of specific protein regions to the D2O solvent, cannot be ruled out. The differences in protein thermal stability can be correlated with the enzymatic activities. Perdeuteration of the protein was expected to affect its dynamics and consequently its stability and activity, and in this study a decrease in stability as well as in relative activity compared with H-HEWL is observed. The differences between D-HEWLEC and D-HEWLPP are likely to be a consequence of the refolding procedure. The additional N-terminal glycine residue in D-HEWLEC may also cause a slight destabilization of the protein. However, the activity results do not allow a conclusive correlation of the effect of refolding on activity, since under the conditions used the difference in activity between the two perdeuterated variants is not statistically significant. This further emphasizes the similarity between the D-HEWL variants and validates the refolding approach to obtain stable and active D-HEWL.

While a large number of HEWL crystal structures have been published, the detailed comparisons needed for this study of <span class="Chemical">perdeuterated and <span class="Chemical">hydrogenated HEWL required the growth of crystals under closely comparable conditions, with only minor variations relating to the seeding procedure and precipitant concentrations. The atomic resolution X-ray data for both perdeuterated samples, as well as for the reference unlabelled sample, have been analyzed in detail, revealing structural features that can be related to the observations on stability and activity. The crystal packing and overall structures were, as expected, found to be essentially identical, with negligible differences in the unit-cell parameters. Moreover, the nitrate and acetate ions that are essential to crystallization were located and refined in identical positions in the three models, with similar B factors (Table 1 ▸). However, despite the close similarity between the three structures, there are some clear variations in hydrogen-bond distances, which appear to be related to the differences in protein stability.

An important factor contributing to the reduced thermal stability of the <span class="Chemical">D-HEWL structures is the effect of H/D substitution on hydrophobic interactions. As <span class="Chemical">described by Hattori et al. (1965 ▸), deuterium-substituted nonpolar amino-acid side chains have a reduced steric requirement due to the smaller amplitudes of vibration of the C—D bond compared with C—H, leading to weaker hydrophobic interactions between the residue side chains; this has also been noted in mass-spectrometric studies (Yee et al., 2016 ▸). Additionally, D2O has a stronger hydrophobic effect than H2O, leading to changes in solvation, more compact structures and a decrease in protein flexibility (Svergun et al., 1998 ▸; Sasisanker et al., 2004 ▸; Efimova et al., 2007 ▸; Jasnin et al., 2008 ▸). This is observed in the crystal structures, where a larger number of structural water molecules were identified in H-HEWL compared with both D-HEWL variants. Moreover, the molecular surface and solvent-accessible surface areas of D-HEWLPP were 15 555 and 8 200 Å2, respectively, whereas those for H-HEWL were 15 725 and 8 274 Å2. The corresponding values for D-HEWLEC are not directly comparable due to the presence of the additional Gly0 residue. Finally, protein dynamics are expected to be influenced by deuteration since D is twice as heavy as H, which in the case of HEWL corresponds to a mass increase of at least ∼700 Da. All of these factors play a role in the interaction with substrate molecules, since the enzymatic activity is strongly dependent on protein dynamics and the displacement of water molecules to accommodate the substrate, consistent with the decreased activity observed in the perdeuterated variants.

The disorder observed in the structures is evidently linked to the intricate networks of <span class="Chemical">hydrogen bonds. However, only a few regions of the models show distinct disorder due to variations in the <span class="Chemical">hydrogen-bond patterns. These are the cases of the Thr40 N–Lys1 O and Gly22 N–Asn19 O hydrogen bonds and the His15 side chain. The differences observed in the Thr40 N–Lys1 O interaction are due to the presence of Gly0 at the N-terminus of D-HEWLEC, leading to increased disorder. In the case of the Gly22 N–Asn19 O hydrogen bond, the alternate conformation of Asn19 is favoured by the side-chain disorder of Gln41 that is present in D-HEWLPP and H-HEWL, resulting in a weaker Gly22 N–Asn19 O inter­action. Finally, the His15 side-chain disorder, with differentiation between the two conformational networks A and B, appears to be linked to partial occupancies of waters 57 and 81 and of nitrate ion 9, and potentially to variations in protonation states. In D-HEWLPP, the absence of water 81 seems to promote the disorder of Thr89 and subsequently the flipping of Asp87 to stabilize His15A. The protonation states are not evident, even in the 0.65 Å resolution structure (Wang et al., 2007 ▸), and obtaining an unambiguous picture of the proton­ation of lysozyme will require high-quality and high-resolution neutron diffraction data. In conclusion, these minor variations in the protein structure alone are not likely to explain the decrease in stability observed in the D-HEWL structures.

The main difference in the crystal structures that can be correlated with variations in protein stability is the disorder of the <span class="Chemical">Lys97–<span class="Chemical">Gly104 region due to the partial peptide-plane flip of Asn103. Peptide-plane flipping occurs in the early stages of protein folding, particularly when glycine is in the i + 1 position, since the structure is not yet restrained by hydrogen bonds between protein residues (Hayward, 2001 ▸). Although not frequent due to its energetically unfavored conformation, peptide flipping remains underrepresented in the PDB (Berman et al., 2000 ▸). This was found to be correlated, among other factors, with the resolution of the X-ray data available to determine the crystal structures (Stewart et al., 1990 ▸; Weiss et al., 1998 ▸). Peptide flipping can be responsible for amyloid formation (Milner-White et al., 2006 ▸; Yang et al., 2006 ▸) or can confer structural flexibility that is essential for protein function (Weiss et al., 1998 ▸; Ludwig et al., 1997 ▸; Keedy et al., 2015 ▸). As described by Wang et al. (2007 ▸), the backbone disorder in this region is a consequence of the Asn103 peptide-plane flip. In their H-HEWL crystal structure determined from X-ray data at 0.65 Å resolution, the flipped conformation has a refined occupancy of 35%, which is consistent with our H-HEWL model in which the flipped conformation of Asn103 was refined with an occupancy of 33%. This observation suggests that the likelihood of Asn103 peptide flipping in native H-HEWL is constant. Conversely, in the D-HEWL models the refined occupancies for the flipped conformation are greater: 46% in D-HEWLEC and 38% in D-HEWLPP. While D-HEWLEC was chemically unfolded and then refolded by slowly changing its buffer from 6 M guanidine–HCl to a 2 M urea H2O solution, D-HEWLPP was folded in deuterated conditions during expression. Thus, both D-HEWL variants were subjected to different folding environments compared with H-HEWL, which are associated with slower solvent dynamics and the H/D-isotope effect, which could favour the peptide-plane flip of Asn103. Interestingly, when the protein is completely unfolded, as is the case for D-HEWLEC, it appears that the probability of the peptide flip occurring or not is identical, suggesting a high degree of freedom between the two conformations. In the case of D-HEWLPP, the solvent-isotope effect may be responsible for this by slowing down the folding dynamics and increasing the likelihood of peptide flipping. This destabilized region is not only part of the enzyme active site, and therefore relevant to substrate binding, as reported by Strynadka & James (1991 ▸), but also protects a hydrophobic pocket containing Trp28, Trp62, Trp63 and Trp108. The increase in disorder of this loop region may therefore be correlated with the decrease in protein thermal stability measured for D-HEWLEC when compared with D-HEWLPP.

The results presented here support the wi<span class="Chemical">despread understanding that perdeuteration has no significant effect on secon<span class="Chemical">dary and tertiary protein structures. Nevertheless, the hydrophobic effect and the slower dynamics caused by perdeuteration have an impact on protein stability and activity. Ultimately, this study emphasizes the capability to use E. coli for the expression of recombinant insoluble protein and subsequent refolding for the production of large amounts of perdeuterated material, enabling a wide range of new science in the future. In addition, this work highlights the fact that studies of deuterated proteins can reveal crucial and highly specific aspects of protein conformation related to variations in protein thermal stability.

Data accessibility

The X-ray diffraction <span class="Chemical">data and models have been deposited in the <span class="Chemical">PDB with accession codes 7ave (D-HEWLEC), 7avf (H-HEWL) and 7avg (D-HEWLPP).

<span class="Chemical">PDB reference: hen egg-white lysozyme, <span class="Chemical">hydrogenated, 7avf

<span class="Chemical">PDB reference: <span class="Chemical">perdeuterated, expressed in

<span class="Chemical">PDB reference: <span class="Chemical">perdeuterated, produced in

Supplementary Figures. DOI: 10.1107/S2052252521001299/jt5055sup1.<span class="Chemical">pdf