Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis

Lack of controls and understanding in nucleation, which proceeds crystal growth and other phase transitions, has been a bottleneck challenge in chemistry, materials, biology, and other fields. The exemplary needs for better methods for biomacromolecule crystallization include (1) synthesizing crystals for high-resolution structure determinations in fundamental research and (2) tuning the crystal habit and thus the corresponding properties in materials and pharmaceutical applications. Herein, a deterministic method is established capable of sustaining the nucleation and growth of a single crystal using the protein lysozyme as a prototype. The supersaturation is localized at the interface between a sample and a precipitant solution, spatially confined by the tip of a single nanopipette. The exchange of matter between the two solutions determines the supersaturation, which is controlled by electrokinetic ion transport driven by an external potential waveform. Nucleation and subsequent crystal growth disrupt the ionic current limited by the nanotip and are detected. The nucleation and growth of individual single crystals are measured in real time. Electroanalytical and optical signatures are elucidated as feedbacks with which active controls in crystal quality and method consistency are achieved: five out of five crystals diffract at a true atomic resolution of up to 1.2 Å. As controls, those synthesized under less optimized conditions diffract poorly. The crystal habits during the growth process are tuned successfully by adjusting the flux. The universal mechanism of nano-transport kinetics, together with the correlations of the diffraction quality and crystal habit with the crystallization control parameters, lay the foundation for the generalization to other materials systems.

Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature

Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium-calmodulin dependent kinase II (CaMKIIβ).

Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography

Hen egg-white lysozyme (HEWL) is an enzymatic protein with two acidic amino acids, Glu35 and Asp52, in its active site. Glu35 acts as a proton donor to the substrate and Asp52 interacts with the positively charged substrate, suggesting different protonation states of these residues. However, neutron crystallographic studies thus far have not provided a consistent picture of the protonation states of these residues. Only one study succeeded in observing the active protonation states of Glu35 and Asp52 in the triclinic crystal system. However, their active states in the most widely studied tetragonal crystal system are still unknown. The application of the D/H contrast technique in neutron crystallography improves the ability to locate exchangeable D/H atoms in proteins. In the present study, D2O and H2O solvent crystals were prepared. Each neutron data set was collected for only five days by combining a time-of-flight diffractometer (iBIX) and the spallation neutron source at the Japan Proton Accelerator Research Complex. The D/H contrast map provided better visualization of the D/H atoms in HEWL than the conventional neutron scattering length density map. The neutron D/H contrast map demonstrated the alternative protonation of the OE1 and OE2 atoms in the carboxyl group of Glu35. This alternative protonation occurs in the absence of a substrate, where high selectivity of the protonation site does not occur. In this case, only the OE1—HE1 bond attacks the substrate in an equilibrium between OE1—HE1 and OE2—HE2, or the H+ ion of the OE2—HE2 bond moves to the OE1 atom just before or after substrate binding to initiate the catalytic reaction. In contrast, the carboxyl group of Asp52 is not protonated. Protonation of the carboxyl group was not observed for other Asp and Glu residues. These results are consistent with results from NMR spectroscopy and explain the protonation states at the active site in the apo form of HEWL.

Serial macromolecular crystallography at ALBA Synchrotron Light Source

The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.

The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme

The biological function of a protein is intimately related to its structure and dynamics, which in turn are determined by the way in which it has been folded. In vitro refolding is commonly used for the recovery of recombinant proteins that are expressed in the form of inclusion bodies and is of central interest in terms of the folding pathways that occur in vivo. Here, biophysical data are reported for in vitro-refolded hydrogenated hen egg-white lysozyme, in combination with atomic resolution X-ray diffraction analyses, which allowed detailed comparisons with native hydrogenated and refolded perdeuterated lysozyme. Distinct folding modes are observed for the hydrogenated and perdeuterated refolded variants, which are determined by conformational changes to the backbone structure of the Lys97-Gly104 flexible loop. Surprisingly, the structure of the refolded perdeuterated protein is closer to that of native lysozyme than that of the refolded hydrogenated protein. These structural differences suggest that the observed decreases in thermal stability and enzymatic activity in the refolded perdeuterated and hydrogenated proteins are consequences of the macromolecular deuteration effect and of distinct folding dynamics, respectively. These results are discussed in the context of both in vitro and in vivo folding, as well as of lysozyme amyloidogenesis.

Insights into the Protein Ruthenation Mechanism by Antimetastatic Metallodrugs: High-Resolution X-ray Structures of the Adduct Formed between Hen Egg-White Lysozyme and at Various Time Points

The pharmacological profile of medicinally relevant Ru(III) coordination compounds has been ascribed to their interactions with proteins, as several studies have provided evidence that DNA is not the primary target. In this regard, numerous spectroscopic and crystallographic studies have indicated that the Ru(III) ligands play an important role in determining the metal binding site, acting as the recognition element in the early stages of the protein-complex formation. Herein, we present a series of near-atomic-resolution X-ray crystal structures of the adducts formed between the antimetastatic metallodrug imidazolium trans-[tetrachlorido(S-dimethyl sufoxide)(1H-imidazole)ruthenate(III)] (NAMI-A) and hen egg-white lysozyme (HEWL). These structures elucidate a series of binding events starting from the noncovalent interaction of intact NAMI-A ions with HEWL (1.5 h), followed by the stepwise exchange of all Ru ligands except for 1H-imidazole (26 h) to the final "ruthenated" protein comprising one aquated Ru ion coordinated to histidine-15 of HEWL (98 h). Our structural data clearly support a two-step mechanism of protein ruthenation, illustrating the ligand-mediated recognition step of the process.

The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors

Crystallographic B-factors provide direct dynamical information on the internal mobility of proteins that is closely linked to function, and are also widely used as a benchmark in assessing elastic network models. A significant question in the field is: what is the exact amount of thermal vibrations in protein crystallographic B-factors? This work sets out to answer this question. First, we carry out a thorough, statistically sound analysis of crystallographic B-factors of over 10 000 structures. Second, by employing a highly accurate all-atom model based on the well-known CHARMM force field, we obtain computationally the magnitudes of thermal vibrations of nearly 1000 structures. Our key findings are: (i) the magnitude of thermal vibrations, surprisingly, is nearly protein-independent, as a corollary to the universality for the vibrational spectra of globular proteins established earlier; (ii) the magnitude of thermal vibrations is small, less than 0.1 Å² at 100 K; (iii) the percentage of thermal vibrations in B-factors is the lowest at low resolution and low temperature (<10%) but increases to as high as 60% for structures determined at high resolution and at room temperature. The significance of this work is that it provides for the first time, using an extremely large dataset, a thorough analysis of B-factors and their thermal and static disorder components. The results clearly demonstrate that structures determined at high resolution and at room temperature have the richest dynamics information. Since such structures are relatively rare in the PDB database, the work naturally calls for more such structures to be determined experimentally.

Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. In this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips

Sample handling and manipulation for cryoprotection currently remain critical factors in X-ray structural determination. While several microchips for macromolecular crystallization have been proposed during the last two decades to partially overcome crystal-manipulation issues, increased background noise originating from the scattering of chip-fabrication materials has so far limited the attainable resolution of diffraction data. Here, the conception and use of low-cost, X-ray-transparent microchips for in situ crystallization and direct data collection, and structure determination at atomic resolution close to 1.0 Å, is presented. The chips are fabricated by a combination of either OSTEMER and Kapton or OSTEMER and Mylar materials for the implementation of counter-diffusion crystallization experiments. Both materials produce a sufficiently low scattering background to permit atomic resolution diffraction data collection at room temperature and the generation of 3D structural models of the tested model proteins lysozyme, thaumatin and glucose isomerase. Although the high symmetry of the three model protein crystals produced almost complete data sets at high resolution, the potential of in-line data merging and scaling of the multiple crystals grown along the microfluidic channels is also presented and discussed.

On the complementarity of X-ray and NMR data

X-ray crystallography and NMR contain complementary information for the structural characterization of biological macromolecules. X-ray diffraction is primarily sensitive to the overall shape of the molecule, whereas NMR is mostly sensitive to the atomic detail. Their combination can therefore provide a stronger justification for the resulting structure. For their combination we have recently proposed REFMAC-NMR, which relies on primary data from both techniques for joint refinement. This possibility raises the compelling question of how far the complementarity can be extended. In this paper, we describe an integrative approach to the refinement with NMR data of four X-ray structures of hen-egg-white lysozyme, solved at atomic resolution in four different crystal forms, and we demonstrate that the outcome critically depends on the crystal form itself, reflecting the sensitivity of NMR to fine details.

The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme

The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl₂ and CuCl₂) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu⁺², Ni⁺² and Na⁺¹ cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector

Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.

Solving a new R2lox protein structure by microcrystal electron diffraction

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

Unit-cell response of tetragonal hen egg white lysozyme upon controlled relative humidity variation

Variation of relative humidity (rH) greatly affects the internal order of solvent-based protein crystals, and the rearrangement of molecules can be efficiently recorded in distinct diffraction patterns. This study focuses on this topic, reporting the effect of rH variation experiments on hen egg white lysozyme (HEWL) polycrystalline precipitates of tetragonal symmetry using X-ray powder diffraction (XRPD). In situ XRPD data were collected on HEWL specimens during dehydration and rehydration processes using laboratory instrumentation. A known polymorph [space group P43212, a = 79.07181 (1), c = 38.0776 (1) Å] was identified during gradual dehydration from 95 to 63% rH and vice versa. Pawley analysis of collected data sets and accurate extraction of unit-cell parameters indicated a characteristic evolution of the tetragonal axes with rH. In addition, there is a low humidity level below which samples do not retain their crystallinity. This work illustrates the accuracy of laboratory XRPD as a probe for time-resolved studies of proteins and in situ investigations of gradual structural modifications upon rH variation. These experiments provide essential information for improving production and post-production practices of microcrystalline protein-based pharmaceuticals.

Critical role of tyrosine-20 in formation of gold nanoclusters within lysozyme: a molecular dynamics study

Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20.

Investigation into the binding of dyes within protein crystals

It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins. Four protein crystals were investigated by X-ray diffraction to ascertain the mode of binding. These were crystals of lysozyme, thaumatin, trypsin inhibited with benzamidine and satellite tobacco mosaic virus. In 30 X-ray analyses of protein crystal-dye complexes, in only three difference Fourier maps was any difference electron density present that was consistent with the binding of dye molecules, and even in these three cases (thaumatin plus thioflavin T, xylene cyanol and m-cresol purple) the amount of dye observed was inadequate to explain the intense color of the crystals. It was concluded that the dye molecules, which are clearly inside the crystals, are disordered but are paradoxically tightly bound to the protein. It is speculated that the dyes, which exhibit large hydrophobic cores and peripheral charged groups, may interact with the crystalline proteins in the manner of conventional detergents.

Prediction of disulfide dihedral angles using chemical shifts

Cystine residues result from the formation of disulfide bonds between pairs of cysteine residues. This cross linking of the backbone is essential for the structure and activity of peptides and proteins. The conformation of a cystine side chain can be described using five dihedral angles, χ1, χ2, χ3, χ2', and χ1', with cystines favouring certain combinations of these angles. 2D NMR spectroscopy is ideally suited for structure determination of disulfide-rich peptides, because of their small size and constrained nature. However, only limited information of the cystine side chain conformation can be determined by NMR spectroscopy, leading to ambiguity in the deduced 3D structures. Resolving accurate structures is important as disulfide-rich peptides have proven to be promising drug candidates in a number of fields, either as bioactive leads or scaffolds. Using a database of NMR chemical shifts combined with crystallographic structures, we have developed a method called DISH that uses support vector machines to predict the dihedral angles of cysteine side chains. It is able to successfully predict χ2 angles with 91% accuracy, and has improved performance over existing prediction methods for χ1 angles, with 87% accuracy. For 81% of cysteine residues, DISH successfully predicted both the χ1 and χ2 angles. By revisiting published solution structures of peptides determined using NMR spectroscopy, we assessed the impact of additional cystine dihedral restraints on the quality of 3D models. DISH improved the resolution and accuracy, highlighting the potential for improving the understanding of structure-activity relationships and rational development of peptide drugs.

Adsorption of Denaturated Lysozyme at the Air-Water Interface: Structure and Morphology

The application of protein deuteration and high flux neutron reflectometry has allowed a comparison of the adsorption properties of lysozyme at the air-water interface from dilute solutions in the absence and presence of high concentrations of two strong denaturants: urea and guanidine hydrochloride (GuHCl). The surface excess and adsorption layer thickness were resolved and complemented by images of the mesoscopic lateral morphology from Brewster angle microscopy. It was revealed that the thickness of the adsorption layer in the absence of added denaturants is less than the short axial length of the lysozyme molecule, which indicates deformation of the globules at the interface. Two-dimensional elongated aggregates in the surface layer merge over time to form an extensive network at the approach to steady state. Addition of denaturants in the bulk results in an acceleration of adsorption and an increase of the adsorption layer thickness. These results are attributed to incomplete collapse of the globules in the bulk from the effects of the denaturants as a result of interactions between remote amino acid residues. Both effects may be connected to an increase of the effective total volume of macromolecules due to the changes of their tertiary structure, that is, the formation of molten globules under the influence of urea and the partial unfolding of globules under the influence of GuHCl. In the former case, the increase of globule hydrophobicity leads to cooperative aggregation in the surface layer during adsorption. Unlike in the case of solutions without denaturants, the surface aggregates are short and wormlike, their size does not change with time, and they do not merge to form an extensive network at the approach to steady state. To the best of our knowledge, these are the first observations of cooperative aggregation in lysozyme adsorption layers.

Structural basis of antigen recognition: crystal structure of duck egg lysozyme

Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.

Graphene-based microfluidics for serial crystallography

Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.

Steering protein adsorption at charged surfaces: electric fields and ionic screening

Protein adsorption at charged surfaces is a common process in the development of functional technological devices.

Current trends in protein crystallization

Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented.

SYNOPSIS

Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.

Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure

Hen Egg White Lysozyme (HEWL) is a widely used exemplar to study protein adsorption on surfaces and interfaces. Here we use fully atomistic Molecular Dynamics (MD) simulations, Multi-Parametric Surface Plasmon Resonance (MP-SPR), contact angle and zeta potential measurements to study HEWL adsorption at a silica surface. The simulations provide a detailed description of the adsorption mechanism and indicate that at pH7 the main adsorption driving force is electrostatics, supplemented by weaker hydrophobic forces. Moreover, they reveal the preferred orientation of the adsorbed protein and show that its structure is only slightly altered at the interface with the surface. This provides the basis for interpreting the experimental results, which indicate the surface adsorbs a close-packed monolayer at about pH10 where the surface has a large negative zeta potential and the HEWL is positively charged. At higher pH, the adsorption amount of the protein layer is greatly reduced due to the loss of charge on the protein. At lower pH, the smaller zeta potential of the surface leads to lower HEWL adsorption. These interpretations are complemented by the contact angle measurements that show how the hydrophobicity of the surface is greatest when the surface coverage is highest. The simulations provide details of the hydrophobic residues exposed to solution by the adsorbed HEWL, completing the picture of the protein layer structure.

Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.

High-resolution structure determination by continuous-rotation data collection in MicroED

MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. An improved data collection protocol for MicroED called “continuous rotation” is presented. Here microcrystals are continuously rotated during data collection yielding improved data, and allowing data processing with MOSFLM resulting in improved resolution for the model protein lysozyme. These improvements pave the way for the implementation and application of MicroED with wide applicability in structural biology.

Room-temperature macromolecular serial crystallography using synchrotron radiation

A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.

Three-dimensional electron crystallography of protein microcrystals

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology.

DOI:http://dx.doi.org/10.7554/eLife.01345.001

X-ray crystallography has been used to work out the atomic structure of a large number of proteins. In a typical X-ray crystallography experiment, a beam of X-rays is directed at a protein crystal, which scatters some of the X-ray photons to produce a diffraction pattern. The crystal is then rotated through a small angle and another diffraction pattern is recorded. Finally, after this process has been repeated enough times, it is possible to work backwards from the diffraction patterns to figure out the structure of the protein.

The crystals used for X-ray crystallography must be large to withstand the damage caused by repeated exposure to the X-ray beam. However, some proteins do not form crystals at all, and others only form small crystals. It is possible to overcome this problem by using extremely short pulses of X-rays, but this requires a very large number of small crystals and ultrashort X-ray pulses are only available at a handful of research centers around the world. There is, therefore, a need for other approaches that can determine the structure of proteins that only form small crystals.

Electron crystallography is similar to X-ray crystallography in that a protein crystal scatters a beam to produce a diffraction pattern. However, the interactions between the electrons in the beam and the crystal are much stronger than those between the X-ray photons and the crystal. This means that meaningful amounts of data can be collected from much smaller crystals. However, it is normally only possible to collect one diffraction pattern from each crystal because of beam induced damage. Researchers have developed methods to merge the diffraction patterns produced by hundreds of small crystals, but to date these techniques have only worked with very thin two-dimensional crystals that contain only one layer of the protein of interest.

Now Shi et al. report a new approach to electron crystallography that works with very small three-dimensional crystals. Called MicroED, this technique involves placing the crystal in a transmission electron cryo-microscope, which is a fairly standard piece of equipment in many laboratories. The normal ‘low-dose’ electron beam in one of these microscopes would normally damage the crystal after a single diffraction pattern had been collected. However, Shi et al. realized that it was possible to obtain diffraction patterns without severely damaging the crystal if they dramatically reduced the normal low-dose electron beam. By reducing the electron dose by a factor of 200, it was possible to collect up to 90 diffraction patterns from the same, very small, three-dimensional crystal, and then—similar to what happens in X-ray crystallography—work backwards to figure out the structure of the protein. Shi et al. demonstrated the feasibility of the MicroED approach by using it to determine the structure of lysozyme, which is widely used as a test protein in crystallography, with a resolution of 2.9 Å. This proof-of principle study paves the way for crystallographers to study protein that cannot be studied with existing techniques.

DOI:http://dx.doi.org/10.7554/eLife.01345.002

Liesegang-like patterns of Toll crystals grown in gel

Generating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. It was observed that crystallization occurred with a peculiar pattern along the capillary resembling Liesegang bands; this phenomenon is described at both macroscopic and atomic levels. It was found that bands appeared for native protein as well as for co-crystals of magic triangle (I3C)-bound protein even though they crystallize in different space groups. Crystallization occurred with a linear recurrence independent of the precipitant concentration and a protein-specific spacing coefficient. Bandwidth varied along the capillary, oscillating between large precipitation areas and single crystals. The reported data suggest that repetitive patterns can be generated with biological macromolecules in the presence of sodium malonate as a crystallization agent. A comparison with typical Liesegang patterns and the possible mechanism underlying this phenomenon are discussed.

Improved Generalized Born Solvent Model Parameters for Protein Simulations

The generalized Born (GB) model is one of the fastest implicit solvent models and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with tradeoffs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to non-protein systems will be explored in the future.

Protein diffusion and long-term adsorption states at charged solid surfaces

The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.

The effect of ionic strength, temperature, and pressure on the interaction potential of dense protein solutions: from nonlinear pressure response to protein crystallization

Understanding the intermolecular interaction potential, V(r), of proteins under the influence of temperature, pressure, and salt concentration is essential for understanding protein aggregation, crystallization, and protein phase behavior in general. Here, we report small-angle x-ray scattering studies on dense lysozyme solutions of high ionic strength as a function of temperature and pressure. We show that the interaction potential changes in a nonlinear fashion over a wide range of temperatures, salt, and protein concentrations. Neither temperature nor protein and salt concentration lead to marked changes in the pressure dependence of V(r), indicating that changes of the water structure dominate the pressure dependence of the intermolecular forces. Furthermore, by analysis of the temperature, pressure, and ionic strength dependence of the normalized second virial coefficient, b2, we show that the interaction can be fine-tuned by pressure, which can be used to optimize b2 values for controlled protein crystallization.

Fast high-pressure freezing of protein crystals in their mother liquor

High-pressure freezing (HPF) is a method which allows sample vitrification without cryoprotectants. In the present work, protein crystals were cooled to cryogenic temperatures at a pressure of 210 MPa. In contrast to other HPF methods published to date in the field of cryocrystallography, this protocol involves rapid sample cooling using a standard HPF device. The fast cooling rates allow HPF of protein crystals directly in their mother liquor without the need for cryoprotectants or external reagents. HPF was first attempted with hen egg-white lysozyme and cubic insulin crystals, yielding good to excellent diffraction quality. Non-cryoprotected crystals of the membrane protein photosystem II have been successfully cryocooled for the first time. This indicates that the presented HPF method is well suited to the vitrification of challenging systems with large unit cells and weak crystal contacts.

Aggregation and fibrillogenesis of proteins not associated with disease: a few case studies

While amyloid structures have been well characterised in a medical context, there is increasing interest in studying amyloid-like aggregates in other areas, such as food science and nanomaterials. Several proteins relevant to food processing, including serum albumen, lactoglobulin, lysozyme, ovalbumin, casein, and soy protein isolate have been shown to form fibrillar structures under both physiological and non-physiological conditions. These structures are likely to contribute to the structural characteristics of the final food product. In a biotechnological context, proteins such as insulin and eye lens crystallins can be induced to form amyloid structures which can subsequently be used in biotechnology. One example of this is the use of amyloid fibrils as a scaffold for the immobilisation of enzymes. Another current interest in amyloid fibrils is as a storage form for peptide hormones, including insulin, glucagon and calcitonin. Here, we give an overview of a selection of well characterised proteins that have been studied outside the context of disease.

Multiprotein interactions during surface adsorption: a molecular dynamics study of lysozyme aggregation at a charged solid surface

Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein-protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein-protein and protein-surface), and gives an insight into processes to be considered in the development of new functionalized material systems.

High-resolution structure of the recombinant sweet-tasting protein thaumatin I

Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at a concentration of 50 nM. The crystal structure of a recombinant form of thaumatin I produced in the yeast Pichia pastoris has been determined to a resolution of 1.1 Å. The model was refined with anisotropic B parameters and riding H atoms. A comparison of the diffraction data and refinement statistics for recombinant thaumatin I with those for plant thaumatin I revealed no significant differences in the diffraction data. The R values for recombinant thaumatin I and plant thaumatin I (F(o) > 4σ) were 9.11% and 9.91%, respectively, indicating the final model to be of good quality. Notably, the electron-density maps around Asn46 and Ser63, which differ between thaumatin variants, were significantly improved. Furthermore, a number of H atoms became visible in an OMIT map and could be assigned. The high-quality structure of recombinant thaumatin with H atoms should provide details about sweetness determinants in thaumatin and provide valuable insights into the mechanism of its interaction with taste receptors.

Temperature dependence of lysozyme hydration and the role of elastic energy

Water plays a critical role in protein dynamics and functions. However, the most basic property of hydration--the water sorption isotherm--remains inadequately understood. Surface adsorption is the commonly adopted picture of hydration. Since it does not account for changes in the conformational entropy of proteins, it is difficult to explain why protein dynamics and activity change upon hydration. The solution picture of hydration provides an alternative approach to describe the thermodynamics of hydration. Here, the flexibility of proteins could influence the hydration level through the change of elastic energy upon hydration. Using nuclear magnetic resonance to measure the isotherms of lysozyme in situ between 18 and 2 °C, the present work provides evidence that the part of water uptake associated with the onset of protein function is significantly reduced below 8 °C. Quantitative analysis shows that such reduction is directly related to the reduction of protein flexibility and enhanced cost in elastic energy upon hydration at lower temperature. The elastic property derived from the water isotherm agrees with direct mechanical measurements, providing independent support for the solution model. This result also implies that water adsorption at charged and polar groups occurring at low vapor pressure, which is known for softening the protein, is crucial for the later stage of water uptake, leading to the activation of protein dynamics. The present work sheds light on the mutual influence of protein flexibility and hydration, providing the basis for understanding the role of hydration on protein dynamics.

Mechanism of hen egg white lysozyme adsorption on a charged solid surface

The mechanism of hen egg white lysozyme (HEWL) adsorption on a negatively charged, hydrophilic surface has been studied using atomistic molecular dynamics (MD) simulation. Sixteen 90 ns trajectories provide adequate data to allow a detailed description of the adsorption process to be formulated. Two distinct adsorption sites have been identified. The main one is located on the N,C-terminal protein face and comprises Arg128 (the crucial one), supplemented by Arg125, Arg5, and Lys1; the minor one is used accidentally and contains only Arg68. Adsorption of this protein is driven by electrostatics, where the orientation of the protein dipole moment defines the direction of protein movement. The diffusion range on the surface depends on protein side-chain penetration through the surface water layers. This is facilitated by the long-range electric field of the charged surface, which can align polar side chains to be perpendicular to the surface. A simulation of adsorption onto a neutral ionic surface shows no such surface water layer penetration. Therefore, protein flexibility is seen to be an important factor, and to adsorb the HEWL has to adjust its structure. Nevertheless, at a flat surface only a slight loss of α-helical content is required. The adsorbed HEWL molecule is oriented between side-on and end-on ways, where the angle between the protein long axis (which mostly approximates the dipole moment) and the surface varies between 45° and 90°. Simulations with targeted mutations confirm the picture that emerges from these studies. The active site is located on the opposite face to the main adsorption site; hence, the activity of the immobilized HEWL should not be affected by the surface interactions. Our results provide a detailed insight into the adsorption mechanism and protein mobility at the surface. This knowledge will aid the proper interpretation of experimental results and the design of new experiments and functional systems.

High-quality crystals of human haematopoietic prostaglandin D synthase with novel inhibitors

Human haematopoietic prostaglandin D synthase (H-PGDS; EC 5.3.99.2) produces prostaglandin D(2), an allergic and inflammatory mediator, in mast cells and Th2 cells. H-PGDS has been crystallized with novel inhibitors with half-maximal inhibitory concentrations (IC(50)) in the low nanomolar range by the counter-diffusion method onboard the Russian Service Module on the International Space Station. The X-ray diffraction of a microgravity-grown crystal of H-PGDS complexed with an inhibitor with an IC(50) value of 50 nM extended to 1.1 A resolution at 100 K using SPring-8 synchrotron radiation, which is one of the highest resolutions obtained to date for this protein.

What governs protein adsorption and immobilization at a charged solid surface?

The adsorption of hen egg white lysozyme at a model charged surface is studied using fully atomistic molecular dynamics simulations. The simulations are performed over a 90 ns time scale which is sufficient to observe rotational and translational steps in the adsorption process. Electrostatics is found to play a key role in guiding the protein to the favorable binding orientation with the N,C-terminal face against the substrate. However, full immobilization appears to only occur through the strong interaction of Arg128 with the surface, facilitated by the protein's flexibility at the terminal face. Simulated mutation at this residue confirms its crucial role. This work demonstrates that electrostatics alone might not be sufficient to guide the development of material systems that exploit protein adsorption and immobilization.

The solubility of hen lysozyme in ethylammonium nitrate/H2O mixtures and a novel approach to protein crystallization

We report on the solubility of hen lysozyme (HEWL) in aqueous ethylammonium nitrate (EAN) as a function of water content. We find the solubility behavior to be complex, exhibiting both a maximum (400 mg/mL) at very high EAN content) and a minimum at intermediate EAN content. We exploit this solubility profile in a novel approach to generating crystals of hydrophilic proteins, based on rehydration of a high concentration protein solution. We describe the production of crystals of X-ray diffraction quality. Two related ionic liquid solvent systems, with the same solubility profiles but different effective pH characteristics, are identified for future evaluation.

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

A cyclic olefin homopolymer-based microfluidics system has been established for protein crystallization and in situ X-ray diffraction.

Microfluidics is a promising technology for the rapid iden­tification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus’ molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5 Å resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts.