X-ray crystal structures of a severely desiccated protein

Protein vibrations and their localization behaviour. A numerical scaling analysis

Using a classical force field, we investigate the localization properties of protein normal modes. For a set of eighteen proteins that cover five classes of increasing size, we compute the participation ratio as a measure of the spatial extent of protein vibrations. In this scaling analysis, we find extended low-frequency far-infrared and Terahertz modes, in contrast to localized high-frequency near-infrared vibrations. These regimes are separated by a broad crossover around a wave number of 260 cm^-1. Biophysical and biochemical implications are discussed, and the vibrational localization properties are compared to those of amorphous solids.

In situ detection of a novel lysozyme monoclinic crystal form upon controlled relative humidity variation

The effect of relative humidity (rH) on protein crystal structures, an area that has attracted high scientific interest during the past decade, is investigated in this study on hen egg-white lysozyme (HEWL) polycrystalline precipitates via in situ laboratory X-ray powder diffraction (XRPD) measurements. For this purpose, HEWL was crystallized at room temperature and pH 4.5, leading to a novel monoclinic HEWL phase which, to our knowledge, has not been reported before. Analysis of XRPD data collected upon rH variation revealed several structural modifications. These observations, on a well-studied molecule like HEWL, underline not only the high impact of humidity levels on biological crystal structures, but also the significance of in-house XRPD as an analytical tool in industrial drug development and its potential to provide information for enhancing manufacturing of pharmaceuticals.

Effects of protein-crystal hydration and temperature on side-chain conformational heterogeneity in monoclinic lysozyme crystals

The modulation of main-chain and side-chain conformational heterogeneity and solvent structure in monoclinic lysozyme crystals by dehydration (related to water activity) and temperature is examined. Decreasing the relative humidity (from 99 to 11%) and decreasing the temperature both lead to contraction of the unit cell, to an increased area of crystal contacts and to remodeling of primarily contact and solvent-exposed residues. Both lead to the depopulation of some minor side-chain conformers and to the generation of new conformations. Side-chain modifications and main-chain r.m.s.d.s associated with cooling from 298 to 100 K depend on relative humidity and are minimized at 85% relative humidity (r.h.). Dehydration from 99 to 93% r.h. and cooling from 298 to 100 K result in a comparable number of remodeled residues, with dehydration-induced remodeling somewhat more likely to arise from contact interactions. When scaled to equivalent temperatures based on unit-cell contraction, the evolution of side-chain order parameters with dehydration shows generally similar features to those observed on cooling to T = 100 K. These results illuminate the qualitative and quantitative similarities between structural perturbations induced by modest dehydration, which routinely occurs in samples prepared for 298 and 100 K data collection, and cryocooling. Differences between these perturbations in terms of energy landscapes and occupancies, and implications for variable-temperature crystallography between 180 and 298 K, are discussed. It is also noted that remodeling of a key lysozyme active-site residue by dehydration, which is associated with a radical decrease in the enzymatic activity of lysozyme powder, arises due to a steric clash with the residue of a symmetry mate.

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

X-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electrons inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(000), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(000) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75±12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.

Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.

Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein

Cytomegalovirus immediate-early 1 (IE1) protein is a key viral effector protein that reprograms host cells. Controlled dehydration experiments with IE1 crystals not only extended their diffraction limit from 2.85 to 2.3 Å resolution but also triggered a monoclinic to tetragonal space-group transition with only minor alterations in the unit-cell parameters. An analysis of the pre-dehydration and post-dehydration crystal structures shows how dehydration rearranges the packing of IE1 molecules to meet the unit-cell constraints of the higher lattice symmetry. The transition from P21 to P43 reduces the number of copies in the asymmetric unit from four to two, and molecules previously related by noncrystallographic symmetry merge into identical crystallographic copies in the tetragonal space group. At the same time, dehydration considerably alters the tertiary structure of one of the two remaining IE1 chains in the asymmetric unit. It appears that this conformational switch is required to compensate for a transition that is assumed to be unfavourable, namely from a highly preferred to a rarely observed space group. At the same time, the dehydration-triggered molecular reshaping could reveal an inherent molecular flexibility that possibly informs on the biological function of IE1, namely on its binding to target proteins from the host cell.

Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.

A novel cross-linked RNase A dimer with enhanced enzymatic properties

A new cross-linked ribonuclease A (RNase A) dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of Lys(66) and Glu(9) is described. The dimer was prepared in the absence of water by incubating a lyophilized preparation of RNase, sealed under vacuum, in an oven at 85 degrees C. It was determined that the in vacuo procedure does not induce any significant conformational changes to the overall structure of RNase A, yet the amide cross-link has an increased acid lability, indicating that it is exposed and conformationally strained. Examination of X-ray crystallographic structures indicates that Lys(66) and Glu(9) are not close enough for the in vacuo dimer to adopt any of the known domain-swapped conformations. Therefore, the in vacuo RNase A dimer appears to be a novel dimeric structure. The in vacuo RNase A dimer also exhibits a twofold increase in activity over monomeric RNase A on a per monomer basis. This doubling of enzymatic activity was shown using dsRNA and ssRNA as substrates. In addition to this enhanced ability to degrade RNA, the dimer is not inhibited by the cellular ribonuclease inhibitor protein (cRI).

Evidence for Macromolecular Protein Rings in the Absence of Bulk Water

We have examined the architecture of a protein complex in the absence of bulk water. By determining collision cross sections of assemblies of the trp RNA binding protein, TRAP, we established that the 11-membered ring topology of the complex can be maintained within a mass spectrometer. We also found that the binding of tryptophan enhances the stability of the ring structure and that addition of a specific RNA molecule increases the size of the complex and prevents structural collapse. These results provide definitive evidence that protein quaternary structure can be maintained in the absence of bulk water and highlight the potential of ion mobility separation for defining shapes of heterogeneous macromolecular assemblies.

Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration

The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.

Investigation of the stabilisation of freeze-dried lysozyme and the physical properties of the formulations

The long-term stability of a protein formulation requires that the glass transition temperature (Tg) of the formulation should be maximised and the perturbation of the protein native structure in the dried form after processing minimised. In the present study, the stabilisation of lysozyme structure conferred by excipients was monitored using second derivative Fourier transform infrared spectroscopy and the physical properties of protein formulations were investigated using differential scanning calorimetry. The results showed that the preservation of protein native structure during freeze-drying and the Tg of freeze-dried formulations were excipient- and excipient to enzyme mass ratio-dependent. The freeze-dried lysozyme appeared to be less effectively stabilised compared with the spray-dried enzyme when the excipients and the excipient to enzyme mass ratios were the same. In terms of the preservation of the secondary structure of lysozyme, glycerol and sucrose seemed to be more efficient than trehalose, although the Tg of trehalose-containing formulations were found to be higher than the Tg of the equivalent sucrose-based ones. With adding either trehalose or dextran to sucrose-containing formulations, the stabilisation of lysozyme native structure could be as effective as with sucrose alone, whilst the Tg could be enhanced. The results in this study suggested that lysozyme, processed by freeze-drying, is stabilised primarily by the water substitution mechanism.

Preparation of protein nanocrystals and their characterization by solid state NMR

Preparation of proteins in their crystalline state has been found to be important in producing stable therapeutic protein formulations, cross-linked enzyme crystals for application in industrial processes, generating novel porous media for separations, and of course in structure elucidation. Of these applications only X-ray crystallography requires large crystals, defined here as being crystals 100s of microns or greater in size. Smaller crystals have attractive attributes in many instances, and are just as useful in structure determination by solid state NMR (ssNMR) as are large crystals. In this paper we outline a simple set of procedures for preparing nanocrystalline protein samples for ssNMR or other applications and describe the characterization of their crystallinity by ssNMR and X-ray powder diffraction. The approach is demonstrated in application to five different proteins: ubiquitin, lysozyme, ribonuclease A, streptavidin, and cytochrome c. In all instances the nanocrystals produced are found to be highly crystalline as judged by natural abundance 13C ssNMR and optical and electron microscopy. We show for ubiquitin that nanocrystals prepared by rapid batch crystallization yield equivalent 13C ssNMR spectra to those of larger X-ray diffraction quality crystals. Single crystal and powder X-ray diffraction measurements are made to compare the degree of order present in polycrystalline, nanocrystalline, and lyophilized ubiquitin. Solid state 13C NMR is also used to show that ubiquitin nanocrystals are thermally robust, giving no indication of loss of local order after repeated temperature cycling between liquid nitrogen and room temperature. The methods developed are rapid and should scale well from the tenths of milligram to multi-gram scales, and as such should find wide utility in the preparation of protein nanocrystals for applications in catalysis, separations, and especially in sample preparation for structural studies using ssNMR.

Crystine: fibrous biomolecular material from protein crystals cross-linked in a specific geometry

Cysteine substitutions were engineered on the surface of maltose binding protein to produce crystine fibers, linear polymers of folded protein formed within a crystal. Disulfide bond formation between adjacent protein molecules within the lattice was monitored by X-ray crystallography. The cross-linked crystals were resistant to dissolution in water or neutral buffer solutions, even though the cross-linking was one-dimensional. However, crystine fibers were observed by transmission electron microscopy to dissociate from the crystals in acidic solutions. Some fibers remained associated as two-dimensional bundles or sheets, with a repeat unit along the fibers consistent with the packing of the individual protein molecules in the crystal. Neutralization of the acidic solutions caused the fibers to re-associate as a solid. Crystine threads were drawn out of this solution. In scanning electron microscopy images, many individual fibers could be seen unwinding from the ends of some threads. Crystine fibers are a new type of biomolecular material with potential applications wherever the use of proteins in a fibrous form is desirable, for example, the incorporation of enzymes into cloth or filtration material.

Investigation of protein/carbohydrate interactions in the dried state. 2. Diffuse reflectance FTIR studies

Upon freeze-drying in the absence of lyoprotectants, Fourier transform infrared (FTIR) spectroscopy has detected changes in the secondary structures of proteins. Such FTIR studies have been typically conducted using protein/KBr pellets, where additional protein degradation could potentially occur due to pressure effects and partial dissolution of the chaotropic KBr. Diffuse reflectance FTIR spectroscopy, in which no sample preparation is necessary, was evaluated as an alternative spectroscopic method to examine protein structure upon freeze-drying. The therapeutic proteins recombinant human deoxyribonuclease I (rh-DNase) and recombinant human insulin like growth factor I (rh-IGF-I) were freeze-dried with mannitol, sucrose, trehalose, and two molecular weight dextrans (69 and 503 kDa) separately, at concentrations ranging from 0 to 100% (w/w). Upon freeze-drying, rh-DNase and rh-IGF-I underwent significant changes in their secondary structure. For both proteins, the presence of intermolecular beta-sheets due to aggregation was detected and the alpha-helix content decreased significantly. The addition of carbohydrates to the formulations inhibited the protein secondary structure rearrangement in a concentration-dependent manner. Sucrose and trehalose appeared to be the most efficient excipients in preventing secondary structure changes. The conformational changes observed for both proteins appeared to be reversible upon rehydration.