Deuterium exchange in lysozyme at 1.4-A resolution

Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals

The hydrogen/deuterium (H/D) exchange of main-chain amide hydrogens in the protein that denatured and refolded in deuterated solvent is considered to contain the traces of hydrogen bond cleavages or the exposure to solvent of the buried part of the protein during the denaturing and refolding (denaturing/refolding) processes. Here, we report the H/D exchange behaviors in hen egg-white lysozymes denatured under acidic conditions, basic conditions, and thermal conditions and then refolded in deuterated solvents, using crystallographic methods. The results indicate that the space containing the Trp28 side chain was hardly exposed to the solvent in acidic conditions, but exposed under basic or heated conditions. Moreover, the β-bridges between Tyr53 and Ile58 in strands β2 and β3, which are in a highly conserved region, show some tolerance to changes in pD. The results indicate that crystallographic method is one of the powerful tools to analyze the denaturing/refolding processes of proteins.

Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state

Neutron diffraction studies of hydrogen/deuterium-exchanged hen egg-white lysozyme were performed by a joint X-ray and neutron refinement to elucidate the hydrogen/deuterium exchange behavior. Large crystals for neutron work, consisting of molecules that were exchanged before crystallization, were obtained by repeatedly adding protein solution to the crystal batch using deuterated precipitant reagent. There are differences in hydrogen/deuterium exchange behavior compared with previous crystallographic or NMR studies, which could be due to intermolecular interactions in the crystal or to different lengths of exchange period.

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness

A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.

Preliminary time-of-flight neutron diffraction study of human deoxyhemoglobin

Human hemoglobin (HbA) is an intricate system that has evolved to efficiently transport oxygen molecules (O(2)) from lung to tissue. Its quaternary structure can fluctuate between two conformations, T (tense or deoxy) and R (relaxed or oxy), which have low and high affinity for O(2), respectively. The binding of O(2) to the heme sites of HbA is regulated by protons and by inorganic anions. In order to investigate the role of the protonation states of protein residues in O(2) binding, large crystals of deoxy HbA (approximately 20 mm(3)) were grown in D(2)O under anaerobic conditions for neutron diffraction studies. A time-of-flight neutron data set was collected to 1.8 A resolution on the Protein Crystallography Station (PCS) at the spallation source run by Los Alamos Neutron Science Center (LANSCE). The HbA tetramer (64.6 kDa; 574 residues excluding the four heme groups) occupies the largest asymmetric unit (space group P2(1)) from which a high-resolution neutron data set has been collected to date.

Neutron protein crystallography: beyond the folding structure of biological macromolecules

Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.

Neutron Laue macromolecular crystallography

Recent progress in neutron protein crystallography such as the use of the Laue technique and improved neutron optics and detector technologies have dramatically improved the speed and precision with which neutron protein structures can now be determined. These studies are providing unique and complementary insights on hydrogen and hydration in protein crystal structures that are not available from X-ray structures alone. Parallel improvements in modern molecular biology now allow fully (per)deuterated protein samples to be produced for neutron scattering that essentially eradicate the large-and ultimately limiting-hydrogen incoherent scattering background that has hampered such studies in the past. High quality neutron data can now be collected to near atomic resolution (approximately 2.0 A) for proteins of up to approximately 50 kDa molecular weight using crystals of volume approximately 0.1 mm3 on the Laue diffractometer at ILL. The ability to flash-cool and collect high resolution neutron data from protein crystals at cryogenic temperature (15 K) has opened the way for kinetic crystallography on freeze trapped systems. Current instrument developments now promise to reduce crystal volume requirements by a further order of magnitude, making neutron protein crystallography a more accessible and routine technique.

A model for water motion in crystals of lysozyme based on an incoherent quasielastic neutron-scattering study

This paper reports an incoherent quasielastic neutron scattering study of the single particle, diffusive motions of water molecules surrounding a globular protein, the hen egg-white lysozyme. For the first time such an analysis has been done on protein crystals. It can thus be directly related and compared with a recent structural study of the same sample. The measurement temperature ranged from 100 to 300 K, but focus was on the room temperature analysis. The very good agreement between the structural and dynamical studies suggested a model for the dynamics of water in triclinic crystals of lysozyme in the time range approximately 330 ps and at 300 K. Herein, the dynamics of all water molecules is affected by the presence of the protein, and the water molecules can be divided into two populations. The first mainly corresponds to the first hydration shell, in which water molecules reorient themselves fivefold to 10-fold slower than in bulk solvent, and diffuse by jumps from hydration site to hydration site. The long-range diffusion coefficient is five to sixfold less than for bulk solvent. The second group corresponds to water molecules further away from the surface of the protein, in a second incomplete hydration layer, confined between hydrated macromolecules. Within the time scale probed they undergo a translational diffusion with a self-diffusion coefficient reduced approximately 50-fold compared with bulk solvent. As protein crystals have a highly crowded arrangement close to the packing of macromolecules in cells, our conclusion can be discussed with respect to solvent behavior in intracellular media: as the mobility is highest next to the surface, it suggests that under some crowding conditions, a two-dimensional motion for the transport of metabolites can be dominant.

Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography

Neutron quasi-Laue diffraction data (2 A resolution) from tetragonal hen egg-white lysozyme were collected in ten days with neutron imaging plates. The data processing Laue software, LAUEGEN, developed for X-ray Laue diffractometry, was adapted for neutron diffractometry with a cylindrical detector. The data analysis software, X-PLOR, was modified and used for the refinement of hydrogen atoms, and the positions of 960 hydrogen atoms in the protein and 157 bound water molecules, were determined. Several examples are given of the methods used to identify hydrogen atoms and water molecules.

Lysozyme: a model enzyme in protein crystallography

The review concentrates on the crystal structure results from several protein crystallography laboratories on three different lysozymes, the type-c lysozymes such as hen egg-white lysozyme (HEWL), the type-g lysozyme, such as goose egg-white lysozyme (GEWL), and the lysozyme from T4 bacteriophage (T4L). The crystallographic studies on HEWL in several different crystal forms have shown that the lysozyme molecule is relatively rigid with the residues of the active site Glu35 and Asp52 adopting almost identical conformations in all structures and species variants. The NMR results also confirm the presence of a similar conformation of HEWL in solution. All three enzymes, HEWL, GEWL and T4L are composed of two domains, one that is predominantly alpha-helical and a smaller domain that is mainly beta-sheet in nature. The general acid/general base residue in each lysozyme (Glu35 in HEWL, Glu73 in GEWL and Glu11 in T4L) is contributed by the larger alpha-helical domain. The beta-sheet domains of HEWL and T4L contribute an aspartate to their respective active sites, which is likely involved in electrostatic stabilization of the oxycarbonium ion intermediate of the site D sugar on the hydrolytic pathway of oligosaccharides. There is no analogous aspartate carboxylate group in GEWL although minor conformational changes could position one or other of Asp86 or Asp97 for such a stabilization role. The binding of substrate analogues, transition state mimics and oligosaccharide products of hydrolysis to HEWL, GEWL and T4L have contributed greatly to our understanding of sugar binding to proteins. The observed subtle conformational differences of the free vs bound forms of these enzymes are best described by a narrowing of the active site clefts in the presence of the inhibitors. Details of the binding interactions of those residues lining the oligosaccharide binding clefts of the three-enzymes HEWL, GEWL and T4L with the sugar residues in sites A, B, C and D are presented and discussed. Oligosaccharides of (GlcNAc)n and alternating MurNAc-GlcNAc-MurNAc have been bound to these three enzymes and the structures determined at high resolution. These binding studies have contributed greatly to our understanding of the catalytic mechanism of the lysozyme glycosidase activity. The currently accepted view of this mechanism is presented and discussed in this review.

Carboxyl group hydrogen bonding in X-ray protein structures analysed using neutron studies on amino acids

A method is proposed to make a distinction between ionized and neutral carboxyl groups in X-ray protein structures. This is based on an analysis of the relative hydrogen bonding populations and bond-length bond-valence correlations in high-precision neutron studies of amino acids and small peptides. With the help of this method, four amino acid residues containing carboxyl groups in the refined structure of triclinic hen egg-white lysozyme have been analysed. Two of these, Glu-35 and Asp-52, are involved in lysozyme function, while the other two, Glu-7 and Asp-101, form a protein-protein inter-molecular contact in the triclinic structure.

Water structure in vitamin B12 coenzyme crystals. I. Analysis of the neutron and x-ray solvent densities

The disordered solvent distribution in crystals of vitamin B12 coenzyme was examined using the methods of high-resolution neutron and x-ray diffraction. One set of neutron (0.95 A) and two sets of x-ray (0.94 and 1.1 A) data were collected and the resulting models were extensively refined using least-squares and Fourier syntheses. The solvent regions were analyzed in two stages: first, main sites were assigned to the well defined regions of solvent density and refined using least squares; second, continuous sites were assigned representing the more disordered diffuse and elongated regions of solvent density. During the analysis an acetone molecule was also located. Water networks were formulated from the assigned sites in the above models and also from those assigned in the original structure determination (Lenhert, 1968), using criteria that included hydrogen bonding (derived from small crystal hydrates), van der Waals contact distances, side-chain disorder, water molecule orientations, and the presence or absence of foreign solvent. The well established networks extend throughout all the solvent regions of the crystal with interesting orientational arrangements of the individual waters around both polar and apolar groups of the coenzyme molecule. The networks were seen to be consistent among each of the four models in terms of occupying relatively similar positions. However, the occupancy values of the individual networks varied between the models; some networks were clearly visible in one but attenuated in another. The specific details of the water structure (bonding geometries, short-range nonbonded contacts, orientations of the waters, polar and apolar interactions, etc.) are described in the following paper.