Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.

Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.

Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant.

Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl group via an activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.

Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria.

Considerable progress has been made in recent years in our understanding of the structural basis of glycosyl transfer. Yet the nature and relevance of the conformational changes associated with substrate recognition and catalysis remain poorly understood. We have focused on the glucosyl-3-phosphoglycerate synthase (GpgS), a "retaining" enzyme, that initiates the biosynthetic pathway of methylglucose lipopolysaccharides in mycobacteria. Evidence is provided that GpgS displays an unusually broad metal ion specificity for a GT-A enzyme, with Mg(2+), Mn(2+), Ca(2+), Co(2+), and Fe(2+) assisting catalysis. In the crystal structure of the apo-form of GpgS, we have observed that a flexible loop adopts a double conformation L(A) and L(I) in the active site of both monomers of the protein dimer. Notably, the L(A) loop geometry corresponds to an active conformation and is conserved in two other relevant states of the enzyme, namely the GpgS·metal·nucleotide sugar donor and the GpgS·metal·nucleotide·acceptor-bound complexes, indicating that GpgS is intrinsically in a catalytically active conformation. The crystal structure of GpgS in the presence of Mn(2+)·UDP·phosphoglyceric acid revealed an alternate conformation for the nucleotide sugar ß-phosphate, which likely occurs upon sugar transfer. Structural, biochemical, and biophysical data point to a crucial role of the ß-phosphate in donor and acceptor substrate binding and catalysis. Altogether, our experimental data suggest a model wherein the catalytic site is essentially preformed, with a few conformational changes of lateral chain residues as the protein proceeds along the catalytic cycle. This model of action may be applicable to a broad range of GT-A glycosyltransferases.

Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes.

MeCP2 is a highly abundant chromatin architectural protein with key roles in post-natal brain development in humans. Mutations in MeCP2 are associated with Rett syndrome, the main cause of mental retardation in girls. Structural information on the intrinsically disordered MeCP2 protein is restricted to the methyl-CpG binding domain; however, at least four regions capable of DNA and chromatin binding are distributed over its entire length. Here we use small angle X-ray scattering (SAXS) and other solution-state approaches to investigate the interaction of MeCP2 and a truncated, disease-causing version of MeCP2 with nucleosomes. We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present. MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA. In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex. We present ab initio envelope reconstructions of nucleosomes and their complexes with MeCP2 from SAXS data. SAXS studies also revealed unexpected sequence-dependent conformational variability in the nucleosomes themselves.

Laplace Variational Approximation for Semiparametric Regression in the Presence of Heteroskedastic Errors.

Variational approximations provide fast, deterministic alternatives to Markov Chain Monte Carlo for Bayesian inference on the parameters of complex, hierarchical models. Variational approximations are often limited in practicality in the absence of conjugate posterior distributions. Recent work has focused on the application of variational methods to models with only partial conjugacy, such as in semiparametric regression with heteroskedastic errors. Here, both the mean and log variance functions are modeled as smooth functions of covariates. For this problem, we derive a mean field variational approximation with an embedded Laplace approximation to account for the non-conjugate structure. Empirical results with simulated and real data show that our approximate method has significant computational advantages over traditional Markov Chain Monte Carlo; in this case, a delayed rejection adaptive Metropolis algorithm. The variational approximation is much faster and eliminates the need for tuning parameter selection, achieves good fits for both the mean and log variance functions, and reasonably reflects the posterior uncertainty. We apply the methods to log-intensity data from a small angle X-ray scattering experiment, in which properly accounting for the smooth heteroskedasticity leads to significant improvements in posterior inference for key physical characteristics of an organic molecule.

Structural and biophysical studies of human PARP-1 in complex with damaged DNA.

The enzyme poly(ADP-ribose) polymerase-1 (PARP-1) is a global monitor of chromatin structure and DNA damage repair. PARP-1 binds to nucleosomes and poly(ADP-ribosylates) histones and several chromatin-associated factors to expose specific DNA sequences to the cellular machinery involved in gene transcription and/or DNA damage repair. While these processes are critical to genomic stability, the molecular mechanisms of how DNA damage induces PARP-1 activation are poorly understood. We have used biochemical and thermodynamic measurements in conjunction with small-angle X-ray scattering to determine the stoichiometry, affinity, and overall structure of a human PARP-1 construct containing the entire DNA binding region, the zinc ribbon domain, and automodification domains (residues 1-486). The interaction of this PARP-1 protein construct with three different DNA damage models (DNA constructs containing a nick, a blunt end, or a 3' extension) was evaluated. Our data indicate that PARP-1 binds each DNA damage model as a monomer and with similar affinity, in all cases resulting in robust activation of the catalytic domain. Using small-angle X-ray scattering, we determined that the N-terminal half of PARP-1 behaves as an extended and flexible arrangement of individually folded domains in the absence of DNA. Upon binding DNA, PARP-1 undergoes a conformational change in the area surrounding the zinc ribbon domain. These data support a model in which PARP-1, upon binding DNA, undergoes a conformational change to become an active nuclear enzyme.

Non-invasive measurement of X-ray beam heating on a surrogate crystal sample.

Cryocooling is a technique routinely used to mitigate the effects of secondary radiation damage on macromolecules during X-ray data collection. Energy from the X-ray beam absorbed by the sample raises the temperature of the sample. How large is the temperature increase and does this reduce the effectiveness of cryocooling? Sample heating by the X-ray beam has been measured non-invasively for the first time by means of thermal imaging. Specifically, the temperature rise of 1 mm and 2 mm glass spheres (sample surrogates) exposed to an intense synchrotron X-ray beam and cooled in a laminar flow of nitrogen gas is experimentally measured. For the typical sample sizes, photon energies, fluxes, flux densities and exposure times used for macromolecular crystallographic data collection at third-generation synchrotron radiation sources and with the sample accurately centered in the cryostream, the heating by the X-ray beam is only a few degrees. This is not sufficient to raise the sample above the amorphous-ice/crystalline-ice transition temperature and, if the cryostream cools the sample to 100 K, not even enough to significantly enhance radiation damage from secondary effects.

A quasi-Laue neutron crystallographic study of D-xylose isomerase.

The location of hydrogen atoms in enzyme structures can bring critical understanding of catalytic mechanism. However, whilst it is often difficult to determine the position of hydrogen atoms using X-ray crystallography even with subatomic (<1.0 A) resolution data available, neutron crystallography provides an experimental tool to directly localize hydrogen/deuterium atoms in biological macromolecules at resolution of 1.5-2.0 A. D-Xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) is a 43 kDa enzyme that catalyses the first reaction in the catabolism of D-xylose. Linearization and isomerization of D-xylose at the active site of D-xylose isomerase rely upon a complex hydrogen transfer. Neutron quasi-Laue data at 2.2 A resolution were collected at room temperature on a partially deuterated Streptomyces rubiginosus D-xylose isomerase crystal using the LADI instrument at ILL with the objective to provide insight into the enzymatic mechanism. The neutron structure shows unambiguously that residue His 53 is doubly protonated at the active site of the enzyme. This suggests that the reaction proceeds through an acid catalyzed opening of the sugar ring, which is in accord with the mechanism suggested by Fenn et al. (Biochemistry 43(21): 6464-6474, 2004). This is the first report of direct observation of double protonation of His 53 and the first validation of the ring opening mechanism at the active site of D-xylose isomerase.

Optimizing crystal volume for neutron diffraction: D-xylose isomerase.

Neutron diffraction is uniquely sensitive to hydrogen positions and protonation state. In that context structural information from neutron data is complementary to that provided through X-ray diffraction. However, there are practical obstacles to overcome in fully exploiting the potential of neutron diffraction, i.e. low flux and weak scattering. Several approaches are available to overcome these obstacles and we have investigated the simplest: increasing the diffracting volume of the crystals. Volume is a quantifiable metric that is well suited for experimental design and optimization techniques. By using response surface methods we have optimized the xylose isomerase crystal volume, enabling neutron diffraction while we determined the crystallization parameters with a minimum of experiments. Our results suggest a systematic means of enabling neutron diffraction studies for a larger number of samples that require information on hydrogen position and/or protonation state.

Extracting trends from two decades of microgravity macromolecular crystallization history.

Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

Seeing the heat -- preliminary studies of cryocrystallography using infrared imaging.

As preparation for an extensive study that aims to image the cryocooling process of macromolecular crystals, the ability to thermally image solid objects and liquids at temperatures far below 273 K is demonstrated. In the case of a large lysozyme crystal (1.0 x 0.7 x 0.2 mm), qualitative measurements show the cooling process to take about 0.6 s with the cooling taking place in a wave starting from the face of the crystal nearest to the origin of the cryostream and ending at the point furthest away from the origin. Annealing of this lysozyme crystal, cooled under good cryoprotectant conditions, shows that cold striations form perpendicular to the cooling stream. These striations become more pronounced after successive annealing. Cryocooling of a non-cryoprotected crystal of glucose isomerase displayed an 'S-shaped' cold front wave traveling across the sample. These preliminary results are qualitative but show the power of infrared imaging as a new tool for fundamental and practical cryocrystallography studies.