Direct assignment of the absolute configuration of molecules from crystal morphology

A method for direct assignment of the absolute configuration of molecules and the absolute structures of polar crystals, independent to that of Bijvoet, is described. The method correlates between the two-dimensional packing arrangement of specific faces, that delineate crystals during their growth and dissolution, with molecules present in the environment. The structural information stored in these faces is transferred to "tailor-made" molecules added to the solvent by controlled morphological changes induced to the growing crystals and by the creation of etch pits at specific crystal faces during their dissolution. In addition, the "tailor-made" molecules are occluded enantioselectively as guests within specific sectors of the host crystals. The method is illustrated for a variety of molecules and crystals including the assignment of the absolute configuration of several alpha-amino acids as "tailor-made" additives in centrosymmetric crystals of glycine and serine, for the absolute structure of polar crystals of sugars and alpha-amino acids and consequently the absolute configuration of molecules packed in such crystals.     

The use of X-ray crystallography to determine absolute configuration

Essential background on the determination of absolute configuration by way of single-crystal X-ray diffraction (XRD) is presented. The use and limitations of an internal chiral reference are described. The physical model underlying the Flack parameter is explained. Absolute structure and absolute configuration are defined and their similarities and differences are highlighted. The necessary conditions on the Flack parameter for satisfactory absolute-structure determination are detailed. The symmetry and purity conditions for absolute-configuration determination are discussed. The physical basis of resonant scattering is briefly presented and the insights obtained from a complete derivation of a Bijvoet intensity ratio by way of the mean-square Friedel difference are exposed. The requirements on least-squares refinement are emphasized. The topics of right-handed axes, XRD intensity measurement, software, crystal-structure evaluation, errors in crystal structures, and compatibility of data in their relation to absolute-configuration determination are described. Characterization of the compounds and crystals by the physicochemical measurement of optical rotation, CD spectra, and enantioselective chromatography are presented. Some simple and some complex examples of absolute-configuration determination using combined XRD and CD measurements, using XRD and enantioselective chromatography, and in multiply-twinned crystals clarify the technique. The review concludes with comments on absolute-configuration determination from light-atom structures.     

The enduring legacy of Koji Nakanishi's research on natural products and bioorganic chemistry. Part 2. Inception and establishment of the ECD exciton chirality method in 1960s to 1970s: A marvel of Nakanishi's Japanese team

The electronic circular dichroism (ECD) exciton chirality method is very useful for determining the absolute configuration (AC) of chiral compounds. In the ECD spectroscopy, the chromophore-chromophore interaction, ie, exciton coupling, is very important. For example, Harada and Nakanishi first discovered in 1969 that chiral dibenzoates exhibit exciton split bisignate Cotton effects, from the sign of which the screw sense between two long axes of benzoate chromophores, ie, the AC of dibenzoate, can be determined. This method was named the dibenzoate chirality rule and has been successfully applied to various natural products to determine their ACs. During these studies, it was also found that this CD method was expanded to encompass other aromatic and olefin chromophores like naphthalene, diene, enone, etc. Therefore, the name of the dibenzaote chirality rule was changed to the CD exciton chirality method. In 1970s, there were heated controversies about the inconsistency between X-ray Bijvoet and CD exciton chirality methods, which was a shocking and serious problem in the community of molecular chirality research. Harada and coworkers synthesized the most ideal cage compound with two anthracene chromophores to connect X-ray Bijvoet and CD exciton chitality methods and proved that these two methods are consistent with each other.     

The iron content of iron superoxide dismutase: determination by anomalous scattering

The number of iron atoms in the dimeric iron-containing superoxide dismutase from Pseudomonas ovalis and their atomic positions have been determined directly from anomalous scattering measurements on crystals of the native enzyme. To resolve the long-standing question of the total amount of iron per molecule for this class of dismutase, the occupancy of each site was refined against the measured Bijvoet differences. The enzyme is a symmetrical dimer with one iron site in each subunit. The iron position is 9 A from the intersubunit interface. The total iron content of the dimer is 1.2 +/- 0.2 moles per mole of protein. This is divided between the subunits in the ratio 0.65:0.55; the difference between them is probably not significant. Since each subunit contains, on average, slightly more than half an iron atom we conclude that the normal state of this enzyme is two iron atoms per dimer but that some of the metal is lost during purification of the protein. Although the crystals are obviously a mixture of holo- and apo-enzymes, the 2.9 A electron density map is uniformly clean, even at the iron site. We conclude that the three-dimensional structures of the iron-bound enzyme and the apo-enzyme are identical.     

Structure and absolute configuration of pyrophen, a novel pryrone derivative of L-phenylalanine from Aspergillus niger

Pyrophen, a novel 4-methoxy-2-pyrone derivative of L-phenylalanine isolated from cultures of Aspergillus niger, crystallizes in the orthorhombic space group P2(1)2(1)2(1), with a = 8.918(1), b = 9.199(3), and c = 18.092(4) A. The structure was solved by direct methods and the absolute configuration assigned by the Bijvoet method. Refinement gave R = 0.045 and S = 1.78 for 1677 reflections with I greater than 3 sigma (I). Though numerous other pyrone natural products are known, including other products of A. niger, this is the first report of an amino acid-pyrone derivative.     

Determination of absolute configurations by X-ray crystallography and 1H NMR anisotropy

To determine the absolute configurations of chiral compounds, many spectroscopic and diffraction methods have been developed. Among them, X-ray crystallographic Bijvoet method, CD exciton chirality method, and the combination of vibrational circular dichroism and quantum mechanical calculations are of nonempirical nature. On the other hand, X-ray crystallography using a chiral internal reference, and 1H NMR spectroscopy using chiral anisotropy reagents are relative and/or empirical methods. In addition to absolute configurational determinations, preparations of enantiopure compounds are strongly desired. As chiral reagents useful for both the preparation of enantiopure compounds by HPLC separation and the simultaneous determination of their absolute configurations, we have developed camphorsultam dichlorophthalic acid (CSDP acid) for X-ray crystallography and 2-methoxy-2-(1-naphthyl)propionic acid (MalphaNP acid) for 1H NMR spectroscopy. In this review, the principles and applications of these X-ray and NMR methods are explained using mostly our own data.     

Isolation of Festuclavine and Three New Indole Alkaloids,Roquefortine A,B and C from the Cultures of Penicillium roqueforti

The structure and absolute configuration of a metabolite isolated from Aspergillus silvaticus was studied by an X-ray diffraction method. Crystals were orthorhombic, with space group P2₁2₁2₁, and a=9.894 (5), b = 6.803 (4), c=22.519 (6) Å, and Z=4. The structure was solved by a direct method and refined by a block-diagonal least-square method to R=0.07 for 1143 non-zero reflections. The metabolite was identified as naphthalic anhydride obtained from atrovenetin. The absolute configuration determined by the Bijvoet method is consistent with that shown chemically. The molecule has two intramolecular hydrogen bonds.     

Chiral Molecular Science: How were the absolute configurations of chiral molecules determined? “Experimental results and theories”

Molecular chirality is a key concept in chemistry, bioscience, and molecular technology, like the invention of a light‐powered chiral molecular motor explained in this review. Thus, the primary research subject is how to determine the absolute configuration (AC) of chiral compounds. This review article focuses on the principle, theory, and practice of the nonempirical methods for determining ACs of chiral compounds, i.e., the Bijvoet method in X‐ray crystallography and the circular dichroism (CD) exciton chirality method, together with the historical aspects of AC determination. The theoretical equations of X‐ray crystallography and exciton CD spectroscopy are explained in detail, and these equations are useful for readers to understand the principle and mechanism of these methods. This review also focuses on the relative methods, where the internal reference with known AC is used and the relative configuration is determined by X‐ray crystallography and/or ¹H nuclear magnetic resonance (NMR) diamagnetic anisotropy method. In these cases, CSDP acid and MαNP acid are useful for the chiral resolution of racemic alcohols, where their diastereomeric esters are easily separable by high‐performance liquid chromatography (HPLC) on silica gel. Thus, these methods are useful for the preparation of enantiopure compounds and simultaneous determination of their ACs. In this review article, the above methods are explained mainly based on the author's own research results.     

CYTOLOGICAL STUDIES OF OEDOGONIUM. I. OOSPORE GERMINATION IN O. FOVEOLATUM

Details of oospore germination, including meiosis, are described and illustrated as they appear in the homothallic Oedogonium foveolatum. Unequivocal meiotic division is demonstrated to occur within 12 hr prior to the liberation of the motile tetrad cells. The development and liberation of the meiotic products are described as are instances of anomalous oospore germination. In some cases, meiosis apparently fails to occur, and a single, diploid germling invariably results. Various factors influencing oospore germination are discussed, including an apparent absolute light requirement.     

Light microscopic morphometric analysis of peroxisomes by automatic image analysis: advantages of immunostaining over the alkaline DAB method.

The feasibility of light microscopic post-embedding immunocytochemistry for morphometry of peroxisomes using automatic image analysis was investigated and compared with the classical alkaline DAB method. Perfusion-fixed rat liver tissue was either embedded in LR White or incubated in the alkaline diaminobenzidine (DAB) medium for cytochemical visualization of catalase. Sections from the LR White-embedded material were incubated with a monospecific antibody against catalase, followed by protein A-gold and silver intensification. Determination of peroxisomal volume density in sections of different thickness revealed that the values increased with section thickness in DAB-stained sections but were unaffected in immunostained preparations. Moreover, the absolute value for volume density of peroxisomes, as determined by light microscopy in immunostained sections, was quite close to the value obtained by analysis of electron microscopic preparations. Finally, morphometric analysis of bezafibrate-induced peroxisome proliferation revealed that the ratio of proliferation obtained by light microscopy in immunostained sections was very close to the results obtained by electron microscopic morphometry. The main advantage of post-embedding immunostaining for light microscopic morphometry is that it restricts the immunocytochemical reaction product to the surface of the section, thus making it independent of section thickness.     

Preliminary x-ray analysis of Escherichia coli GMP synthetase: Determination of anomalous scattering factors for a cysteinyl mercury derivative

We have initiated a project to determine the three-dimensional structure of GMP synthetase (GMPS) from Escherichia coli. GMPS catalyzes the conversion of XMP to GMP in the final step of de novo guanine nucleotide biosynthesis, and is a member of the glutamine amidotransferase family: a group of enzymes responsible for the assimilation of nitrogen into compounds such as amino acids, purine and pyrimidine bases, amino sugars, and antibiotics. The E. coli guaA gene encoding GMPS was cloned into a tac expression vector, overexpressed, and its gene product purified. Conditions for the growth of protein crystals were developed using recombinant GMPS in the presence of MgCl₂, ATP, and XMP. The crystals are monoclinic, space group P2₁, with cell parameters of a = 156.0 Å, b = 102.0 Å, c = 78.8 Å, β= 96.7°. Diffraction data to 2.8 Å spacings were collected on a Xuong-Hamlin area detector with an overall R_sym of 5.2%. Both the volume of the unit cell and the peaks in the self-rotation function are consistent with one GMPS tetramer of D₂ symmetry in the crystallographic asymmetric unit. Previously, GMPS has been observed only as a dimer in solution. GMPS was covalently modified with p-chloromercuribenzylsulfonic acid (PCMBS), and its X-ray fluorescence spectrum was measured through the L_III absorption edge of mercury Anomalous scattering factors for cysteinyl mercury were derived from this spectrum, and the feasibility of structure determination by multi-wavelength anomalous diffraction was evaluated. The optimal MAD dispersive signal is 4.5% of |F|, and the optimal MAD Bijvoet signal is 7.5% of |F| at a concentration of approximately 1 mercury per 10-kDa protein. The anomalous scattering factors tabulated here should be transferable to cysteinyl mercury in other proteins. © 1994 John Wiley & Sons, Inc.     

Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination.

We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 A resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 A resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.     

The light: nutrient ratio in lakes: the balance of energy and materials affects ecosystem structure and process

The amounts of solar energy and materials are two of the chief factors determining ecosystem structure and process. Here, we examine the relative balance of light and phosphorus in a set of freshwater pelagic ecosystems. We calculated a ratio of light: phosphorus by putting mixed-layer mean light in the numerator and total P concentration in the denominator. This light: phosphorus ratio was a good predictor of the C:P ratio of particulate matter (seston), with a positive correlation demonstrated between these two ratios. We argue that the balance between light and nutrients controls "nutrient use efficiency" at the base of the food web in lakes. Thus, when light energy is high relative to nutrient availability, the base of the food web is carbon rich and phosphorus poor. In the opposite case, where light is relatively less available compared to nutrients, the base of the food web is relatively P rich. The significance of this relationship lies in the fact that the composition of sestonic material is known to influence a large number of ecosystem processes such as secondary production, nutrient cycling, and (we hypothesize) the relative strength of microbial versus grazing processes. Using the central result of increased C:P ratio with an increased light: phosphorus ratio, we make specific predictions of how ecosystem structure and process should vary with light and nutrient balance. Among these predictions, we suggest that lake ecosystems with low light: phosphorus ratios should have several trophic levels simultaneously carbon or energy limited, while ecosystems with high light: phosphorus ratios should have several trophic levels simultaneously limited by phosphorus. Our results provide an alternative perspective to the question of what determines nutrient use efficiency in ecosystems.     

The tertiary structure of azurin from Pseudomonas denitrificans as determined by Cu resonant diffraction using synchrotron radiation

The structure of Pseudomonas denitrificans azurin has been solved at 3.0 A resolution by film data collection methods using synchrotron radiation. Bijvoet pairs of reflections were collected using 8.98 keV radiation where both delta f' and delta f", the real and imaginary corrections to azurin's Cu prosthetic group scattering, respectively, are large, and using 8.00 keV radiation where these corrections are smaller. The Cu atom was located by difference Patterson syntheses and used to phase the observed protein structure-factor moduli of selected reflections. An atomic model of the protein was built using a restricted data set and phases for all observed reflections to 3.0 A resolution were subsequently calculated from the initial model. The atomic model was subsequently rebuilt using all observed data. The results of this work are presented here and illustrate the utility of synchrotron radiation phasing techniques in solving the structures of metalloproteins without recourse to multiple isomorphous replacement.     

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

This protocol provides a method for quantitating the intracellular concentrations of endogenous metabolites in cultured cells. The cells are grown in stable isotope-labeled media to near-complete isotopic enrichment and then extracted in organic solvent containing unlabeled internal standards in known concentrations. The ratio of endogenous metabolite to internal standard in the extract is determined using mass spectrometry (MS). The product of this ratio and the unlabeled standard amount equals the amount of endogenous metabolite present in the cells. The cellular concentration of the metabolite can then be calculated on the basis of intracellular volume of the extracted cells. The protocol is exemplified using Escherichia coli and primary human fibroblasts fed uniformly with (13)C-labeled carbon sources, with detection of (13)C-assimilation by liquid chromatography-tandem MS. It enables absolute quantitation of several dozen metabolites over approximately 1 week of work.     

Isotopic difference spectra as an aide in determining absolute configuration using vibrational optical activity: vibrational circular dichroism of 13C- and 2H-labelled nonamethoxy cyclotriveratrylene

The use of isotopic difference spectra in vibrational optical activity is demonstrated as a supplemental aide in determining the absolute configuration of chiral molecules. It is shown that IR and VCD difference spectra associated with isotopic substitution observed in experimental spectra can be accurately reproduced by density functional theory calculations when the IR and VCD spectra of the original isotopomer are calculated to reasonable accuracy. Results for isotopically substituted nonamethoxy cyclotriveratrylene are presented to illustrate the degree of agreement between measured and calculated IR and VCD difference spectra for several isotopomers of this molecule. These findings highlight the utility of isotoptic substitution as an aide to verifying the determination of absolute configuration using vibrational optical activity.     

Human ferrochelatase: crystallization, characterization of the [2Fe-2S] cluster and determination that the enzyme is a homodimer

Ferrochelatase (protoheme ferrolyase, EC 4.99.1.1) catalyzes the terminal step in the heme biosynthetic pathway, the insertion of ferrous iron into protoporphyrin IX to form protoheme IX. Previously we have demonstrated that the mammalian enzyme is associated with the inner surface of the inner mitochondrial membrane and contains a nitric oxide sensitive [2Fe-2S] cluster that is coordinated by four Cys residues whose spacing in the primary sequence is unique to animal ferrochelatase. We report here the characterization and crystallization of recombinant human ferrochelatase with an intact [2Fe-2S] cluster. Gel filtration chromatography and dynamic light scattering measurements revealed that the purified recombinant human ferrochelatase in detergent solution is a homodimer. EPR redox titrations of the enzyme yield a midpoint potential of -453+/-10 mV for the [2Fe-2S] cluster. The form of the protein that was crystallized has a single Arg to Leu substitution. This mutation has no detectable effect on enzyme activity but is critical for crystallization. The crystals belong to the space group P2(1)2(1)2(1) and have unit cell constants of a=93.5 A, b=87.7 A, and c=110.2 A. There are two molecules in the asymmetric unit and the crystals diffract to better than 2.0 A resolution. The Fe to Fe distance of the [2Fe-2S] cluster is calculated to be 2.7 A based upon the Bijvoet difference Patterson map.     

The nutrient-load hypothesis: patterns of resource limitation and community structure driven by competition for nutrients and light

Resource competition theory predicts that the outcome of competition for two nutrients depends on the ratio at which these nutrients are supplied. Yet there is considerable debate whether nutrient ratios or absolute nutrient loads determine the species composition of phytoplankton and plant communities. Here we extend the classical resource competition model for two nutrients by including light as additional resource. Our results suggest the nutrient-load hypothesis, which predicts that nutrient ratios determine the species composition in oligotrophic environments, whereas nutrient loads are decisive in eutrophic environments. The underlying mechanism is that nutrient enrichment shifts the species interactions from competition for nutrients to competition for light, which favors the dominance of superior light competitors overshadowing all other species. Intermediate nutrient loads can generate high biodiversity through a fine-grained patchwork of two-species and three-species coexistence equilibria. Depending on the species traits, however, competition for nutrients and light may also produce multiple alternative stable states, suppressing the predictability of the species composition. The nutrient-load hypothesis offers a solution for several discrepancies between classical resource competition theory and field observations, explains why eutrophication often leads to diversity loss, and provides a simple conceptual framework for patterns of biodiversity and community structure observed in nature.     

Photosynthetic Activity of Chloroplasts Isolated From Bermudagrass (Cynodon dactylon L.), a Species With a High Photosynthetic Capacity

Chloroplasts have been isolated from bermudagrass (Cynodon dactylon L.) leaves and assayed for photophosphorylation and electron transport activity. These chloroplasts actively synthesize adenosine triphosphate during cyclic electron flow with phenazine methosulfate and noncyclic electron flow concurrent with the reduction of such Hill oxidants as nicotinamide adenosine dinucleotide phosphate, cytochrome c, and ferricyanide. Apparent Km values for the cofactors of photophosphorylation have been determined to be 5 × 10⁻⁵ M for phosphate and 2.5 × 10⁻⁵ M for adenosine diphosphate. The influence of light intensity on photophosphorylation has been studied and the molar ratio of cyclic to noncyclic phosphorylation calculated. It is concluded that the high photosynthetic capacity of bermudagrass leaves probably could be supported by the photophosphorylation capacities indicated in these chloroplast studies and the anomalous lack of data in chlorolast studies on the production of sufficient reductant for CO₂ assimilation at high light intensities has been noted.     

The Levels of Organization of the Photosynthetic Apparatus and the Control of Production Processes in Phytocenoses under Artificial-Light Culture

The processes limiting the production in higher plant phytocenoses under an artificial-light culture are analyzed in relation to the multilevel organization of the photosynthetic apparatus (PA). The authors consider the feasibility of overcoming these limitations by optimizing the physical parameters of irradiation (the structure of the light spectrum, the rate, and the ratio of radiation fluxes in photosynthetically active radiation (PAR) and infrared (IR) regions) at the molecular, leaf, plant, and cenotic levels of PA organization. To illustrate this approach, the authors used a complex experiment in an artificial ecosystem to evaluate the efficiency of the light control of production processes in multispecies phytocenoses by alleviating or removing the factors that limit plant production at the various levels of PA organization. An artificial-light culture is seen as an instrument for solving several problems of theoretical and applied plant physiology and related disciplines in the future.