Identification of Anticryptococcal Bornyl Compounds from Verbesina turbacensis and Their Structure-Activity Relationships

Cryptococcus neoformans is an opportunistic fungal pathogen that has limited treatment options. Natural product plant extracts offer a cost-effective option for the discovery of new anticryptococcal lead compounds. The acetone bark extract of Verbesina turbacensis was found to potently inhibit C. neoformans and was subjected to bioautography. Two compounds that inhibited the growth of C. neoformans were isolated and displayed minimum inhibitory concentration values of 10 and 310 µg/mL. The compounds were identified as the bornyl hydroxycinnamic esters bornyl caffeate and bornyl ferulate, respectively. To better understand initial structure-activity relationships, anticryptococcal activity was characterized for similar compounds. All compounds were further evaluated for mammalian cell toxicity using the MTT assay with MCF-7 and HEK-293 cell lines. Overall, bornyl caffeate demonstrated promising anticryptococcal potential given its potent inhibition of C. neoformans and low mammalian cell toxicity.

Natural Product Inhibition and Enzyme Kinetics Related to Phylogenetic Characterization for Bacterial Peptidyl-tRNA Hydrolase 1

With the relentless development of drug resistance and re-emergence of many pathogenic bacteria, the need for new antibiotics and new antibiotic targets is urgent and growing. Bacterial peptidyl-tRNA hydrolase, Pth1, is emerging as a promising new target for antibiotic development. From the conserved core and high degree of structural similarity, broad-spectrum inhibition is postulated. However, Pth1 small-molecule inhibition is still in the earliest stages. Focusing on pathogenic bacteria, herein we report the phylogenetic classification of Pth1 and natural product inhibition spanning phylogenetic space. While broad-spectrum inhibition is found, narrow-spectrum and even potentially clade-specific inhibition is more frequently observed. Additionally reported are enzyme kinetics and general in vitro Pth1 solubility that follow phylogenetic boundaries along with identification of key residues in the gate loop region that appear to govern both. The studies presented here demonstrate the sizeable potential for small-molecule inhibition of Pth1, improve understanding of Pth enzymes, and advance Pth1 as a much-needed novel antibiotic target.

Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins

How the distinctive lipid composition of mammalian plasma membranes impacts membrane protein structure is largely unexplored, partly because of the dearth of isotropic model membrane systems that contain abundant sphingolipids and cholesterol. This gap is addressed by showing that sphingomyelin and cholesterol-rich (SCOR) lipid mixtures with phosphatidylcholine can be cosolubilized by n-dodecyl-β-melibioside to form bicelles. Small-angle X-ray and neutron scattering, as well as cryo-electron microscopy, demonstrate that these assemblies are stable over a wide range of conditions and exhibit the bilayered-disc morphology of ideal bicelles even at low lipid-to-detergent mole ratios. SCOR bicelles are shown to be compatible with a wide array of experimental techniques, as applied to the transmembrane human amyloid precursor C99 protein in this medium. These studies reveal an equilibrium between low-order oligomer structures that differ significantly from previous experimental structures of C99, providing an example of how ordered membranes alter membrane protein structure.

Structure and physiological function of the human KCNQ1 channel voltage sensor intermediate state

Voltage-gated ion channels feature voltage sensor domains (VSDs) that exist in three distinct conformations during activation: resting, intermediate, and activated. Experimental determination of the structure of a potassium channel VSD in the intermediate state has previously proven elusive. Here, we report and validate the experimental three-dimensional structure of the human KCNQ1 voltage-gated potassium channel VSD in the intermediate state. We also used mutagenesis and electrophysiology in Xenopus laevisoocytes to functionally map the determinants of S4 helix motion during voltage-dependent transition from the intermediate to the activated state. Finally, the physiological relevance of the intermediate state KCNQ1 conductance is demonstrated using voltage-clamp fluorometry. This work illuminates the structure of the VSD intermediate state and demonstrates that intermediate state conductivity contributes to the unusual versatility of KCNQ1, which can function either as the slow delayed rectifier current (IKs) of the cardiac action potential or as a constitutively active epithelial leak current.

Volatile Compositions and Antifungal Activities of Native American Medicinal Plants: Focus on the Asteraceae

In the past, Native Americans of North America had an abundant traditional herbal legacy for treating illnesses, disorders, and wounds. Unfortunately, much of the ethnopharmacological knowledge of North American Indians has been lost due to population destruction and displacement from their native lands by European-based settlers. However, there are some sources of Native American ethnobotany remaining. In this work, we have consulted the ethnobotanical literature for members of the Asteraceae used in Cherokee and other Native American traditional medicines that are native to the southeastern United States. The aerial parts of Eupatorium serotinum, Eurybia macrophylla, Eutrochium purpureum, Polymnia canadensis, Rudbeckia laciniata, Silphium integrifolium, Smallanthus uvedalia, Solidago altissima, and Xanthium strumarium were collected from wild-growing plants in north Alabama. The plants were hydrodistilled to obtain the essential oils and the chemical compositions of the essential oils were determined by gas chromatography-mass spectrometry. The essential oils were tested for in-vitro antifungal activity against Aspergillus niger, Candida albicans, and Cryptococcus neoformans. The essential oil of E. serotinum showed noteworthy activity against C. neoformans with a minimum inhibitory concentration (MIC) value of 78 μg/mL, which can be attributed to the high concentration of cyclocolorenone in the essential oil.

Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space

Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda-Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC1/2) at high resolutions, decreased Rfree factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. These results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography.

Expedited isolation of natural product peptidyl-tRNA hydrolase inhibitors from a Pth1 affinity column

New antibiotics and new antibiotic targets are needed to counter the development of bacterial drug resistance that threatens to return the human population to the pre-antibiotic era. Bacterial peptidyl-tRNA hydrolase (Pth1) is a promising new antibiotic target in the early stages of development. While inhibitory activity has been observed in a variety of natural products, bioactive fractionation has been a bottleneck for inhibitor isolation. To expedite the isolation of inhibitory compounds from complex mixtures, we constructed a Pth1 affinity column and used it to isolate inhibitory compounds from crude natural products. Recombinantly produced S. typhimurium Pth1 was covalently attached to a column matrix and the inhibitory activity isolated from ethanol extracts of Salvinia minima. The procedure reported here demonstrates that isolation of Pth1 inhibitory compounds from complex natural product extracts can be greatly expedited over traditional bioactive fractionation, decreasing time and expense. The approach is generally applicable to Pth1s from other bacterial species and opens an avenue to advance and accelerate inhibitor development against this promising antimicrobial target.

Novel Antifungal Activity for the Lectin Scytovirin: Inhibition of Cryptococcus neoformans and Cryptococcus gattii

Pathogenic cryptococci are encapsulated yeast that can cause severe meningoencephalitis. Existing therapeutic options are dated and there is a growing need for new alternative antifungal agents for these fungi. Here we report novel inhibition of pathogenic cryptococci by the antimicrobial lectin Scytovirin. Inhibition was most potent against Cryptococcus neoformans var neoformans and C. gattii, with MFC values of 500 nM. Scytovirin binding was localized to the cell wall and shown to affect capsule size and release. No effect was observed on melanization or with cells grown in the presence the cell wall stressor Congo red. Synergy with existing antifungals was indicated, most strongly for amphotericin B. Overall, Scytovirin serves as a much needed new avenue for anticryptococcal development.

Structural and biochemical differences between the Notch and the amyloid precursor protein transmembrane domains

γ-Secretase cleavage of the Notch receptor transmembrane domain is a critical signaling event for various cellular processes. Efforts to develop inhibitors of γ-secretase cleavage of the amyloid-β precursor C99 protein as potential Alzheimer's disease therapeutics have been confounded by toxicity resulting from the inhibition of normal cleavage of Notch. We present biochemical and structural data for the combined transmembrane and juxtamembrane Notch domains (Notch-TMD) that illuminate Notch signaling and that can be compared and contrasted with the corresponding traits of C99. The Notch-TMD and C99 have very different conformations, adapt differently to changes in model membrane hydrophobic span, and exhibit different cholesterol-binding properties. These differences may be exploited in the design of agents that inhibit cleavage of C99 while allowing Notch cleavage.

Bacterial production of site specific 13C labeled phenylalanine and methodology for high level incorporation into bacterially expressed recombinant proteins

Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific ¹³C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles. Aromatic side chains have many of the same advantages as methyl containing amino acids including distinct ¹³C chemical shifts and multiple magnetically equivalent ¹H positions. Herein we report economical bacterial production and one-step purification of phenylalanine with ¹³C incorporation at the Cα, Cγ and Cε positions, resulting in two isolated ¹H-¹³C spin systems. We also present methodology to maximize incorporation of phenylalanine into recombinantly overexpressed proteins in bacteria and demonstrate compatibility with ILV-methyl labeling. Inexpensive, site specific isotope labeled phenylalanine adds another dimension to biomolecular NMR, opening new avenues of study.

Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1

Peptidyl-tRNA hydrolases (Pths) play ancillary yet essential roles in protein biosynthesis by recycling peptidyl-tRNA. In E. coli, inhibition of bacterial Pth1 leads to accumulation of peptidyl-tRNA, depletion of aminoacyl-tRNA, and cell death. Eukaryotes have multiple Pths and Pth1 knock out was shown to have no effect on viability in yeast. Thereby, bacterial Pth1 is a promising target for novel antibiotic development. With the abundance of Pth1 structural data, molecular docking was used for virtual screening of existing, commercially available antibiotics to map potential interactions with Pth enzymes. Overall, 83 compounds were docked to eight different bacterial Pth1 and three different Pth2 structures. A variety of compounds demonstrated favorable docking with Pths. Whereas, some compounds interacted favorably with all Pths (potential broad spectrum inhibition), more selective interactions were observed for Pth1 or Pth2 and even specificity for individual Pth1s. While the correlation between computational docking and experimentation still remains unknown, these findings support broad spectrum inhibition, but also point to the possibility of narrow spectrum Pth1 inhibition. Also suggested is that Pth1 can be distinguished from Pth2 by small molecule inhibitors. The findings support continued development of Pth1 as an antibiotic target.

Neutron diffraction analysis of Pseudomonas aeruginosa peptidyl-tRNA hydrolase 1

Perdeuterated peptidyl-tRNA hydrolase 1 from Pseudomonas aeruginosa was crystallized for structural analysis using neutron diffraction. Crystals of perdeuterated protein were grown to 0.15 mm(3) in size using batch crystallization in 22.5% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol with a 20-molar excess of trilysine as an additive. Neutron diffraction data were collected from a crystal at room temperature using the MaNDi single-crystal diffractometer at Oak Ridge National Laboratory.

Antifungal Activity of Plant Extracts against Aspergillus niger and Rhizopus stolonifer

Despite recent advances in antifungal development, fungi remain a devastating threat to human health and compromise viability of the food supply. Plant based antimicrobials represent a vast untapped source with tremendous potential. Herein we present the antifungal properties of more than 50 plant extracts against two important human and agricultural pathogens, Aspergillus niger and Rhizopus stolonifer. Multiple extracts exhibit promising MIC values of less than 100 μg/mL and are reported for both fungal species.

Antifungal activity of plant extracts against Aspergillus niger and Rhizopus stolonifer

Despite recent advances in antifungal development, fungi remain a devastating threat to human health and compromise viability of the food supply. Plant based antimicrobials represent a vast untapped source with tremendous potential. Herein we present the antifungal properties of more than 50 plant extracts against two important human and agricultural pathogens, Aspergillus niger and Rhizopus stolonifer. Multiple extracts exhibit promising MIC values of less than 100 μg/mL and are reported for both fungal species.

Recombinant production, crystallization and X-ray crystallographic structure determination of peptidyl-tRNA hydrolase from Salmonella typhimurium

Peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) from the pathogenic bacterium Salmonella typhimurium has been cloned, expressed in Escherichia coli and crystallized for X-ray analysis. Crystals were grown using hanging-drop vapor diffusion against a reservoir solution consisting of 0.03 M citric acid, 0.05 M bis-tris propane, 1% glycerol, 3% sucrose, 25% PEG 6000 pH 7.6. Crystals were used to obtain the three-dimensional structure of the native protein at 1.6 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P2₁2₁2₁ with unit-cell parameters a=62.1, b=64.9, c=110.5 Å, α=β=γ=90°. The asymmetric unit of the crystallographic lattice was composed of two copies of the enzyme molecule with a 51% solvent fraction, corresponding to a Matthews coefficient of 2.02 Å3 Da(-1). The structural coordinates reported serve as a foundation for computational and structure-guided efforts towards novel small-molecule Pth1 inhibitors and potential antibacterial development.

Expression, purification, and solubility optimization of peptidyl-tRNA hydrolase 1 from Bacillus cereus

Peptidyl-tRNA hydrolase 1 cleaves the ester bond of peptidyl-tRNA thereby recycling peptidyl-tRNAs generated from premature termination of translation and expression of minigenes and short ORFs. Bacterial Pth1 is essential, highly conserved, and has no essential eukaryotic homolog making it a good target for antibacterial development. Herein we describe the cloning of pth1 gene from Bacillus cereus as an N-terminal hexahistidine fusion protein. Solubility was optimized for overexpression in Escherichia coli. Purity greater than 95% was achieved in one chromatography step. Yields greater than 12mg of purified Pth1 per liter of minimal media were achieved and buffer conditions for long-term solubility were determined. Enzymatic activity of Pth1 from B. cereus was confirmed and quantification of Michaelis-Menten parameters reported.

Small molecule binding, docking, and characterization of the interaction between Pth1 and peptidyl-tRNA

Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition.

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6(1)22 with unit-cell parameters a=b=63.62, c=155.20 Å, α=β=90, γ=120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da(-1). The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.

Inhibition of Essential Bacterial Peptidyl-tRNA Hydrolase Activity by Tropical Plant Extracts

Peptidyl-tRNA Hydrolase (Pth) is a highly conserved, essential enzyme in bacteria. It removes the peptide portion from peptidyl-tRNA, returning free tRNAs to participate in translation. Build-up of peptidyl-tRNAs is toxic and defects in Pth function result in cell death. Herein we use in vitro activity of recombinant E. coli Pth to screen tropical plant extracts for inhibition. Multiple extracts were found to have inhibitory activity with some exhibiting different inhibitory effects depending on extraction conditions. IC50values ranged from 0.02 to > 53.8 μg of extract per 1 unit of Pth, holding promise for in vivo screening. The inhibitory components in these extracts may serve as lead compounds for development of novel antibacterials.

Inhibition of essential bacterial peptidyl-tRNA hydrolase activity by tropical plant extracts

Peptidyl-tRNA Hydrolase (Pth) is a highly conserved, essential enzyme in bacteria. It removes the peptide portion from peptidyl-tRNA, returning free tRNAs to participate in translation. Build-up of peptidyl-tRNAs is toxic and defects in Pth function result in cell death. Herein we use in vitro activity of recombinant E. coli Pth to screen tropical plant extracts for inhibition. Multiple extracts were found to have inhibitory activity with some exhibiting different inhibitory effects depending on extraction conditions. IC50 values ranged from 0.02 to > 53.8 microg of extract per 1 unit of Pth, holding promise for in vivo screening. The inhibitory components in these extracts may serve as lead compounds for development of novel antibacterials.

Thermal coefficients of the methyl groups within ubiquitin

Physiological processes such as protein folding and molecular recognition are intricately linked to their dynamic signature, which is reflected in their thermal coefficient. In addition, the local conformational entropy is directly related to the degrees of freedom, which each residue possesses within its conformational space. Therefore, the temperature dependence of the local conformational entropy may provide insight into understanding how local dynamics may affect the stability of proteins. Here, we analyze the temperature dependence of internal methyl group dynamics derived from the cross-correlated relaxation between dipolar couplings of two CH bonds within ubiquitin. Spanning a temperature range from 275 to 308 K, internal methyl group dynamics tend to increase with increasing temperature, which translates to a general increase in local conformational entropy. With this data measured over multiple temperatures, the thermal coefficient of the methyl group order parameter, the characteristic thermal coefficient, and the local heat capacity were obtained. By analyzing the distribution of methyl group thermal coefficients within ubiquitin, we found that the N-terminal region has relatively high thermostability. These results indicate that methyl groups contribute quite appreciably to the total heat capacity of ubiquitin through the regulation of local conformational entropy.

Peptidyl-tRNA hydrolase screening combined with molecular docking reveals the antibiotic potential of Syzygium johnsonii bark extract

With the rapid rise of antibiotic resistance in pathogenic bacteria, the need for new antibacterial agents is overwhelming. Herein we report the limited screening of tropical plant extracts for inhibitory activity against the essential enzyme peptidyl-tRNA hydrolase (Pth). Initial screening was conducted through an electrophoretic mobility assay and Northern blot detection. The ability of Pth to cleave the peptide-tRNA ester bond was assessed. The ethanol bark extract of Syzygium johnsonii showed strong inhibitory potential. Molecular docking studies point to Syzygium polyphenolics as the potential source of inhibition. This work is the forerunner of activity-directed isolation, purification, and structure elucidation of the inhibitory components from Syzygium johnsonii extracts and studies of compound interaction with Pth.

Peptidyl-tRNA Hydrolase Screening Combined with Molecular Docking Reveals the Antibiotic Potential ofSyzygium johnsoniiBark Extract

With the rapid rise of antibiotic resistance in pathogenic bacteria, the need for new antibacterial agents is overwhelming. Herein we report the limited screening of tropical plant extracts for inhibitory activity against the essential enzyme peptidyl-tRNA hydrolase (Pth). Initial screening was conducted through an electrophoretic mobility assay and Northern blot detection. The ability of Pth to cleave the peptide-tRNA ester bond was assessed. The ethanol bark extract of Syzygium johnsonii showed strong inhibitory potential. Molecular docking studies point to Syzygium polyphenolics as the potential source of inhibition. This work is the forerunner of activity-directed isolation, purification, and structure elucidation of the inhibitory components from Syzygium johnsonii extracts and studies of compound interaction with Pth.

Critical-point universality in adsorption: the effect of charcoal on a mixture of isobutyric acid and water near the consolute point

The mixture of isobutyric acid and water has a consolute point at a temperature of 25.75 °C and mole fraction 0.1148 isobutyric acid. When charcoal is added to this mixture, the concentration of isobutyric acid is reduced by adsorption. We have measured the action of charcoal on solutions of isobutyric acid and water as a function of isobutyric acid mole fraction at temperatures of 25.85 and 32.50 °C. At the higher temperature, the specific adsorption density (y(2)(α)/m) satisfies the Freundlich equation (y(2)(α)/m)=KX(2)(1/n), where y(2)(α) is the mass of isobutyric acid adsorbed, m is the mass of charcoal, X(2) is the equilibrium mole fraction of isobutyric acid, n is the Freundlich index, and K=K(T) is an amplitude that depends upon the temperature T. At 25.85 °C, a critical endpoint is located at an isobutyric acid mole fraction X(2)(ce)=0.09. When compared with the Freundlich equation at this temperature, a plot of the specific adsorption density as a function of X(2) in the vicinity of the critical-endpoint composition assumes a shape which is reminiscent of the derivative of a Dirac delta function. Using critical-point scaling theory, we show that this divergent pattern is consistent with the principle of critical point universality.

Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78

The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Through structural and functional analyses, we determine that this occurs on a region of Ube2g2 distinct from binding sites for ubiquitin-activating enzyme (E1) and RING fingers. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2:G2BR interaction also causes an approximately 50-fold increase in affinity between the E2 and RING finger. This results in markedly increased ubiquitylation by Ube2g2 and the gp78 RING finger. The significance of this G2BR effect is underscored by enhanced ubiquitylation observed when Ube2g2 is paired with other RING finger E3s. These findings uncover a mechanism whereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiquitylation.

Efficient and precise measurement of H(alpha)-C(alpha), C(alpha)-C', C(alpha)-C(beta) and H(N)-N residual dipolar couplings from 2D H(N)-N correlation spectra

A suite of experiments are presented for the measurement of H(alpha)-C(alpha), C(alpha)-C', C(alpha)-C(beta) and H(N)-N couplings from uniformly 15N, 13C labeled proteins. Couplings are obtained from a series of intensity modulated two-dimensional H(N)-N spectra equivalent to the common 1H-15N-HSQC spectra, alleviating many overlap and assignment issues associated with other techniques. To illustrate the efficiency of this method, H(alpha)-C(alpha), C(alpha)-C', and H(N)-N isotropic scalar couplings were determined for ubiquitin from data collected in less than 4.5 h, C(alpha)-C(beta) data collection required 10 h. The resulting couplings were measured with an average error of +/-0.06, +/-0.05, +/-0.04 and +/-0.10 Hz, respectively. This study also shows H(alpha)-C(alpha) and C(alpha)-C(beta) couplings, valuable because they provide orientation of bond vectors outside the peptide plane, can be measured in a uniform and precise way. Superior accuracy and precision to existing 3D measurements for C(alpha)-C' couplings and increased precision compared to IPAP measurements for H(N)-N couplings are demonstrated. Minor modifications allow for acquisition of modulated H(N)-C' 2D spectra, which can yield additional well resolved peaks and significantly increase the number of measured RDCs for proteins with crowded 1H-15N resonances.

Emerging structural explanations of ionotropic glutamate receptor function

High-resolution studies of ionotropic glutamate receptor (iGluR) extracellular domains are beginning to bridge the gap between structure and function. Crystal structures have defined the ligand binding pocket well beyond what was suggested by mutational analysis and homology models alone, providing initial suggestions about the mechanisms of channel gating and desensitization. NMR-derived backbone dynamics and molecular dynamics simulations have added further insights into the role of protein dynamics in receptor function. As a whole, the current knowledge of iGluR structure in conjunction with new advances in the understanding of K+ channels provides a vastly improved understanding of iGluR function. This review focuses on structural and dynamic studies of the extracellular ligand binding domain of iGluRs and the pore region of K+ channels that have contributed to mechanistic insights into the processes of iGluR gating and desensitization

Structural mobility of the extracellular ligand-binding core of an ionotropic glutamate receptor. Analysis of NMR relaxation dynamics

Ionotropic glutamate receptors play important roles in a variety of neuronal processes and have been implicated in multiple neurodegenerative diseases. The extracellular ligand-binding (S1S2) core of the GluR2 subtype can be expressed in bacteria as a soluble, monomeric protein with binding properties essentially identical to those of the intact receptor. The crystal structure of this protein has been determined in the presence and absence of various agonists and antagonists [Armstrong, N., Sun, Y., Chen, G. Q., and Gouaux, E. (1998) Nature 395, 913-917; Armstrong, N., and Gouaux, E. (2000) Neuron 28, 165-181]. The protein consists of two lobes, with the S1 segment composing the majority of lobe 1 and the S2 segment composing most of lobe 2. A domain closure upon ligand binding has been postulated, but details of intradomain motions have not been investigated. In this paper, the backbone motions of the ligand-binding core of GluR2 bound to glutamate were studied using (15)N longitudinal (T1) and transverse (T2) relaxation measurements as well as [1H]-15N nuclear Overhauser effects at 500 and 600 MHz. Residues in the agonist-binding pocket exhibited two main classes of motion. Those contacting the alpha-substituents of the ligand glutamate exhibited minimal internal motion, while those contacting the gamma-constituents exhibited exchange dynamics, indicating two dynamically distinct portions of the binding pocket. Also, two residues in transdomain linkers between lobes 1 and 2 show exchange, lending new insight into the previously proposed domain closure hypothesis. Finally, concerted motion of helix F suggests a pathway for ligand dissociation without the necessity of domain reopening.

Isolation and structural analysis of two-dimensional crystals of photosystem II from Hordeum vulgare viridis zb63

Photosystem II (PS II), found in the photosynthetic membranes of plants, has the unique ability to split water, evolving atmospheric oxygen as a byproduct. In the photosystem I deficient barley mutant, viridis zb63, PS II is found in 2D crystals but has normal activity [D. Simpson, (1983) Eur. J. Cell Biol. 31, 305-314]. We have isolated these PS II crystals from the mutants and obtained a projection map at 2.0 nm resolution. This map was compared to a projection map of PS II in crystals derived from spinach. The unit cell for the barley crystal was 16.1 x 24.1 nm; for spinach, the unit cell was 11.9 x 16.6 nm. In both cases, there was p2 symmetry and each half of the unit cell included five subareas. After isolation, the barley crystals were unstable, suggesting that, in this case, interactions across membranes within the grana are required to retain ordering of PS II. A comparison of the estimated masses within the PS II dimer from each species indicated that the two crystals probably did not contain the same complement of polypeptides, suggesting that PS II is labile. Nevertheless, the projection maps contained similar structural features, suggesting that PS II lability is restricted and that there is an underlying stable structure.