Characterization of triterpenoidic saponin mixture in crude extracts from leaves of Acanthopanax senticosus Harms by saponin structural correlation and mass spectrometry

Eighteen triterpenoidic saponins in crude extracts from leaves of Acanthopanax senticous Harms have been investigated by electrospray ionization multi-stage tandem mass spectrometry and high-resolution mass spectrometry. In ESI-MS spectra, predominant [M + Na](+) ions in the positive ion mode have been observed for molecular mass information. Meanwhile, specific structural correlations between these ions are firstly found. The 18 peaks (ions) can be classified into three groups (group D, E, and F with mass increase) with each group including six peaks. There is a mass difference of 132 Da between group D and E for each corresponding peak in turn (for example peak 1 to peak 7), indicating one more pentose residue was attached to saponins in group E than those corresponding in group D. The mass difference of 146 Da between group E and F implies one more deoxy-hexose attached to saponins in group F than those corresponding in group E. The structural correlations of the corresponding ions are confirmed by tandem mass spectrometry and high-re solution mass spectrometry. These structural features can not only facilitate the rapid characterization of the native known saponins in crude plant extracts, thus avoiding tedious derivation and separation of saponins, but also help find novel compounds of the same type in a specific medicinal plant.

Characterization of the structural and functional changes of hemoglobin in dimethyl sulfoxide by spectroscopic techniques

Circular dichroism (CD), fourier transform infrared (FTIR), and fluorescence spectroscopy were used to explore the effect of dimethyl sulfoxide (DMSO) on the structure and function of hemoglobin (Hb). The native tertiary structure was disrupted completely when the concentration of DMSO reached 50% (v/v), which was determined by loss of the characteristic Soret CD spectrum. Loss of the native tertiary structure could be mainly caused by breaking the hydrogen bonds, between the heme propionate groups and nearby surface amino acid residues, and by disorganizing the hydrophobic interior of this protein. Upon exposure of Hb to 52% DMSO for ca. 12 h in a D2O medium no significant change in 1652 cm(-1) band of the FTIR spectrum was produced, which demonstrated that alpha-helical structure predominated. When the concentration of DMSO increased to 57%: (1) the band at 1652 cm(-1) disappeared with the appearance of two new bands located at 1661 and 1648 cm(-1); (2) another new band at 1623 cm(-1) was attributed to the formation of intermolecular beta-sheet or aggregation, which was the direct consequence of breaking of the polypeptide chain by the competition of S=O groups in DMSO with C=O groups in amide bonds. Further increasing the DMSO concentration to 80%, the intensity at 1623 cm(-1) increased, and the bands at 1684, 1661 and 1648 cm(-1) shifted to 1688, 1664 and 1644 cm(-1), respectively. These changes showed that the native secondary structure of Hb was last and led to further aggregation and increase of the content of 'free' amide C=O groups. In pure DMSO solvent, the major band at 1664 cm(-1) indicated that almost all of both the intermolecular beta-sheet and any residual secondary structure were completely disrupted. The red shift of the fluorescence emission maxima showed that the tryptophan residues were exposed to a greater hydrophilic environment as the DMSO content increased. GO-binding experiment suggested that the biological function of Hb was disrupted seriously even if the content of DMSO was 20%. (C) 1998 Elsevier Science B.V. All rights reserved.

Structural and thermodynamic characterization of pre- and postpolymerization states in the F4 fimbrial subunit FaeG.

Enterotoxigenic Escherichia coli expressing F4 fimbriae are the major cause of porcine colibacillosis and are responsible for significant death and morbidity in neonatal and postweaned piglets. Via the chaperone-usher pathway, F4 fimbriae are assembled into thin, flexible polymers mainly composed of the single-domain adhesin FaeG. The F4 fimbrial system has been labeled eccentric because the F4 pilins show some features distinct from the features of pilins of other chaperone-usher-assembled structures. In particular, FaeG is much larger than other pilins (27 versus approximately 17 kDa), grafting an additional carbohydrate binding domain on the common immunoglobulin-like core. Structural data of FaeG during different stages of the F4 fimbrial biogenesis process, combined with differential scanning calorimetry measurements, confirm the general principles of the donor strand complementation/exchange mechanisms taking place during pilus biogenesis via the chaperone-usher pathway.

Structural and Functional Characterization of a Novel Heterodimeric Kinesin in Candida albicans

Kinesins are molecular motors that transport intracellular cargos along microtubules (MTs) and influence the organization and dynamics of the MT cytoskeleton. Their force-generating functions arise from conformational changes in their motor domain as ATP is bound and hydrolyzed, and products are released. In the budding yeast Saccharomyces cerevisiae, the Kar3 kinesin forms heterodimers with one of two non-catalytic kinesin-like proteins, Cik1 and Vik1, which lack the ability to bind ATP, and yet they retain the capacity to bind MTs. Cik1 and Vik1 also influence and respond to the MT-binding and nucleotide states of Kar3, and differentially regulate the functions of Kar3 during yeast mating and mitosis. The mechanism by which Kar3/Cik1 and Kar3/Vik1 dimers operate remains unknown, but has important implications for understanding mechanical coordination between subunits of motor complexes that traverse cytoskeletal tracks. In this study, we show that the opportunistic human fungal pathogen Candida albicans (Ca) harbors a single version of this unique form of heterodimeric kinesin and we present the first in vitro characterization of this motor. Like its budding yeast counterpart, the Vik1-like subunit binds directly to MTs and strengthens the MT-binding affinity of the heterodimer. However, in contrast to ScKar3/Cik1 and ScKar3/Vik1, CaKar3/Vik1 exhibits weaker overall MT-binding affinity and lower ATPase activity. Preliminary investigations using a multiple motor motility assay indicate CaKar3/Vik1 may not be motile. Using a maltose binding protein tagging system, we determined the X-ray crystal structure of the CaKar3 motor domain and observed notable differences in its nucleotide-binding pocket relative to ScKar3 that appear to represent a previously unobserved state of the active site. Together, these studies broaden our knowledge of novel kinesin motor assemblies and shed new light on structurally dynamic regions of Kar3/Vik1-like motor complexes that help mediate mechanical coordination of its subunits.

Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli

Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.

Promoter region of the Escherichia coli O7-specific lipopolysaccharide gene cluster:structural and functional characterization of an upstream untranslated mRNA sequence

We report the identification of the promoter region of the Escherichia coli O7-specific lipopolysaccharide (LPS) gene cluster (wbEcO7). Typical -10 and -35 sequences were found to be located in the intervening region between galF and rlmB, the first gene of the wbEcO7 cluster. Data from RNase protection experiments revealed the existence of an untranslated leader mRNA segment of 173 bp, including the JUMPStart and two ops sequences. We characterized the structure of this leader mRNA by using the program Mfold and a combination of nested and internal deletions transcriptionally fused to a promoterless lac operon. Our results indicated that the leader mRNA may fold into a series of complex stem-loop structures, one of which includes the JUMPStart element. We have also found that one of the ops sequences resides on the predicted stem and the other resides on the loop region, and we confirmed that these sequences are essential for the RfaH-mediated regulation of the O polysaccharide cluster. A very similar stem-loop structure could be predicted in the promoter region of the LPS core operon encoding the waaQGPSBIJYZK genes. We observed another predicted stem-loop, located immediately downstream from the wbEcO7 transcription initiation site, which appeared to be involved in premature termination of transcription. This putative stem-loop is common to many other O polysaccharide gene clusters but is not present in core oligosaccharide genes. wbEcO7-lac transcriptional fusions in single copy numbers were also used to determine the effects of various environmental cues in the transcriptional regulation of O polysaccharide synthesis. No effects were detected with temperature, osmolarity, Mg2+ concentration, and drugs inducing changes in DNA supercoiling. We therefore conclude that the wbEcO7 promoter activity may be constitutive and that regulation takes place at the level of elongation of the mRNA in a RfaH-mediated manner.

Structural-Functional Studies of Burkholderia cenocepacia D-Glycero-beta-D-manno-heptose 7-Phosphate Kinase (HldA) and Characterization of Inhibitors with Antibiotic Adjuvant and Antivirulence Properties

As an essential constituent of the outer membrane of Gram-negative bacteria, lipopolysaccharide contributes significantly to virulence and antibiotic resistance. The lipopolysaccharide biosynthetic pathway therefore serves as a promising therapeutic target for antivirulence drugs and antibiotic adjuvants. Here we report the structural-functional studies of D-glycero-beta-D-manno-heptose 7-phosphate kinase (HldA), an absolutely conserved enzyme in this pathway, from Burkholderia cenocepacia. HldA is structurally similar to members of the PfkB carbohydrate kinase family and appears to catalyze heptose phosphorylation via an in-line mechanism mediated mainly by a conserved aspartate, Asp270. Moreover, we report the structures of HldA in complex with two potent inhibitors in which both inhibitors adopt a folded conformation and occupy the nucleotide-binding sites. Together, these results provide important insight into the mechanism of HldA-catalyzed heptose phosphorylation and necessary information for further development of HldA inhibitors.

Structural and chemical characterization of corals grown under present day and naturally elevated pCO2 conditions in Papua New Guinea - a window into the future

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Structural and functional characterization of the gene products responsible for phototrophic iron oxidation by purple bacteria

Dissertação para a obtenção de grau de doutor em Bioquímica pelo Instituto de Tecnologia Química e Biológica. Universidade Nova de Lisboa

Synthesis, Spectral Characterization, Structural Studies and Biological Investigations of Transition Metal Complexes of Some Acid Hydrazones

This study concentrates the chemical properties of hydrazones due to its chelating capability and their pharmacological applications. Studies cover the preparation of different acid hydrazones and their structural studies and studies on their antimicrobial activity, synthesis and spectral characterization of different complexes of copper oxovanadium, manganese, nickel etc. Effect of incorporation of heterocyclic bases to the coordination sphere, change in the biological activity of acid hydrazones upon coordination, development of X-ray quality single crystals and its X-ray diffraction studies, studies on the redox behavior of the coordinated metal ions and correlation between the stereochemistry and biological activities.

Structural, electrical and electrochemical characterization of high frequency magnetron sputtered spinel oxide cathode films for lithium ion battery applications

The main challenges in the deposition of cathode materials in thin film form are the reproduction of stoichiometry close to the bulk material and attaining higher rates of deposition and excellent crystallinity at comparatively lower annealing temperatures. There are several methods available to develop stoichiometric thin film cathode materials including pulsed laser deposition; plasma enhanced chemical vapor deposition, electron beam evaporation, electrostatic spray deposition and RF magnetron sputtering. Among them the most versatile method is the sputtering technique, owing to its suitability for micro-fabricating the thin film batteries directly on chips in any shape or size, and on flexible substrates, with good capacity and cycle life. The main drawback of the conventional sputtering technique using RF frequency of 13.56MHz is its lower rate of deposition, compared to other deposition techniques A typical cathode layer for a thin film battery requires a thickness around one micron. To deposit such thick layers using convention RF sputtering, longer time of deposition is required, since the deposition rate is very low, which is typically 10-20 Å/min. This makes the conventional RF sputtering technique a less viable option for mass production in an economical way. There exists a host of theoretical and experimental evidences and results that higher excitation frequency can be efficiently used to deposit good quality films at higher deposition rates with glow discharge plasma. The effect of frequencies higher than the conventional one (13.56MHz) on the RF magnetron sputtering process has not been subjected to detailed investigations. Attempts have been made in the present work, to sputter deposit spinel oxide cathode films, using high frequency RF excitation source. Most importantly, the major challenge faced by the thin film battery based on the LiMn2O4 cathode material is the poor capacity retention during charge discharge cycling. The major causes for the capacity fading reported in LiMn2O4cathode materials are due to, Jahn-Teller distortion, Mn2+ dissolution into the electrolyte and oxygen loss in cathode material during cycling. The work discussed in this thesis is an attempt on overcoming the above said challenges and developing a high capacity thin film cathode material.