Biomedical subjects

Da-Cheng Wang

Publications and source records attributed to Da-Cheng Wang.

32 records · Page 2Linked to original sources

PubMed2004

Structural mechanism governing cis and trans isomeric states and an intramolecular switch for cis/trans isomerization of a non-proline peptide bond observed in crystal structures of scorpion toxins.

Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. While some external factors, such as metal binding or co-factor interaction, have been identified that appear to induce cis/trans isomerization of non-proline peptide bonds, the intrinsic structural basis for their existence and the mechanism governing cis/trans isomerization in proteins remains poorly understood. Here, we report the crystal structure of a newly isolated neurotoxin, the scorpion alpha-like toxin Buthus martensii Karsch (BmK) M7, at 1.4A resolution. BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. We also determined the crystal structures of several mutants of BmK M1, a representative scorpion alpha-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. Substitution of an aspartic acid residue for lysine at residue 8 in the BmK M1 (K8D) mutant converted the cis form of the non-proline peptide bond 9-10 into the trans form, revealing an intramolecular switch for cis-to-trans isomerization. Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. The structural interconversion of the isomeric states of the BmK M1 non-proline cis peptide bond may relate to the conversion of the scorpion alpha-toxins subgroups.

Amino Acid Sequence↗

PubMed2004

Solution structure of Eucommia antifungal peptide: a novel structural model distinct with a five-disulfide motif.

The three-dimensional structure in aqueous solution of Eucommia antifungal peptide 2 (EAFP2) from Eucommia ulmoides Oliv was determined using (1)H NMR spectroscopy. EAFP2 is a newly discovered 41-residue peptide distinct with a five-disulfide cross-linked motif. This peptide exhibits chitin-binding activity and inhibitory effects on the growth of cell wall chitin-containing fungi and chitin-free fungi. The structure was calculated by using torsion angle dynamic simulated annealing with a total of 614 distance restraints and 16 dihedral restraints derived from NOESY and DQF-COSY spectra, respectively. The five disulfide bonds were assigned from preliminary structures using a statistical analysis of intercystinyl distances. The solution structure of EAFP2 is presented as an ensemble of 20 conformers with a backbone RMS deviation of 0.65 (+/-0.13) A for the well-defined Cys3-Cys39 segment. The tertiary structure of EAFP2 represents the first five-disulfide cross-linked structural model of the plant antifungal peptide. EAFP2 adopts a compact global fold composed of a 3(10) helix (Cys3-Arg6), an alpha-helix (Gly26-Cys30), and a three-strand antiparallel beta-sheet (Cys16-Ser18, Tyr22-Gly24, and Arg36-Cys37). The tertiary structure of EAFP2 shows a chitin-binding domain (residues 11-30) with a hydrophobic face and a characteristic sector formed by the N-terminal 10 residues and the C-terminal segment cross-linked through the unique disulfide bond Cys7-Cys37, which brings all four positively charged residues (Arg6, Arg9, Arg36, and Arg40) onto a cationic face. On the basis of such a structural feature, the possible structural basis for the functional properties of EAFP2 is discussed.

Amino Acid Sequence↗

PubMed2004

Mass spectrometric strategy for primary structure determination of N-terminally blocked peptides.

The mass spectrometric strategy including three steps is presented for primary structure determination of the N-terminally blocked peptides. First, the C-terminal sequencing is performed by using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry coupled with carboxypeptidase Y digestion. Then, the peptide is cleaved according to the obtained C-terminal sequence information and the resulting peptides are identified by mass spectrometry and Edman degradation after fractionation by reverse-phase chromatography. Finally, the N-terminal fragment is sequenced by tandem mass spectrometry. The strategy was successfully applied to the sequence determination of two novel N-terminally blocked peptides named EAFP1 and EAFP2.

Amino Acid Sequence↗

PubMed2004

Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution.

EAFP2 is a novel antifungal protein isolated from the bark of the tree Eucommia ulmoides Oliver. It consists of 41 residues and is characterized with a five-disulfide motif and the inhibitory effects on the growth of both cell wall chitin-containing and chitin-free fungi. The crystal structure of EAFP2 at an atomic resolution of 0.84 A has been determined by using Shake-and-Bake direct methods with the program SnB. The phases obtained were of sufficient quality to permit the initial model built automatically and the structural refinement carried out using anisotropic displacement parameters resulted in a final crystallographic R factor of 6.8%. In the resulting structural model, all non-hydrogen protein atoms including an unusual pyroglutamyl acid residue at the N-terminal can fit to the articulated electron densities with one centre and more than 65% of the hydrogen atoms in the protein can be observed as individual peaks in the difference map. The general fold of EAFP2 is composed of a 3(10) helix (Cys3-Arg6), an alpha-helix (Ala27-Cys31) and a three-stranded antiparallel beta-sheet (Cys16-Ser18, Cys23-Ser25, and Cys35-Cys37) and cross-linked by five disulfide bridges. The tertiary structure of EAFP2 can be divided into two structural sectors, A and B. Sector A composed of residues 11-30 adopts a conformation similar to the chitin-binding domain in the hevein-like proteins and features a hydrophobic surface embraced a chitin-binding site (Tyr20, 22, 29, and Ser18). The distinct disulfide bridge Cys7-Cys37 connects the N-terminal ten residues with the C-terminal segment 35-41 to form the sector B, which features a cationic surface distributing all four positively charged residues, Arg6, 9, 36, and 40. Based on these structural features, the possible structural basis of the functional properties of EAFP2 is discussed.

Amino Acid Sequence↗

PubMed2003

Exploration of the functional site of a scorpion alpha-like toxin by site-directed mutagenesis.

Scorpion alpha-neurotoxins can be classified into distinct subgroups according to their sequence and pharmacological properties. Using toxicity tests, binding studies, and electrophysiological recordings, BmK M1, a toxin from the Asian scorpion Buthus martensi Karsch, was experimentally identified as an alpha-like toxin. Being the first alpha-like toxin available in a recombinant form, BmK M1 was then modified by site-directed mutagenesis for investigation of the molecular basis of its activity. The results suggested a functional site which protrudes from the molecular scaffold as a unique tertiary arrangement, constituted by the five-residue reverse turn 8-12 and the C-terminal segment. The C-terminal basic residues Lys62 and His64 together with Lys8 in the turn, which are critical for the bioactivities, may directly interact with the receptor site on the sodium channel. Residues Asn11 and Arg58, indispensable for the activities, are mainly responsible for stabilizing the distinct conformation of the putative bioactive site. Among others, His10 and His64 seem to be involved in the preference of BmK M1 for phylogenetically distinct target sites. The comparison of BmK M1 with Aah2 (classical alpha-toxin) and Lqh(alpha)IT (alpha-insect toxin) showed that the specific orientation of the C-terminus mediated by the reverse turn might be relevant to the preference of alpha-toxin subgroups for phylogenetically distinct yet closely related receptor sites. The Y5G mutation indicated the "conserved hydrophobic surface" might be structurally important for stabilizing the beta-sheet in the alpha/beta-scaffold. The observations in this work shed light on the nature and roles of the residues possibly involved in the biological activity of a scorpion alpha-like toxin.

Action Potentials↗

PubMed2003

Importance of the conserved aromatic residues in the scorpion alpha-like toxin BmK M1: the hydrophobic surface region revisited.

About one-third of the amino acid residues conserved in all scorpion long chain Na+ channel toxins are aromatic residues, some of which constitute the so-called "conserved hydrophobic surface." At present, in-depth structure-function studies of these aromatic residues using site-directed mutagenesis are still rare. In this study, an effective yeast expression system was used to study the role of seven conserved aromatic residues (Tyr5, Tyr14, Tyr21, Tyr35, Trp38, Tyr42, and Trp47) from the scorpion toxin BmK M1. Using site-directed mutagenesis, all of these aromatic residues were individually substituted with Gly in association with a more conservative substitution of Phe for Tyr5, Tyr14, Tyr35, or Trp47. The mutants, which were expressed in Saccharomyces cerevisiae S-78 cells, were then subjected to a bioassay in mice, electrophysiological characterization on cloned Na+ channels (Nav1.5), and CD analysis. Our results show an eye-catching correlation between the LD50 values in mice and the EC50 values on Nav1.5 channels in oocytes, indicating large mutant-dependent differences that emphasize important specific roles for the conserved aromatic residues in BmK M1. The aromatic side chains of the Tyr5, Tyr35, and Trp47 cluster protruding from the three-stranded beta-sheet seem to be essential for the structure and function of the toxin. Trp38 and Tyr42 (located in the beta2-sheet and in the loop between the beta2- and beta3-sheets, respectively) are most likely involved in the pharmacological function of the toxin.

Amino Acid Sequence↗

PubMed2003

Primary structural determination of N-terminally blocked peptides from the bark of Eucommia ulmoides Oliv by mass spectrometric analysis.

Sequencing of N-terminally blocked proteins/peptides is a challenge since these molecules inhibit processing by Edman degradation. By using high accuracy Fourier transform ion cyclotron resonance (FTICR) tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), the primary structures of two novel N-terminally blocked antifungal peptides (EAFP1 and EAFP2), purified from the bark of Eucommia ulmoides Oliv, have been determined. The results show that the high mass accuracy provided by FTICR mass spectrometry is effective to determine the N-terminally blocking group, and can simplify the task of spectral interpretation and improve the precision of sequence determination. The combination of MALDI-TOFMS with carboxyl peptidase Y digestion was used to determine the C-terminal 36- and 27-residue sequences of EAFP1 and EAFP2, respectively, to provide the sequence linkage information for tryptic fragments. Compared with traditional peptide chemistry the advantage of mass spectrometric techniques is their simplicity, speed and sensitivity.

Alkylation↗

PubMed2003

Crystal structure of pokeweed antiviral protein with well-defined sugars from seeds at 1.8A resolution.

The crystal structure of pokeweed antiviral protein from seeds of Phytolacca americana (PAP-S) was solved at 1.8A. PAP-S is a one-chain ribosome-inactivating protein (RIP) and distinctively contains three well-defined N-acetylglucosamines, each covalently linked to an asparagine residue at positions, 10, 44, and 255, respectively. The high-resolution structure clearly shows the three mono-sugars to have either an alpha- or a beta-conformation. Two of sugars are located on the same side of the molecule with the active pocket. Except one hydrogen bond, there are no intermolecular interactions between the polypeptide chain and the sugars. Instead the sugar conformations appear to be stabilized by intermolecular interactions. The sugar structure defined at high resolution provides a structural basis for understanding their possible biological activity. The structural comparisons of PAP-S with other PAPs reveal that the major disparity of these homologous molecules is the different charge distribution on the upper right side of the front side near the active pocket. Based on the available structure of the 50S ribosomal subunit, the possible interactions between PAPs and the ribosome are discussed.

Acetylglucosamine↗

PubMed2002

Purification, crystallization and preliminary X-ray diffraction analysis of a novel mannose-binding lectin from Gastrodia elata with antifungal properties.

A plant antifungal protein, Gastrodia antifungal protein (GAFP-1) has been isolated from terminal corms of the orchid Gastrodia elata B1 f. elata, purified to homogeneity and crystallized by means of the hanging-drop vapour-diffusion method. The best quality crystals grew over several months at 277 K. The crystal used for data collection belongs to the space group P2(1)2(1)2, with unit-cell parameters a = 61.087, b = 91.488, c = 81.132 A. Using a synchrotron-radiation source, the resolution limit of the data reached 2.0 A, with an overall R(merge) of 0.097 and a completeness of 99.8%. Four independent molecules were estimated to be present in the asymmetric unit, with a solvent content of 46.3%. This data will help to solve the first structure of a monomeric monocot mannose-binding lectin.

Amino Acid Sequence↗

PubMed2002

Two novel antifungal peptides distinct with a five-disulfide motif from the bark of Eucommia ulmoides Oliv.

Two antifungal peptides, named EAFP1 and EAFP2, have been purified from the bark of Eucommia ulmoides Oliv. Each of the sequences consists of 41 residues with a N-terminal blockage by pyroglutamic acid determined by automated Edman degradation in combination with the tandem mass spectroscopy and the C-terminal ladder sequencing analysis. The primary structurs all contain 10 cysteines, which are cross-linked to form five disulfide bridges with a pairing pattern (C1-C5, C2-C9, C3-C6, C4-C7, C8-C10). This is the first finding of a plant antifungal peptide with a five-disulfide motif. EAFP1 and EAFP2 show characteristics of hevein domain and exhibit chitin-binding properties similar to the previously identified hevein-like peptides. They exhibit relatively broad spectra of antifungal activities against eight pathogenic fungi from cotton, wheat, potato, tomato and tobacco. The inhibition activity of EAFP1 and EAFP2 can be effective on both chitin-containing and chitin-free fungi. The values of IC(50) range from 35 to 155 microg/ml for EAFP1 and 18 to 109 microg/ml for EAFP2. Their antifungal effects are strongly antagonized by calcium ions.

Alternaria↗

PubMed2002

cDNA cloning, high-level expression, purification, and characterization of an avian Cu,Zn superoxide dismutase from Peking duck.

As a special species of avian, Peking duck is often used as a model for exploring effective factors against cardio-cerebrovascular diseases, and therefore investigations of antioxidant enzymes including superoxide dismutase are intriguing. By using 3(')-RACE with a gene-specific primer, a cDNA encoding duck Cu,Zn SOD was amplified from the total RNA extracted from Peking duck liver. Three free cysteine residues are found in the deduced amino acid sequence of duck SOD, among which Cys153 at the carbonyl-terminal is a distinctive feature. Production with a high yield of recombinant duck Cu,Zn SOD was achieved in Escherichia coli after the reconstituted expression vector pET-3a-dSOD was transformed into the bacterial strain BL21(DE3)pLysS. After two steps of anion exchange chromatography, a great quantity of the purified enzyme (100mg/L fermented culture) with an enzymatic activity comparable to that of native duck and bovine SOD was finally obtained. Duck SOD is a homodimer with 153 residues for each subunit. The molecular mass of the recombinant enzyme is 15,540.0Da measured by mass spectrum, which well coincides with the estimated size of the sequence but significantly differs from that of the native counterpart. Five charge isomers were observed on isoelectricfocusing (IEF). The most interesting observation is that the thermal stability of duck SOD is much lower than that of the bovine enzyme as revealed by irreversible heat inactivation at 70 degrees C. These properties are discussed in relation to the distinctive free Cys residues in duck Cu,Zn SOD.

Amino Acid Sequence↗

PubMed2002

Crystallization and preliminary crystallographic studies of a novel antifungal protein with five disulfide bridges from Eucommia ulmoides Oliver.

Two antifungal proteins, named Eucommia antifungal peptides 1 and 2 (EAFP1 and EAFP2), have been purified from the bark of the tree E. ulmoides Oliver and show a relatively broad spectrum of antifungal activity against several agriculturally important plant pathogens. One of these small proteins (EAFP2) has been crystallized. The crystal belongs to space group P2(1), with unit-cell parameters a = 19.01, b = 23.16, c = 30.69 A, beta = 98.54 degrees. 1.0 A resolution data were collected from an EAFP2 crystal and have been used to obtain phase information directly by an ab initio method.

Antifungal Agents↗

PubMed2002

Purification, crystallization and initial structural solution of a new alpha-like toxin with cardiac toxicity from scorpion Buthus martensii Karsch.

An alpha-like toxin named BmK M7 active on both mammals and insects has been purified from the venom of scorpion Buthus martensii Karsch (BmK) recently. The electrophysiological experiments showed that M7 can bind to human cardiac Na+-channel and modify its normal properties, hence can be considered as a cardiotoxin. Single crystals of M7 have been obtained by hanging-drop vapor diffusion method using ammonium sulfate as precipitant in Tris-HCl buffer at pH 8.5. A data set to 1.40 A resolution was collected using synchrotron radiation and CCD detector in Photon Factory in Japan. Data analysis showed that the crystals belonged to space group P3(1)21/P3(1)21, with cell dimensions a=b=32.76 A, c=176.82 A. Assuming two molecules per asymmetric unit, the Vm value is 1.92 A3/Da. The initial structural analysis was carried out by molecular replacement, which showed the correct space group (P3(1)21), and the orientations and positions of the two molecules in the asymmetric unit.

Animals↗

PubMed1997

cDNA Sequences of Two Anti-mammals Neurotoxins from Scorpion Buthus martensii Karsch.

The total mRNA was prepared and purified from the venom gland of scorpion Buthus martensii Karsch (BmK). The cDNA library of this venom gland was then constructed using reverse transcription. Two cDNAs encoding the anti-mammalian neurotoxins, named as BmK M1 and BmK M9, were selectively amplified by PCR and sequenced. Both have open reading frames of 252 bp encoding 84 residues of the toxin precursors, including a 19 amino acid signal peptide, the mature toxin with 64 residues, and an additional Arg tail at the carboxyl-terminus which was removed during post-protein processing. The deduced amino acid sequence of BmK M1 was completely identical with the known sequence of the natural toxin BmK M4, whereas the other BmK M9 shared a high homology with the natural toxin BmK M4, differing only in two residues. The cDNA of BmK M1 showed 87.2% homology with that of the African scorpion Lqh alphaIT.

Journal Article↗