Jya-Wei Cheng

Base pairing geometry in GA mismatches depends entirely on the neighboring sequence

We have synthesized nine self-complementary DNA oligomers containing different flanking sequences adjacent to a pair of contiguous GA mismatches, and have used high resolution nuclear magnetic resonance (n.m.r.) to investigate the GpA phosphodiester backbone conformation and mismatch pairing schemes in these duplexes. We found dramatic effects of the flanking base pair on the hydrogen bonding and backbone conformation, which appear to be coupled. Thus the Ganti-Aanti base pairing scheme in a NAGATN sequence switches to a more stable sheared GA base pairing scheme in a NCGAGN or NTGAAN context, while no duplex is formed (or only GA bulges occur) when NAGATN is changed to NGGACN. Furthermore, the more stable sheared GA pairing in NPyGAPuN sequences is associated with a BII rather than BI backbone conformation for the phosphodiester between the adjacent mismatched GA pairs. The overall stability of these adjacent GA mismatches as measured by imino proton n.m.r. studies is Py-GA-Pu > A-GA-T > G-GA-C.

Solution Structure of a Novel Tryptophan-Rich Peptide with Bidirectional Antimicrobial Activity

Trp-rich antimicrobial peptides play important roles in the host innate defense mechanisms of many plants, insects, and mammals. A new type of Trp-rich peptide, Ac-KWRRWVRWI-NH(2), designated Pac-525, was found to possess improved activity against both gram-positive and -negative bacteria. We have determined that the solution structures of Pac-525 bound to membrane-mimetic sodium dodecyl sulfate (SDS) micelles. The SDS micelle-bound structure of Pac-525 adopts an alpha-helical segment at residues Trp2, Arg3, and Arg4. The positively charged residues are clustered together to form a hydrophilic patch. The three hydrophobic residues Trp2, Val6, and Ile9 form a hydrophobic core. The surface electrostatic potential map indicates the three tryptophan indole rings are packed against the peptide backbone and form an amphipathic structure. Moreover, the reverse sequence of Pac-525, Ac-IWRVWRRWK-NH(2), designated Pac-525(rev), also demonstrates similar antimicrobial activity and structure in membrane-mimetic micelles and vesicles. A variety of biophysical and biochemical methods, including circular dichroism, fluorescence spectroscopy, and microcalorimetry, were used to show that Pac-525 interacted strongly with negatively charged phospholipid vesicles and induced efficient dye release from these vesicles, suggesting that the antimicrobial activity of Pac-525 may be due to interactions with bacterial membranes.

Boosting Salt Resistance of Short Antimicrobial Peptides

ABSTRACT The efficacies of many antimicrobial peptides are greatly reduced under high salt concentrations, therefore limiting their use as pharmaceutical agents. Here, we describe a strategy to boost salt resistance and serum stability of short antimicrobial peptides by adding the nonnatural bulky amino acid β-naphthylalanine to their termini. The activities of the short salt-sensitive tryptophan-rich peptide S1 were diminished at high salt concentrations, whereas the activities of its β-naphthylalanine end-tagged variants were less affected.

Easy Strategy To Increase Salt Resistance of Antimicrobial Peptides

ABSTRACT The efficacies of many antimicrobial peptides are greatly reduced under high salt concentrations, limiting their development as pharmaceutical compounds. Here, we describe an easy strategy to increase salt resistance of antimicrobial peptides by replacing tryptophan or histidine residues with the bulky amino acids β-naphthylalanine and β-(4,4′-biphenyl)alanine. The activities of the salt-sensitive peptide P-113 were diminished at high salt concentrations, whereas the activities of its β-naphthylalanine and β-(4,4′-biphenyl)alanine-substituted variant were less affected.

Palladium-catalyzed cyclization of alkenyl and aryl halides containing α,β-unsaturated carbonyl groups via intramolecular carbopalladation

Abstract Treatment of alkenyl and aryl iodides and bromides containing an appropriate α, β-unsaturated carbonyl group with a catalytic amount (3–5 mol %) of either a Pd(O) or a Pd(II) complex, e.g., Pd(PPh 3 ) 4 , and a base, e.g., NEt 3 , can induce highly regioselective cyclization via intramolecular carbopalladation; formation of exocyclic alkenes can also be highly stereoselective.

Novel Antimicrobial Peptides with High Anticancer Activity and Selectivity

We describe a strategy to boost anticancer activity and reduce normal cell toxicity of short antimicrobial peptides by adding positive charge amino acids and non-nature bulky amino acid β-naphthylalanine residues to their termini. Among the designed peptides, K4R2-Nal2-S1 displayed better salt resistance and less toxicity to hRBCs and human fibroblast than Nal2-S1 and K6-Nal2-S1. Fluorescence microscopic studies indicated that the FITC-labeled K4R2-Nal2-S1 preferentially binds cancer cells and causes apoptotic cell death. Moreover, a significant inhibition in human lung tumor growth was observed in the xenograft mice treated with K4R2-Nal2-S1. Our strategy provides new opportunities in the development of highly effective and selective antimicrobial and anticancer peptide-based therapeutics.

Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein

Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein Kuo-Chun Huang, Ming-Che Lee, Chih-Wei Wu, Kao-Jean Huang, Huan-Yao Lei, and Jya-Wei Cheng* 1 Institute of Biotechnology and Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan 2Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan

Stability and folding of the SH3 domain of bruton's tyrosine kinase

Brutons tyrosine kinase (BTK) plays an important role in B cell development. Deletion of C‐terminal 14 amino acids of the SH3 domain of BTK results in X‐linked agammaglobulinemia (XLA), an inherited disease. We report here on the stability and folding of SH3 domain of BTK. Peptides corresponding to residues 216–273 (58 residues) and 216–259 (44 residues) of BTK SH3 domain were synthesized by solid phase methods; the first peptide constitutes the entire SH3 domain of BTK while the latter peptide lacks 14 amino acid residues of the C‐terminal. The 58 amino acid peptide forms mainly a β‐barrel type folding unit. Although small and lacking disulfide bonds, this peptide is extremely stable to thermal denaturation. Based on circular dichroism measurements, its melting temperature was found to be high, 82°C at pH 6.0. However, the Gibbs free energy (ΔG  H 2O ) of the intrinsic stability and thermodynamic spontaneity of unfolding were found to be low, 2.6 kcal/mol by Gdn·HCl denaturation experiments, as compared to 12 kcal/mol obtained for larger single domain proteins, indicating poor stability of SH3 domain. Addition of 500 mM of Na2SO4 increased the free energy change ΔG  H 2O to 4.0 kcal/mol, suggesting an ionic strength effect. The truncated peptide fails to fold correctly and adopts random coil conformation in contrast to 58 amino acid β‐barrel peptide, which exhibits high thermal stability but normal or low stability at ambient temperature. These results, to our knowledge the first to delineate the importance of C‐terminal in structural integrity of SH3 domains, indicate also that improper folding and/or poor stability of mutant SH3 domain in BTK likely causes XLA. Proteins 28:465–471

Efficacy of a novel antimicrobial peptide against periodontal pathogens in both planktonic and polymicrobial biofilm states

UNLABELLED Streptococcus gordonii, Fusobacterium nucleatum and Porphyromonas gingivalis represent the early, middle and late colonizers of the bacterial accretion in dental plaque biofilms. These sessile communities constitute a protected mode of growth that promotes survival in a hostile environment. This study describes a novel and unrecognized role for a synthetic cationic antimicrobial peptide, Nal-P-113, which inhibits and kills periodontal bacteria in planktonic state, inhibits the formation of biofilms and eradicates polymicrobial biofilms. Nal-P-113 is also stable in saliva, serum and saline solution. At a concentration less than 320 μg/mL which is harmless to normal oral cells, Nal-P-113 can kill bacteria in planktonic state. At a concentration of antimicrobial peptide Nal-P-113 (1280 μg/mL) which only causes slight damages to normal oral cells is needed to kill bacteria in biofilm state. It is worth mentioning that this concentration of Nal-P-113 is harmless to rat oral mucosa compared to chlorhexidine. The mechanism of Nal-P-113 inhibiting and killing periodontal bacteria might rely on the abilities to permeabilize and/or to form pores within the cytoplasmic membranes, thus causes the death of bacteria. Here, we provided a novel and stable antimicrobial peptide with very low mammalian cytotoxicity, which can inhibit and kill periodontal bacteria in both planktonic and polymicrobial biofilm states. STATEMENT OF SIGNIFICANCE Nal-P-113 is a potent antimicrobial peptide with strong antimicrobial ability, improved deficiency compared with other antibacterial peptides, and remains stable in phosphate buffered saline, saliva, brain-heart infusion medium and bovine calf serum. Nal-P-113 exhibits a broad spectrum of bacteriocidal activity with excellent eradicating capability on oral pathogens and the respective biofilms. In this study, we used propidium iodide staining, scanning electron microscopy and transmission electron microscopy to confirm that Nal-P-113 can perforate plasmalemma thereby resulting in the death of oral pathogens and disintegrate the respective biofilms. Nal-P-113 also showed effective anti-plaque biofilms and cytotoxicity in the rat periodontitis model. No adverse effects can be observed on the gingivomucosa tissue. In short, the antimicrobial peptide Nal-P-113 presented to be an effective yet have low mammalian cytotoxicity agent with potential application in the clinic. This study provides a proof of concept in applying antimicrobial peptides in the clinical perspective.

A new protocol for high-yield purification of recombinant human CXCL8((3-72))K11R/G31P expressed in Escherichia coli.

The ELR-CXC chemokines are important to neutrophil inflammation in many acute and chronic diseases. Among them, CXCL8 (interleukin-8, IL-8), binds to both the CXCR1 and CXCR2 receptors with high affinity and the expression levels of CXCL8 are elevated in many inflammatory diseases. Recently, an analogue of human CXCL8, CXCL8((3-72))K11R/G31P (hG31P) has been developed. It has been demonstrated that hG31P is a high affinity antagonist for both CXCR1 and CXCR2. To obtain large quantities of hG31P, we have successfully constructed and expressed hG31P in Escherichia coli. Moreover, we have developed a new protocol for high-yield purification of hG31P and for the removal of lipopolysaccharide (LPS, endotoxin) associated with hG31P due to the expression in E. coli. The purity of hG31P is more than 95% and the final yield is 9.7mg hG31P per gram of cell paste. The purified hG31P was tested by various biological assays. In addition, the structural properties of hG31P were studied by circular dichroism (CD), ultracentrifuge, isothermal titration calorimetry (ITC), and nuclear magnetic resonance (NMR) spectroscopy. Our results indicate that this purification protocol is very simple and easy to amplify at a large scale. The results of this study will provide an effective route to produce enough hG31P for future clinical studies.