Peptide Assemblies Mimicking Chaperones for Protein Trafficking.

Although peptide assemblies have been explored extensively, the self-assembly of negatively charged peptides (NCPs) received little attention. Stimulated by the fact that acidic stretch is a common feature in the intrinsically disordered regions of histone chaperones, we explored the use of the assemblies of NCPs for trafficking histone proteins. Our results show that the peptides that contain glutamic acid (E)-repeat, at neutral or basic pH, self-assemble to form micelles in solution. Circular dichroism indicates that increasing pH favored the peptides to populate more in disordered and α helix conformations. Being innocuous to cells, the assemblies of these NCPs traffic histone 2B (H2B) to mitochondria. Structure-activity study indicates that self-assembly, proper stereochemistry, and acidic repeats are necessary for trafficking H2B. This work, as the first example of peptide assemblies for protein trafficking, illustrates a supramolecular approach for controlling cellular processes and provides insights for mimicking chaperones and controlling protein-protein interactions.

An Optimized SPME-GC-MS Method for Volatile Metabolite Profiling of Different Alfalfa (Medicago sativa L.) Tissues.

Solid-phase microextraction (SPME) was coupled to gas chromatography mass spectrometry (GC-MS) and a method optimized to quantitatively and qualitatively measure a large array of volatile metabolites in alfalfa glandular trichomes isolated from stems, trichome-free stems, and leaves as part of a non-targeted metabolomics approach. Major SPME extraction parameters optimized included SPME fiber composition, extraction temperature, and extraction time. The optimized SPME method provided the most chemically diverse coverage of alfalfa volatile and semi-volatile metabolites using a DVB/CAR/PDMS fiber, extraction temperature of 60 °C, and an extraction time of 20 min. Alfalfa SPME-GC-MS profiles were processed using automated peak deconvolution and identification (AMDIS) and quantitative data extraction software (MET-IDEA). A total of 87 trichome, 59 stem, and 99 leaf volatile metabolites were detected after background subtraction which removed contaminants present in ambient air and associated with the fibers and NaOH/EDTA buffer solution containing CaCl2. Thirty-seven volatile metabolites were detected in all samples, while 15 volatile metabolites were uniquely detected only in glandular trichomes, 9 only in stems, and 33 specifically in leaves as tissue specific volatile metabolites. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) of glandular trichomes, stems, and leaves showed that the volatile metabolic profiles obtained from the optimized SPME-GC-MS method clearly differentiated the three tissues (glandular trichomes, stems, and leaves), and the biochemical basis for this differentiation is discussed. Although optimized using plant tissues, the method can be applied to other types of samples including fruits and other foods.

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides.

Here, we report the use of an enzymatic reaction to cleave the branch off branched peptides for inducing the morphological transition of the assemblies of the peptides. The attachment of DEDDDLLI sequences to the ε-amine of the lysine residue of a tetrapeptide produces branched peptides that form micelles. Upon the proteolytic cleavage of the branch, catalyzed by proteinase K, the micelles turn into nanofibers. We also found that the acetylation of the N-terminal of the branch increased the stability of the branched peptides. Moreover, these branched peptides facilitate the delivery of the proteins into cells. This work contributes insights for the development of peptide supramolecular assemblies via enzymatic noncovalent synthesis in cellular environment.

Enzymatic Cleavage of Branched Peptides for Targeting Mitochondria.

Most of the reported mitochondria-targeting molecules are lipophilic and cationic, and thus they may become cytotoxic with accumulation. Here we show enzymatic cleavage of branched peptides that carry negative charges for targeting mitochondria. Conjugating a well-established protein tag (i.e., FLAG-tag) to self-assembling motifs affords the precursors that form micelles. Enzymatic cleavage of the hydrophilic FLAG motif (DDDDK) by enterokinase (ENTK) turns the micelles to nanofibers. After being taken up by cells, the micelles, upon the action of intracellular ENTK, turn into nanofibers to locate mainly at mitochondria. The micelles of the precursors are able to deliver cargos (either small molecules or proteins) into cells, largely to mitochondria and within 2 h. Preventing ENTK proteolysis diminishes mitochondria targeting. As the first report of using enzymatic self-assembly for targeting mitochondria and delivery cargos to mitochondria, this work illustrates a fundamentally new way to target subcellular organelles for biomedicine.

Introduction of a bacterial acetyl-CoA synthesis pathway improves lactic acid production in Saccharomyces cerevisiae.

Acid-tolerant Saccharomyces cerevisiae was engineered to produce lactic acid by expressing heterologous lactate dehydrogenase (LDH) genes, while attenuating several key pathway genes, including glycerol-3-phosphate dehydrogenase1 (GPD1) and cytochrome-c oxidoreductase2 (CYB2). In order to increase the yield of lactic acid further, the ethanol production pathway was attenuated by disrupting the pyruvate decarboxylase1 (PDC1) and alcohol dehydrogenase1 (ADH1) genes. Despite an increase in lactic acid yield, severe reduction of the growth rate and glucose consumption rate owing to the absence of ADH1 caused a considerable decrease in the overall productivity. In Δadh1 cells, the levels of acetyl-CoA, a key precursor for biologically applicable components, could be insufficient for normal cell growth. To increase the cellular supply of acetyl-CoA, we introduced bacterial acetylating acetaldehyde dehydrogenase (A-ALD) enzyme (EC 1.2.1.10) genes into the lactic acid-producing S. cerevisiae. Escherichia coli-derived A-ALD genes, mhpF and eutE, were expressed and effectively complemented the attenuated acetaldehyde dehydrogenase (ALD)/acetyl-CoA synthetase (ACS) pathway in the yeast. The engineered strain, possessing a heterologous acetyl-CoA synthetic pathway, showed an increased glucose consumption rate and higher productivity of lactic acid fermentation. The production of lactic acid was reached at 142g/L with production yield of 0.89g/g and productivity of 3.55gL(-1)h(-1) under fed-batch fermentation in bioreactor. This study demonstrates a novel approach that improves productivity of lactic acid by metabolic engineering of the acetyl-CoA biosynthetic pathway in yeast.

Enzymatically Forming Cell Compatible Supramolecular Assemblies of Tryptophan-Rich Short Peptides.

Here we report a new type of tryptophan-rich short peptides, which act as hydrogelators, form supramolecular assemblies via enzymatic dephosphorylation, and exhibit cell compatibility. The facile synthesis of the peptides starts with the production of phosphotyrosine, then uses solid phase peptide synthesis (SPPS) to build the phosphopeptides that contain multiple tryptophan residues. Besides exhibiting excellent solubility, these phosphopeptides, unlike the previously reported cytotoxic phenylalanine-rich phosphopeptides, are largely compatible toward mammalian cells. Our preliminary mechanistic study suggests that the tryptophan-rich peptides, instead of forming pericellular assemblies, largely accumulate in lysosomes. Such lysosomal localization may account for their cell compatibility. Moreover, these tryptophan-rich peptides are able to transiently reduce the cytotoxicity of phenylalanine-rich peptide assemblies. This rather unexpected result implies that tryptophan may act as a useful aromatic building block for developing cell compatible supramolecular assemblies for soft materials and find applications for protecting cells from cytotoxic peptide assemblies.

Bromophenols as Candida albicans isocitrate lyase inhibitors.

A new series of bromophenols was synthesized by reactions of corresponding phenol analogs with bromine. The synthesized compounds were tested for inhibitory activity against isocitrate lyase (ICL) of Candida albicans and antimicrobial activity against gram-positive and, gram-negative bacteria and fungi. Among the synthesized bromophenols, bis(3-bromo-4,5-dihydroxyphenyl)methanone (11) and (3-bromo-4,5-dihydroxyphenyl)(2,3-dibromo-4,5-dihydroxyphenyl)methanone (12) displayed potent inhibitory activities against ICL, showing a stronger inhibitory effects than were found with natural bromophenol 1. The preliminary structure-activity relationships were investigated in order to determine the essential structural requirements for the inhibitory activities of these compounds against ICL of C. albicans.

Branched peptides for enzymatic supramolecular hydrogelation.

Here we show the use of branched peptides (i.e., isopeptides) as the substrates of proteases for generating supramolecular hydrogels via enzymatically clipping the branch off the peptides. As the first report of using a protease to cut branched peptides to enable a molecular process for converting nanostructures, this work illustrates a fundamentally new molecular motif for exploring the applications of protease-instructed self-assembly for soft materials.