Design of a bioactive cell‐penetrating peptide: when a transduction domain does more than transduce

The discovery of cell‐penetrating peptides (CPPs) has facilitated delivery of peptides into cells to affect cellular behavior. Previously, we were successful at developing a phosphopeptide mimetic of the small heat shock‐like protein HSP20 . Building on this success we developed a cell‐permeant peptide inhibitor of mitogen‐activated protein kinase‐activated protein kinase 2 (MK2). It is well documented that inhibition of MK2 may be beneficial for a myriad of human diseases including those involving inflammation and fibrosis. During the optimization of the activity and specificity of the MK2 inhibitor (MK2i) we closely examined the effect of cell‐penetrating peptide identity. Surprisingly, the identity of the CPP dictated kinase specificity and functional activity to an extent that rivaled that of the therapeutic peptide. The results reported herein have wide implications for delivering therapeutics with CPPs and indicate that judicious choice of CPP is crucial to the ultimate therapeutic success. Published in 2009 by John Wiley & Sons, Ltd.     

The effect of conjugation on antitumor activity of vindoline derivatives with octaarginine,a cell‐penetrating peptide

Some Vinca alkaloids (eg, vinblastine, vincristine) have been widely used as antitumor drugs for a long time. Unfortunately, vindoline, a main alkaloid component of Catharanthus roseus (L.) G. Don, itself, has no antitumor activity. In our novel research program, we have prepared and identified new vindoline derivatives with moderate cytostatic activity. Here, we describe the effect of conjugation of vindoline derivative with oligoarginine (tetra‐, hexa‐, or octapeptides) cell‐penetrating peptides on the cytostatic activity in vitro and in vivo. Br‐Vindoline‐(l )‐Trp‐OH attached to the N‐terminus of octaarginine was the most effective compound in vitro on HL‐60 cell line. Analysis of the in vitro activity of two isomer conjugates (Br‐vindoline‐(l )‐Trp‐Arg₈ and Br‐vindoline‐(d )‐Trp‐Arg₈ suggests the covalent attachment of the vindoline derivatives to octaarginine increased the antitumor activity significantly against P388 and C26 tumour cells in vitro. The cytostatic effect was dependent on the presence and configuration of Trp in the conjugate as well as on the cell line studied. The configuration of Trp notably influenced the activity on C26 and P388 cells: conjugate with (l )‐Trp was more active than conjugate with the (d )‐isomer. In contrast, conjugates had very similar effect on both the HL‐60 and MDA‐MB‐231 cells. In preliminary experiments, conjugate Br‐vindoline‐(l )‐Trp‐Arg₈ exhibited some inhibitory effect on the tumor growth in P388 mouse leukemia tumor‐bearing mice. Our results indicate that the conjugation of modified vindoline could result in an effective compound even with in vivo antitumor activity.     

Cyclization of a cell‐penetrating peptide via click‐chemistry increases proteolytic resistance and improves drug delivery

In this work we report synthesis and biological evaluation of a cell‐penetrating peptide (CPP), that is partly cyclized via a triazole bridge. Recently, beneficious properties have been reported for cyclized peptides concerning their metabolic stability and intracellular uptake. A CPP based on human calcitonin was used in this study, and side chain cyclization was achieved via copper catalyzed alkyne‐azide click reaction. Cell viability studies in several cell‐lines revealed no cytotoxic effects. Furthermore, efficient uptake in breast cancer MCF‐7 cells could be determined. Moreover, preliminary studies using this novel peptide as drug transporter for daunorubicin were performed. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Broad‐substrate screen as a tool to identify substrates for bacterial Gcn5‐related N‐acetyltransferases with unknown substrate specificity

Due to a combination of efforts from individual laboratories and structural genomics centers, there has been a surge in the number of members of the Gcn5‐related acetyltransferasesuperfamily that have been structurally determined within the past decade. Although the number of three‐dimensional structures is increasing steadily, we know little about the individual functions of these enzymes. Part of the difficulty in assigning functions for members of this superfamily is the lack of information regarding how substrates bind to the active site of the protein. The majority of the structures do not show ligand bound in the active site, and since the substrate‐binding domain is not strictly conserved, it is difficult to predict the function based on structure alone. Additionally, the enzymes are capable of acetylating a wide variety of metabolites and many may exhibit promiscuity regarding their ability to acetylate multiple classes of substrates, possibly having multiple functions for the same enzyme. Herein, we present an approach to identify potential substrates for previously uncharacterized members of the Gcn5‐related acetyltransferase superfamily using a variety of metabolites including polyamines, amino acids, antibiotics, peptides, vitamins, catecholamines, and other metabolites. We have identified potential substrates for eight bacterial enzymes of this superfamily. This information will be used to further structurally and functionally characterize them.     

O‐GlcNAcylation of protein kinase A catalytic subunits enhances its activity: a mechanism linked to learning and memory deficits in Alzheimer's disease

Alzheimer's disease (AD) is characterized clinically by memory loss and cognitive decline. Protein kinase A (PKA)‐CREB signaling plays a critical role in learning and memory. It is known that glucose uptake and O‐GlcNAcylation are reduced in AD brain. In this study, we found that PKA catalytic subunits (PKAcs) were posttranslationally modified by O‐linked N‐acetylglucosamine (O‐GlcNAc). O‐GlcNAcylation regulated the subcellular location of PKAcα and PKAcβ and enhanced their kinase activity. Upregulation of O‐GlcNAcylation in metabolically active rat brain slices by O‐(2‐acetamido‐2‐deoxy‐d ‐glucopyranosylidenamino) N‐phenylcarbamate (PUGNAc), an inhibitor of N‐acetylglucosaminidase, increased the phosphorylation of tau at the PKA site, Ser214, but not at the non‐PKA site, Thr205. In contrast, in rat and mouse brains, downregulation of O‐GlcNAcylation caused decreases in the phosphorylation of CREB at Ser133 and of tau at Ser214, but not at Thr205. Reduction in O‐GlcNAcylation through intracerebroventricular injection of 6‐diazo‐5‐oxo‐l ‐norleucine (DON), the inhibitor of glutamine fructose‐6‐phosphate amidotransferase, suppressed PKA‐CREB signaling and impaired learning and memory in mice. These results indicate that in addition to cAMP and phosphorylation, O‐GlcNAcylation is a novel mechanism that regulates PKA‐CREB signaling. Downregulation of O‐GlcNAcylation suppresses PKA‐CREB signaling and consequently causes learning and memory deficits in AD.     

Self‐renaturing enzymes: Design of an enzyme‐chaperone chimera as a new approach to enzyme stabilization

Molecular chaperones in aqueous‐organic mixtures can broaden the utility of biocatalysis by stabilizing enzymes in denaturing conditions. We have designed a self‐renaturing enzyme‐chaperone chimera consisting of penicillin amidase and a thermophilic chaperonin that functions in aqueous‐organic mixtures. The flexible linker separating the enzyme and chaperone domains was optimized and the design was extended to incorporate a chitin binding domain to facilitate immobilization of the chimera to a chitin support. The initial specific activity of penicillin amidase was not compromised by the enzyme‐chaperone fusion or by immobilization. The total turnover number of immobilized chimera for amoxicillin synthesis in aqueous‐methanol mixtures was 2.8 times higher after 95 h than the total turnover number of the immobilized penicillin amidase lacking a chaperone domain. Similarly, in 32% methanol the soluble chimera was active for over three times longer than the enzyme alone. This approach could easily be extended to other enzyme systems. Biotechnol. Bioeng. 2009;102: 1316–1322. © 2009 Wiley Periodicals, Inc.     

An integrative approach to examining a homology question: shell structures in soft‐shell turtles

Understanding the patterns of shell reduction in turtles is relevant when examining both fossils and living forms. The soft‐shelled turtles (Trionychidae) are characterized by the general reduction of the peripheral bony elements of the carapace, and some species possess structures of contested homology. By examining Remane's ‘principal criteria’, we addressed the primary homology of the prenuchal and the posterior peripheral ossicles (= PPOs) of the Asian flapshell turtles, Lissemys spp., thus evaluating their topological equivalence, their structural quality, and the presence of intermediate forms in ontogeny and phylogeny. We conducted an analysis of gross morphology, bone histology, and ontogeny of these elements in a large sample of living and fossil trionychids and their sister‐group, the carettochelyids. We conclude that the prenuchal comprises a neomorphic structure that does not fulfil any of the homology criteria examined. The assessment of the homology of PPOs is less straightforward because of the presence of partly conflicting evidence. Nevertheless, PPOs and standard peripherals share an antero‐posterior polarity of the ossification pattern, which we interpret as a significant shared underlying developmental pattern. Depending on the phylogenetic position of Lissemys in trionychid phylogeny, the hypothesis of PPOs homology with standard peripherals is a straightforward one or, alternatively, one involving homologous developmental processes at other levels of the hierarchy, resulting in similar microstructural characteristics of these bony shell features. In this respect, we consider the antero‐posterior polarity of the ossification pattern of both PPOs and standard peripherals as providing potential evidence for the homology of the genetic control regulating the expression of both these structures, and therefore we interpret these structures as homologues on the basis of a deeply homologous underlying developmental process. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 462–476.     

A synthetic peptide corresponding to a region of the human pericentriolar material 1 (PCM‐1) protein binds β‐amyloid (Aβ1‐42) oligomers

We have recently reported that a ~19‐kDa polypeptide, rPK‐4, is a protein kinase Cs inhibitor that is 89% homologous to the 1171–1323 amino acid region of the 228‐kDa human pericentriolar material‐1 (PCM‐1) protein (Chakravarthy et al. 2012). We have now discovered that rPK‐4 binds oligomeric amyloid‐β peptide (Aβ)_1‐42 with high affinity. Most importantly, a PCM‐1‐selective antibody co‐precipitated Aβ and amyloid β precursor protein (AβPP) from cerebral cortices and hippocampi from AD (Alzheimer's disease) transgenic mice that produce human AβPP and Aβ_1‐42, suggesting that PCM‐1 may interact with amyloid precursor protein/Aβ in vivo. We have identified rPK‐4′s Aβ‐binding domain using a set of overlapping synthetic peptides. We have found with ELISA, dot‐blot, and polyacrylamide gel electrophoresis techniques that a ~ 5 kDa synthetic peptide, amyloid binding peptide (ABP)‐p4‐5 binds Aβ_1‐42 at nM levels. Most importantly, ABP‐p4‐5, like rPK‐4, appears to preferentially bind Aβ_1‐42 oligomers, believed to be the toxic AD‐drivers. As expected from these observations, ABP‐p4‐5 prevented Aβ_1‐42 from killing human SH‐SY5Y neuroblastoma cells via apoptosis. These findings indicate that ABP‐p4‐5 is a possible candidate therapeutic for AD.     

Applying computer‐aided photo‐identification to messy datasets: a case study of Thornicroft's giraffe (Giraffa camelopardalis thornicrofti)

Digital photography enables researchers to rapidly compile large quantities of data from individually identifiable animals, and computer software improves the management of such large datasets while aiding the identification process. Wild‐ID software has performed well with uniform datasets controlling for angle and portion of the animal photographed; however, few datasets are collected under such controlled conditions. We examined the effectiveness of Wild‐ID in identifying individual Thornicroft's giraffe from a dataset of photographs (n = 552) collected opportunistically in the Luangwa Valley, Zambia from March to October 2009. We assessed the programme's accuracy in correctly identifying individuals and the effect of five image quality factors on identification success: blurriness, background type and complexity, amount of sky and the presence of other giraffe. The programme correctly identified individuals in 71.6% of photographs. Background complexity was the only significant variable affecting identification success and removing background imagery reduced identification error by 52.8% (from 28.4 to 13.4%). Our results indicate higher levels of error than previously reported for Wild‐ID. However, they also suggest the programme is an effective tool for quickly identifying individuals in large field datasets, especially if photograph backgrounds are removed beforehand and postanalysis visual verification is performed.     

Structures of a highly variable cell‐wall anchored protein‐encoding the spj gene from ST8/SCCmecIVl community‐associated methicillin‐resistant Staphylococcus aureus (CA‐MRSA/J) isolated from 2003 onwards: An indicator of a strongly invasive pathotype

The cell wall‐anchored protein‐encoding spj gene on staphylococcal cassette chromosome mec IVl (SCCmecIVl) was found to vary in size because of its 22‐ and 86‐aa repeat domains. The 22‐aa repeats are the more flexible of the two repeats, comprising three 11‐aa units, and were classified into three groups with eleven types. The 11/22‐aa repeats are longer in individuals with bullous impetigo, shorter in those with invasive disease and were absent in a fatal case, this last one having been rapidly diagnosed by PCR. IS431‐flanking pUB110 (bleO, aadD) is present on SCCmecIVl at 90%. The bacterial surface has the spj product and a unique surface layer.     

Parabolic variation in sexual selection intensity across the range of a cold‐water pipefish: implications for susceptibility to climate change

While an understanding of evolutionary processes in shifting environments is vital in the context of rapid ecological change, one of the most potent selective forces, sexual selection, remains curiously unexplored. Variation in sexual selection across a species range, especially across a gradient of temperature regimes, has the potential to provide a window into the possible impacts of climate change on the evolution of mating patterns. Here, we investigated some of the links between temperature and indicators of sexual selection, using a cold‐water pipefish as model. We found that populations differed with respect to body size, length of the breeding season, fecundity, and sexual dimorphism across a wide latitudinal gradient. We encountered two types of latitudinal patterns, either linear, when related to body size, or parabolic in shape when considering variables related to sexual selection intensity, such as sexual dimorphism and reproductive investment. Our results suggest that sexual selection intensity increases toward both edges of the distribution and that the large differences in temperature likely play a significant role. Shorter breeding seasons in the north and reduced periods for gamete production in the south certainly have the potential to alter mating systems, breeding synchrony, and mate monopolization rates. As latitude and water temperature are tightly coupled across the European coasts, the observed patterns in traits related to sexual selection can lead to predictions regarding how sexual selection should change in response to climate change. Based on data from extant populations, we can predict that as the worm pipefish moves northward, a wave of decreasing selection intensity will likely replace the strong sexual selection at the northern range margin. In contrast, the southern populations will be followed by heightened sexual selection, which may exacerbate the problem of local extinction at this retreating boundary.     

Dynamic size responses to climate change: prevailing effects of rising temperature drive long‐term body size increases in a semi‐arid passerine

Changes in animal body size have been widely reported as a correlate of contemporary climate change. Body size affects metabolism and fitness, so changing size has implications for resilience, yet the climatic factors that drive size variation remain poorly understood. We test the role of mean and extreme temperature, rainfall, and remotely sensed primary productivity (NDVI) as drivers of body size in a sedentary, semi‐arid Australian passerine, Ptilotula (Lichenostomus) penicillatus, over 23 years. To distinguish effects due to differential growth from changes in population composition, we analysed first‐year birds and adults separately and considered climatic variation at three temporal scales (current, previous, and preceding 5 years). The strongest effects related to temperature: in both age classes, larger size was associated with warmer mean temperatures in the previous year, contrary to Bergmann's Rule. Moreover, adults were larger in warmer breeding seasons, while first years was larger after heatwaves; these effects are more likely to be mediated through size‐dependent mortality, highlighting the role of body size in determining vulnerability to extinction. In addition to temperature, larger adult size was associated with lower primary productivity, which may reflect a trade‐off between vegetative growth and nectar production, on which adults rely. Finally, lower rainfall was associated with decreasing size in first year and adults, most likely related to decreased food availability. Overall, body size increased over 23 years, strongly in first‐year birds (2.7%) compared with adults (1%), with size outcomes a balance between competing drivers. As rainfall declined over time and productivity remained fairly stable, the temporal increase in body size appears largely driven by rising mean temperature and temperature extremes. Body size responses to environmental change are thus complex and dynamic, driven by effects on growth as well as mortality.     

The molecular behavior of a single β‐amyloid inside a dipalmitoylphosphatidylcholine bilayer at three different temperatures: An atomistic simulation study: Aβ interaction with DPPC: Atomistic simulation

The behavior of a single Aβ40 molecule within a dipalmitoylphosphatidylcholine (DPPC) bilayer was studied by all‐atom molecular dynamics simulations. The effect of membrane structure was investigated on Aβ40 behavior, secondary structure, and insertion depth. Simulations were performed at three temperatures (323, 310, and 300 K) to probe three different bilayer fluidities. Results show that at all above temperatures, the peptide contains two short helices, coil, bend, and turn structures. At 300 K, the peptide contains a region with β structure in C‐terminal region. Our results also show that Aβ decreases the bilayer thickness and the order of lipids in its vicinity which leads to water insertion into the bilayer and concomitant increase in the local fluidity. The peptide remains embedded in the bilayer at all temperatures, and become inserted into the bilayer up to several residues at 323 and 310 K. At 310 and 300 K, the dominant interaction energy between Aβ and bilayer changes from electrostatic to van der Waals. It can be proposed that at higher temperatures (e.g., 323 K), Lys28 and the C‐terminal region of the peptide play the role of two anchors that keep Aβ inside the top leaflet. This study demonstrates that Aβ molecule can perturb the integrity of cellular membranes. Proteins 2017; 85:1298–1310. © 2017 Wiley Periodicals, Inc.