Different Biological Activities of Histidine-Rich Peptides Are Favored by Variations in Their Design

The protein transduction and antimicrobial activities of histidine-rich designer peptides were investigated as a function of their sequence and compared to gene transfection, lentivirus transduction and calcein release activities. In membrane environments, the peptides adopt helical conformations where the positioning of the histidine side chains defines a hydrophilic angle when viewed as helical wheel. The transfection of DNA correlates with calcein release in biophysical experiments, being best for small hydrophilic angles supporting a model where lysis of the endosomal membrane is the limiting factor. In contrast, antimicrobial activities show an inverse correlation suggesting that other interactions and mechanisms dominate within the bacterial system. Furthermore, other derivatives control the lentiviral transduction enhancement or the transport of proteins into the cells. Here, we tested the transport into human cell lines of luciferase (63 kDa) and the ribosome-inactivating toxin saporin (30 kDa). Notably, depending on the protein, different peptide sequences are required for the best results, suggesting that the interactions are manifold and complex. As such, designed LAH4 peptides assure a large panel of biological and biophysical activities whereby the optimal result can be tuned by the physico-chemical properties of the sequences.

Helixvis: Visualize α-Helical Peptides in Python

Representing three-dimensional objects on a two-dimensional screen or sheet of paper can be challenging. To address this issue in the context of oligopeptide alpha-helical secondary structure, the helical wheel and wenxiang diagram visualizations have been developed. Although there exist graphical interfaces and web servers that generate these visualizations, a Python implementation has not yet been popularized. Here, we introduce the Python helixvis package, a companion to the R helixvis package, as a programmatic implementation of alpha helix visualization. All the code and output in this report is fully reproducible and available at https://github.com/subramv/ helixvis.<br>

Helixvis: Visualize α-Helical Peptides in Python

Representing three-dimensional objects on a two-dimensional screen or sheet of paper can be challenging. To address this issue in the context of oligopeptide alpha-helical secondary structure, the helical wheel and wenxiang diagram visualizations have been developed. Although there exist graphical interfaces and web servers that generate these visualizations, a Python implementation has not yet been popularized. Here, we introduce the Python helixvis package, a companion to the R helixvis package, as a programmatic implementation of alpha helix visualization. All the code and output in this report is fully reproducible and available at https://github.com/subramv/ helixvis.<br>

Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein–derived peptides

Group A streptococcus (Strep A) surface M protein, an α-helical coiled-coil dimer, is a vaccine target and a major determinant of streptococcal virulence. The sequence-variable N-terminal region of the M protein defines the M type and also contains epitopes that promote opsonophagocytic killing of streptococci. Recent reports have reported considerable cross-reactivity among different M types, suggesting the prospect of identifying cross-protective epitopes that would constitute a broadly protective multivalent vaccine against Strep A isolates. Here, we have used a combination of immunological assays, structural biology, and cheminformatics to construct a recombinant M protein–based vaccine that included six Strep A M peptides that were predicted to elicit antisera that would cross-react with an additional 15 nonvaccine M types of Strep A. Rabbit antisera against this recombinant vaccine cross-reacted with 10 of the 15 nonvaccine M peptides. Two of the five nonvaccine M peptides that did not cross-react shared high sequence identity (≥50%) with the vaccine peptides, implying that high sequence identity alone was insufficient for cross-reactivity among the M peptides. Additional structural analyses revealed that the sequence identity at corresponding polar helical-wheel heptad sites between vaccine and nonvaccine peptides accurately distinguishes cross-reactive from non–cross-reactive peptides. On the basis of these observations, we developed a scoring algorithm based on the sequence identity at polar heptad sites. When applied to all epidemiologically important M types, this algorithm should enable the selection of a minimal number of M peptide–based vaccine candidates that elicit broadly protective immunity against Strep A.

NetWheels: A web application to create high quality peptide helical wheel and net projections

Helices are one of the most common secondary structures found in peptides and proteins. The wheel and net projections have been proposed to represent in two dimensions the tridimensional helical structures and facilitate the observation of their properties, especially in terms of residues polarity and intramolecular bonding. Nevertheless, there are few software options to create these projections. We have developed a web-based application that has several futures to create, customize and export these projections and is freely available at http://lbqp.unb.br/NetWheels.

DNA Barcoding and Intra Species Analysis of the Ember Parrot Fish Scarus Rubroviolaceus using mtCO1

<div><p><em>In this study S.rubroviolaceus </em><em>form very ancient family group </em><em>Scorpaenidae with</em><em> structurally diverse group of subphylum Vertebrata</em><em> was collected form from parangipettai (MAB06)for species identification with inter specific variation among barcoding region sequenceing cytochrome oxidase subunit I (</em><em>COI)</em><em> gene comparing with Australia (EF609452), Tonga (FJ584082), South Africa (GU805008), Iran (HQ149928). The intraspecific variation analysis in NCBI screend for COI sequence form different geographical regions results 99% to 100% identity. BOLD’s identification engine shows 99.68% to 100% similar of 20 specimens with conformation of COI species database tree that S.rubroviolaceus belongs to order Carangidae. The molar concentration of nucleotides in the COI region profiling barcoding valuates that high in thymine content are similar in all the samples, Cytosine as second predominant and guanine as least molar concentration. A helical wheel is ploted to illustrate the properties of alpha helices in proteins. Multiple sequence alignments for DNA sequences similarities query were analysed with Clustal W from EMBL tools.</em></p></div>

Lachesana tarabaevi, an expert in membrane-active toxins

In the present study, we show that venom of the ant spider Lachesana tarabaevi is unique in terms of molecular composition and toxicity. Whereas venom of most spiders studied is rich in disulfide-containing neurotoxic peptides, L. tarabaevi relies on the production of linear (no disulfide bridges) cytolytic polypeptides. We performed full-scale peptidomic examination of L. tarabaevi venom supported by cDNA library analysis. As a result, we identified several dozen components, and a majority (∼80% of total venom protein) exhibited membrane-active properties. In total, 33 membrane-interacting polypeptides (length of 18–79 amino acid residues) comprise five major groups: repetitive polypeptide elements (Rpe), latarcins (Ltc), met-lysines (MLys), cyto-insectotoxins (CIT) and latartoxins (LtTx). Rpe are short (18 residues) amphiphilic molecules that are encoded by the same genes as antimicrobial peptides Ltc 4a and 4b. Isolation of Rpe confirms the validity of the iPQM (inverted processing quadruplet motif) proposed to mark the cleavage sites in spider toxin precursors that are processed into several mature chains. MLys (51 residues) present ‘idealized’ amphiphilicity when modelled in a helical wheel projection with sharply demarcated sectors of hydrophobic, cationic and anionic residues. Four families of CIT (61–79 residues) are the primary weapon of the spider, accounting for its venom toxicity. Toxins from the CIT 1 and 2 families have a modular structure consisting of two shorter Ltc-like peptides. We demonstrate that in CIT 1a, these two parts act in synergy when they are covalently linked. This finding supports the assumption that CIT have evolved through the joining of two shorter membrane-active peptides into one larger molecule.

A CLAG3 Mutation in an Amphipathic Transmembrane Domain Alters Malaria Parasite Nutrient Channels and Confers Leupeptin Resistance

Erythrocytes infected with malaria parasites have increased permeability to ions and nutrients, as mediated by the plasmodial surface anion channel (PSAC) and recently linked to parasiteclag3genes. Although the encoded protein is integral to the host membrane, its precise contribution to solute transport remains unclear because it lacks conventional transmembrane domains and does not have homology to ion channel proteins in other organisms. Here, we identified a probable CLAG3 transmembrane domain adjacent to a variant extracellular motif. Helical-wheel analysis revealed strict segregation of polar and hydrophobic residues to opposite faces of a predicted α-helical transmembrane domain, suggesting that the domain lines a water-filled pore. A single CLAG3 mutation (A1210T) in a leupeptin-resistant PSAC mutant falls within this transmembrane domain and may affect pore structure. Allelic-exchange transfection and site-directed mutagenesis revealed that this mutation alters solute selectivity in the channel. The A1210T mutation also reduces the blocking affinity of PSAC inhibitors that bind on opposite channel faces, consistent with global changes in channel structure. Transfected parasites carrying this mutation survived a leupeptin challenge significantly better than a transfection control did. Thus, the A1210T mutation contributes directly to both altered PSAC activity and leupeptin resistance. These findings reveal the molecular basis of a novel antimalarial drug resistance mechanism, provide a framework for determining the channel's composition and structure, and should guide the development of therapies targeting the PSAC.

A simple and novel helical drive in-pipe robot

SUMMARYPipeline grids of various size and material are pervasive in today's modern society. The frequent inspection and maintenance of such pipeline grids have presented a tremendous challenge. It is advocated that only advanced robot design embedded with intelligent electronics and control algorithms could perform the job. Given the ever increasing demands for intelligent in-pipe robots, various in-pipe drive mechanisms have been reported. One of the simplest is helical wheel drives that have only one degree of freedom. All previously reported in-pipe helical drives are based on independent passive wheels that are tilted an angle. One of the major problems of current helical wheel drives is their unstable traction force. In this paper, instead of allowing the wheels to rotate independently, they are synchronized by adding a timing belt. This small change will result in significant improvement which will be highlighted in this paper. In the proposed driving method, tracking force is analyzed together with a comprehensive set of traction force measurement experiments. Both analysis and experiments have shown that the proposed mechanism has great potential for in-pipe robot drive design.