Characterisation of helical structure in AFM micrographs of a trimer of the peptide sequence (ValGlyGlyValGly)

2014 ◽  
Vol 46 (10-11) ◽  
pp. 679-682 ◽  
Author(s):  
James Eric Castle ◽  
Neluta Ibris ◽  
Anna Maria Salvi ◽  
Pasquale Moscarelli ◽  
Brigida Bochicchio ◽  
...  
Keyword(s):  
Helical Structure ◽  
Peptide Sequence ◽  
Afm Micrographs

scholarly journals Identification of Antimicrobial Peptides from the Microalgae Tetraselmis suecica (Kylin) Butcher and Bactericidal Activity Improvement

Marine Drugs ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. 453 ◽  
Author(s):  
Guzmán ◽  
Wong ◽  
Román ◽  
Cárdenas ◽  
Alvárez ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Pathogenic Bacteria ◽  
Bioactive Peptides ◽  
De Novo ◽  
Helical Structure ◽  
Antimicrobial Activities ◽  
Peptide Sequence ◽  
Tetraselmis Suecica ◽  
Defense Strategies ◽  
Key Residues

The outburst of microbial resistance to antibiotics creates the need for new sources of active compounds for the treatment of pathogenic microorganisms. Marine microalgae are of particular interest in this context because they have developed tolerance and defense strategies to resist the exposure to pathogenic bacteria, viruses, and fungi in the aquatic environment. Although antimicrobial activities have been reported for some microalgae, natural algal bioactive peptides have not been described yet. In this work, acid extracts from the microalga Tetraselmis suecica with antibacterial activity were analyzed, and de novo sequences of peptides were determined. Synthetic peptides and their alanine and lysine analogs allowed identifying key residues and increasing their antibacterial activity. Additionally, it was determined that the localization of positive charges within the peptide sequence influences the secondary structure with tendency to form an alpha helical structure.

scholarly journals Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

2012 ◽  
Vol 8 ◽  
pp. 1172-1184 ◽  
Author(s):  
Evan F Haney ◽  
Leonard T Nguyen ◽  
David J Schibli ◽  
Hans J Vogel
Keyword(s):  
Antimicrobial Peptide ◽  
Positive Charge ◽  
Helical Structure ◽  
Physicochemical Characteristics ◽  
Proximal Region ◽  
Peptide Sequence ◽  
Interfacial Region ◽  
Cytotoxic Activities ◽  
Glycoprotein Gp41 ◽  
Membrane Proximal Region

A number of physicochemical characteristics have been described which contribute to the biological activity of antimicrobial peptides. This information was used to design a novel antimicrobial peptide sequence by using an intrinsically inactive membrane-associated peptide derived from the HIV glycoprotein, gp41, as a starting scaffold. This peptide corresponds to the tryptophan-rich membrane-proximal region of gp41, which is known to interact at the interfacial region of the viral membrane and adopts a helical structure in the presence of lipids. Three synthetic peptides were designed to increase the net positive charge and amphipathicity of this 19-residue peptide. Ultimately, the peptide with the greatest degree of amphipathicity and largest positive charge proved to be the most potent antimicrobial, and this peptide could be further modified to improve the antimicrobial activity. However, the other two peptides were relatively ineffective antimicrobials and instead proved to be extremely hemolytic. This work demonstrates a novel approach for the design of unexplored antimicrobial peptide sequences but it also reveals that the biological and cytotoxic activities of these polypeptides depend on a number of interrelated factors.

scholarly journals Iterative optimization yields Mcl-1–targeting stapled peptides with selective cytotoxicity to Mcl-1–dependent cancer cells

2018 ◽  
Vol 115 (5) ◽  
pp. E886-E895 ◽  
Author(s):  
Raheleh Rezaei Araghi ◽  
Gregory H. Bird ◽  
Jeremy A. Ryan ◽  
Justin M. Jenson ◽  
Marina Godes ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cancer Survival ◽  
Cell Transformation ◽  
Helical Structure ◽  
Structural Rearrangement ◽  
Peptide Sequence ◽  
Systematic Sampling ◽  
Stapled Peptides ◽  
Structural Mechanism ◽  
Iterative Optimization

Bcl-2 family proteins regulate apoptosis, and aberrant interactions of overexpressed antiapoptotic family members such as Mcl-1 promote cell transformation, cancer survival, and resistance to chemotherapy. Discovering potent and selective Mcl-1 inhibitors that can relieve apoptotic blockades is thus a high priority for cancer research. An attractive strategy for disabling Mcl-1 involves using designer peptides to competitively engage its binding groove, mimicking the structural mechanism of action of native sensitizer BH3-only proteins. We transformed Mcl-1–binding peptides into α-helical, cell-penetrating constructs that are selectively cytotoxic to Mcl-1–dependent cancer cells. Critical to the design of effective inhibitors was our introduction of an all-hydrocarbon cross-link or “staple” that stabilizes α-helical structure, increases target binding affinity, and independently confers binding specificity for Mcl-1 over related Bcl-2 family paralogs. Two crystal structures of complexes at 1.4 Å and 1.9 Å resolution demonstrate how the hydrophobic staple induces an unanticipated structural rearrangement in Mcl-1 upon binding. Systematic sampling of staple location and iterative optimization of peptide sequence in accordance with established design principles provided peptides that target intracellular Mcl-1. This work provides proof of concept for the development of potent, selective, and cell-permeable stapled peptides for therapeutic targeting of Mcl-1 in cancer, applying a design and validation workflow applicable to a host of challenging biomedical targets.

Single molecule optical diffraction: A tool for understanding the structure of triple stranded left-hand helical cellulose

1989 ◽  
Vol 47 ◽  
pp. 1024-1025
Author(s):  
George C. Ruben ◽  
William Krakow
Keyword(s):  
Single Molecule ◽  
Helical Structure ◽  
Optical Diffraction ◽  
Maximum Diameter ◽  
Primary Cell Wall ◽  
Cellulose Synthesis ◽  
Left Hand ◽  
Left Handed ◽  
Freeze Dried ◽  
Diffraction Patterns

Tobacco primary cell wall and normal bacterial Acetobacter xylinum cellulose formation produced a 36.8±3Å triple-stranded left-hand helical microfibril in freeze-dried Pt-C replicas and in negatively stained preparations for TEM. As three submicrofibril strands exit the wall of Axylinum , they twist together to form a left-hand helical microfibril. This process is driven by the left-hand helical structure of the submicrofibril and by cellulose synthesis. That is, as the submicrofibril is elongating at the wall, it is also being left-hand twisted and twisted together with two other submicrofibrils. The submicrofibril appears to have the dimensions of a nine (l-4)-ß-D-glucan parallel chain crystalline unit whose long, 23Å, and short, 19Å, diagonals form major and minor left-handed axial surface ridges every 36Å.The computer generated optical diffraction of this model and its corresponding image have been compared. The submicrofibril model was used to construct a microfibril model. This model and corresponding microfibril images have also been optically diffracted and comparedIn this paper we compare two less complex microfibril models. The first model (Fig. 1a) is constructed with cylindrical submicrofibrils. The second model (Fig. 2a) is also constructed with three submicrofibrils but with a single 23 Å diagonal, projecting from a rounded cross section and left-hand helically twisted, with a 36Å repeat, similar to the original model (45°±10° crossover angle). The submicrofibrils cross the microfibril axis at roughly a 45°±10° angle, the same crossover angle observed in microflbril TEM images. These models were constructed so that the maximum diameter of the submicrofibrils was 23Å and the overall microfibril diameters were similar to Pt-C coated image diameters of ∼50Å and not the actual diameter of 36.5Å. The methods for computing optical diffraction patterns have been published before.

Liquid Crystal Trimers Incorporating Saturated Isosteres of Benzene and Exhibiting Modulated Nematic Phases

2019 ◽  
Author(s):  
Adam Al-Janabi ◽  
Richard Mandle
Keyword(s):  
Liquid Crystal ◽  
Helical Structure ◽  
Molecular Shape ◽  
Saturated Hydrocarbons ◽  
Fluid System ◽  
Structural Requirement ◽  
Disubstituted Benzene ◽  
Bona Fide ◽  
Nematic Phases ◽  
Bend Angles

<p>The nematic twist-bend (N<sub>TB</sub>) liquid crystal phase possesses a local helical structure with a pitch length of a few nanometres and is the first example of spontaneous symmetry breaking in a fluid system. All known examples of the N­<sub>TB­</sub> phase occur in materials whose constituent mesogenic units are aromatic hydrocarbons. It is not clear if this is due to synthetic convenience or a <i>bona fide</i> structural requirement for a material to exhibit this phase of matter. In this work we demonstrate that materials consisting largely of saturated hydrocarbons could also give rise to this mesophase. Furthermore, replacement of 1,4-disubstituted benzene with <i>trans</i> 1,4-cyclohexane or even 1,4-cubane does not especially alter the transition temperatures of the resulting material nor does it appear to impact upon the heliconical tilt angle, suggesting the local structure of the phase is unperturbed. Calculating the probability distribution of bend angles reveals that the choice of isosteric group has little impact on the overall molecular shape, demonstrating the shape-driven nature of the N<sub>TB</sub> phase. </p>

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

2020 ◽  
Vol 20 (10) ◽  
pp. 831-840
Author(s):  
Weibin Li
Keyword(s):  
Pathogenic Bacteria ◽  
Genetic Diagnosis ◽  
Bloodstream Infections ◽  
High Specificity ◽  
Peptide Sequence ◽  
High Morbidity ◽  
Specificity And Sensitivity ◽  
Prospective Application ◽  
Small Molecule Therapeutics

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

Effect of polymerization degree of oligogalacturonates and D-galacturonans on their circular dichroic spectra

1979 ◽  
Vol 44 (1) ◽  
pp. 167-173 ◽  
Author(s):  
Slavomír Bystrický ◽  
Rudolf Kohn ◽  
Tibor Sticzay
Keyword(s):  
Physicochemical Properties ◽  
Aqueous Solutions ◽  
Helical Structure ◽  
Monomeric Unit ◽  
Polymerization Degree ◽  
Cd Spectra ◽  
Circular Dichroic

The CD spectra of aqueous solutions of homopolymeric sodium oligogalacturonates and D-galacturonans of polymerization degree n = 1-64, as well as lower calcium oligogalacturonates (n = 1-5) were measured. Chiroptic properties were correlated with the polymerization degree in terms of optical superposition of monomeric unit increments. Interpretation of obtained data, respecting further physicochemical properties entitles to conclude that the conformation of macromolecules of D-galacturonan in solution is close to helical structure.

scholarly journals CirBiTree: Citrullination Site Inference Based on a Fuzzy Neural Network and Flexible Neural Tree

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Chuandong Song ◽  
Haifeng Wang
Keyword(s):  
Neural Network ◽  
Fuzzy Neural Network ◽  
Classification Model ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Post Translational Modification ◽  
Fuzzy Neural ◽  
Human Complex ◽  
Better Than

Emerging evidence demonstrates that post-translational modification plays an important role in several human complex diseases. Nevertheless, considering the inherent high cost and time consumption of classical and typical in vitro experiments, an increasing attention has been paid to the development of efficient and available computational tools to identify the potential modification sites in the level of protein. In this work, we propose a machine learning-based model called CirBiTree for identification the potential citrullination sites. More specifically, we initially utilize the biprofile Bayesian to extract peptide sequence information. Then, a flexible neural tree and fuzzy neural network are employed as the classification model. Finally, the most available length of identified peptides has been selected in this model. To evaluate the performance of the proposed methods, some state-of-the-art methods have been employed for comparison. The experimental results demonstrate that the proposed method is better than other methods. CirBiTree can achieve 83.07% in sn%, 80.50% in sp, 0.8201 in F1, and 0.6359 in MCC, respectively.

scholarly journals Primary- and secondary-structural analysis of a unique prokaryotic metallothionein from a Synechococcus sp. cyanobacterium

1988 ◽  
Vol 251 (3) ◽  
pp. 691-699 ◽  
Author(s):  
R W Olafson ◽  
W D McCubbin ◽  
C M Kay
Keyword(s):  
Amino Acid ◽  
Metal Binding ◽  
Helical Structure ◽  
Basic Amino Acid ◽  
Cysteine Residues ◽  
Amino Acid Residues ◽  
C Terminus ◽  
Empirical Relations ◽  
Heavy Metal Binding ◽  
Synechococcus Sp

Biochemical and physiological studies of Synechococcus cyanobacteria have indicated the presence of a low-Mr heavy-metal-binding protein with marked similarity to eukaryotic metallothioneins (MTs). We report here the characterization of a Synechococcus prokaryotic MT isolated by gel-permeation and reverse-phase chromatography. The large number of variants of this molecule found during chromatographic separation could not be attributed to the presence of major isoproteins as assessed by amino acid analysis and amino acid sequencing of isoforms. Two of the latter were shown to have identical primary structures that differed substantially from the well-described eukaryotic MTs. In addition to six long-chain aliphatic residues, two aromatic residues were found adjacent to one another near the centre of the molecule, making this the most hydrophobic MT to be described. Other unusual features included a pair of histidine residues located in repeating Gly-His-Thr-Gly sequences near the C-terminus and a complete lack of association of hydroxylated residues with cysteine residues, as is commonly found in eukaryotes. Similarly, aside from a single lysine residue, no basic amino acid residues were found adjacent to cysteine residues in the sequence. Most importantly, sequence alignment analyses with mammalian, invertebrate and fungal MT sequences showed no statistically significant homology aside from the presence of Cys-Xaa-Cys structures common to all MTs. On the other hand, like other MTs, the prokaryotic molecule appears to be free of alpha-helical structure but has a considerable amount of beta-structure, as predicted by both c.d. measurements and the Chou & Fasman empirical relations. Considered together, these data suggested that some similarity between the metal-thiolate clusters of the prokaryote and eukaryote MTs may exist.

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