Self Assembly of Short Aromatic Peptides into Amyloid Fibrils and Related Nanostructures

The formation of amyloid fibrils is the hallmark of more than twenty human disorders of unrelated etiology. In all these cases, ordered fibrillar protein assemblies with a diameter of 7–10 nm are being observed. In spite of the great clinical important of amyloidassociated diseases, the molecular recognition and self-assembly processes that lead to the formation of the fibrils are not fully understood. One direction to decipher the mechanism of amyloid formation is the use of short peptides fragments as model systems. Short peptide fragments, as short as pentapeptides, were shown to form typical amyloid assemblies in vitro that have ultrastructural, biophysical, and cytotoxic properties, as those of assemblies that are being formed by full length polypeptides. When we analyzed such short fragments, we identified the central role of aromatic moieties in the ability to aggregate into ordered nano-fibrillar structures. This notion allowed us to discover additional very short amyloidogenic peptides as well as other aromatic peptide motifs, which can form various assemblies at the nano-scale (including nanotubes, nanospheres, and macroscopic hydrogels with nano-scale order). Other practical utilization of this concept, together with novel β breakage methods, is their use for the development of novel classes of amyloid formation inhibitors.Key Words: Alzheimer''s disease, amyloid disease, molecular recognition, nanostructures, protein aggregation, protein misfolding, self-assembly, type II diabetes     

Self Assembly of Short Aromatic Peptides into Amyloid Fibrils and Related Nanostructures

The formation of amyloid fibrils is the hallmark of more than twenty human disorders of unrelated etiology. In all these cases, ordered fibrillar protein assemblies with a diameter of 7-10 nm are being observed. In spite of the great clinical important of amyloid-associated diseases, the molecular recognition and self-assembly processes that lead to the formation of the fibrils are not fully understood. One direction to decipher the mechanism of amyloid formation is the use of short peptides fragments as model systems. Short peptide fragments, as short as pentapeptides, were shown to form typical amyloid assemblies in vitro that have ultrastructural, biophysical, and cytotoxic properties, as those of assemblies that are being formed by full length polypeptides. When we analyzed such short fragments, we identified the central role of aromatic moieties in the ability to aggregate into ordered nano-fibrillar structures. This notion allowed us to discover additional very short amyloidogenic peptides as well as other aromatic peptide motifs, which can form various assemblies at the nano-scale (including nanotubes, nanospheres, and macroscopic hydrogels with nano-scale order). Other practical utilization of this concept, together with novel β-breakage methods, is their use for the development of novel classes of amyloid formation inhibitors.     

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.     

RINQ: Reference-based Indexing for Network Queries

We consider the problem of similarity queries in biological network databases. Given a database of networks, similarity query returns all the database networks whose similarity (i.e. alignment score) to a given query network is at least a specified similarity cutoff value. Alignment of two networks is a very costly operation, which makes exhaustive comparison of all the database networks with a query impractical. To tackle this problem, we develop a novel indexing method, named RINQ (Reference-based Indexing for Biological Network Queries). Our method uses a set of reference networks to eliminate a large portion of the database quickly for each query. A reference network is a small biological network. We precompute and store the alignments of all the references with all the database networks. When our database is queried, we align the query network with all the reference networks. Using these alignments, we calculate a lower bound and an approximate upper bound to the alignment score of each database network with the query network. With the help of upper and lower bounds, we eliminate the majority of the database networks without aligning them to the query network. We also quickly identify a small portion of these as guaranteed to be similar to the query. We perform pairwise alignment only for the remaining networks. We also propose a supervised method to pick references that have a large chance of filtering the unpromising database networks. Extensive experimental evaluation suggests that (i) our method reduced the running time of a single query on a database of around 300 networks from over 2 days to only 8 h; (ii) our method outperformed the state of the art method Closure Tree and SAGA by a factor of three or more; and (iii) our method successfully identified statistically and biologically significant relationships across networks and organisms.     

G-specific RNA-cleaving Conjugates of Short Peptides and Oligodeoxyribonucleotides

Abstract

Artificial ribonucleases, conjugates of short oligodeoxyribonucleotides and peptides built of arginine, leucine, proline, and serine, were synthesized and assessed in terms of ribonuclease activity and specificity of RNA cleavage. A specific group of the conjugates was identified that display T1-ribonuclease-like activity and cleave RNA predominantly at G-X sequences. Circular dichroism study of the structures of the most active conjugates, free peptide (LR)4G, and oligonucleotides revealed that conjugation of oligonucleotide to the peptide results in a specific peptide folding that possibly provides ribonuclease activity to the conjugate.     

Designer Amphiphilic Short Peptides Enhance Thermal Stability of Isolated Photosystem-I

Stability of membrane protein is crucial during protein purification and crystallization as well as in the fabrication of protein-based devices. Several recent studies have examined how various surfactants can stabilize membrane proteins out of their native membrane environment. However, there is still no single surfactant that can be universally employed for all membrane proteins. Because of the lack of knowledge on the interaction between surfactants and membrane proteins, the choice of a surfactant for a specific membrane protein remains purely empirical. Here we report that a group of short amphiphilic peptides improve the thermal stability of the multi-domain protein complex photosystem-I (PS-I) in aqueous solution and that the peptide surfactants have obvious advantages over other commonly used alkyl chain based surfactants. Of all the short peptides studied, Ac-I₅K₂-CONH₂ (I₅K₂) showed the best stabilizing effect by enhancing the melting temperature of PS-I from 48.0°C to 53.0°C at concentration of 0.65 mM and extending the half life of isolated PS-I significantly. AFM experiments showed that PS-I/I₅K₂/Triton X-100 formed large and stable vesicles and thus provide interfacial environment mimicking that of native membranes, which may partly explain why I₅K₂ enhanced the thermal stability of PS-I. Hydrophobic and hydrophilic group length of I_xK_y had an important influence on the stabilization of PS-I. Our results showed that longer hydrophobic group was more effective in stabilizing PS-I. These simple short peptides therefore exhibit significant potential for applications in membrane protein studies.     

Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.     

Reference-based pricing: Will other provinces follow the BC lead?

REFERENCE-BASED PRICING has had a major impact on medical practice in British Columbia. Anne Mullens discusses the new system''s first 2 years. She says physicians outside BC should pay attention, because RBP may be heading their way. It is set to land in Australia next month.     

Synthesis of Quantum Dots Labeled Short Peptides and Imaging the T cell Surface Receptors with QDs-Labeled Peptides

Semiconductor quantum dots have been used for labeling many biomacromolecules and small molecules, but it remains a challenge to couple it with short active peptides that play critical roles in many physiological processes. Several binding methods for QDs and short peptides have been reported, but all with some limitations in amino acid sequence. In this paper, we report a method for synthesis of quantum dots labeled short peptides that is appropriate to any short peptide. The quantum dots (CdTe)-labeled short peptides were verified and characterized by RP-HPLC. The QDs-labeled peptides were applied to monitor the specific binding between two immune peptides and T cell surface receptors. The quantum dots-labeled immune peptides provide a powerful method for studying immunological functions of these peptides, and an effective strategy for monitoring their complex modulating processes in vivo.     

Inhibition of Plant-Pathogenic Bacteria by Short Synthetic Cecropin A-Melittin Hybrid Peptides

Short peptides of 11 residues were synthesized and tested against the economically important plant pathogenic bacteria Erwinia amylovora, Pseudomonas syringae, and Xanthomonas vesicatoria and compared to the previously described peptide Pep3 (WKLFKKILKVL-NH₂). The antimicrobial activity of Pep3 and 22 analogues was evaluated in terms of the MIC and the 50% effective dose (ED₅₀) for growth. Peptide cytotoxicity against human red blood cells and peptide stability toward protease degradation were also determined. Pep3 and several analogues inhibited growth of the three pathogens and had a bactericidal effect at low micromolar concentrations (ED₅₀ of 1.3 to 7.3 μM). One of the analogues consisting of a replacement of both Trp and Val with Lys and Phe, respectively, resulted in a peptide with improved bactericidal activity and minimized cytotoxicity and susceptibility to protease degradation compared to Pep3. The best analogues can be considered as potential lead compounds for the development of new antimicrobial agents for use in plant protection either as components of pesticides or expressed in transgenic plants.     

Small Signaling Peptides in Arabidopsis Development: How Cells Communicate Over a Short Distance

To sustain plants’ postembryonic growth and development in a structure of cells fixed in cell walls, a tightly controlled short distance cell–cell communication is required. The focus on phytohormones, such as auxin, has historically overshadowed the importance of small peptide signals, but it is becoming clear that secreted peptide signals are important in cell–cell communication to coordinate and integrate cellular functions. However, of the more than 1000 potential secreted peptides, so far only very few have been functionally characterized or matched to a receptor. Here, we will describe our current knowledge on how small peptide signals can be identified, how they are modified and processed, which roles they play in Arabidopsis thaliana development, and through which receptors they act.     

Unconventional secretion: a stress on GRASP

Most proteins follow the classical secretory pathway from the endoplasmic reticulum, via the Golgi, to the plasma membrane or extracellular medium. However, some proteins reach these final destinations by two alternative routes. One sustains the extracellular delivery of cytoplasmic proteins that lack a signal peptide, the other supports the transport of transmembrane proteins to the plasma membrane in a manner that bypasses the Golgi. Here, we highlight the observation that some unconventional secretion events are triggered by cellular stress. Furthermore, one Golgi protein, Golgi Re-Assembly and Stacking Protein (GRASP), has been shown to be essential to both types of unconventional secretion and we discuss ways in which it may support these events in a Golgi-independent manner.     

Efficient Cargo Delivery into Adult Brain Tissue Using Short Cell-Penetrating Peptides

Zebrafish brains can regenerate lost neurons upon neurogenic activity of the radial glial progenitor cells (RGCs) that reside at the ventricular region. Understanding the molecular events underlying this ability is of great interest for translational studies of regenerative medicine. Therefore, functional analyses of gene function in RGCs and neurons are essential. Using cerebroventricular microinjection (CVMI), RGCs can be targeted efficiently but the penetration capacity of the injected molecules reduces dramatically in deeper parts of the brain tissue, such as the parenchymal regions that contain the neurons. In this report, we tested the penetration efficiency of five known cell-penetrating peptides (CPPs) and identified two– polyR and Trans – that efficiently penetrate the brain tissue without overt toxicity in a dose-dependent manner as determined by TUNEL staining and L-Plastin immunohistochemistry. We also found that polyR peptide can help carry plasmid DNA several cell diameters into the brain tissue after a series of coupling reactions using DBCO-PEG4-maleimide-based Michael’s addition and azide-mediated copper-free click reaction. Combined with the advantages of CVMI, such as rapidness, reproducibility, and ability to be used in adult animals, CPPs improve the applicability of the CVMI technique to deeper parts of the central nervous system tissues.     

Fibrous Aggregates of Short Peptides Containing Two Distinct Aromatic Amino Acid Residues

The aim of the study was the assessment of the ability of short peptides to form aggregates under physiological conditions. The dipeptides studied were derived from different aromatic amino acids (heteroaromatic peptides). Tripeptides were obtained from two distinct aromatic amino acids and cysteine or methionine residue in the C‐terminal, N‐terminal, or central position. The ability of the peptides to form fibrous aggregates under physiological conditions was evaluated using three independent methods: the Congo Red assay, the Thioflavin T assay, and microscopic examinations using normal and polarized light. Materials potentially useful for regenerative medicine were selected based on their cytotoxicity to the endothelial cell line EA.hy 926 and physicochemical properties of films formed by peptides. The required parameters of biocompatibility were fulfilled by H?PheCysTrp?OH, H?PheCysTyr?OH, H?PheTyrMet?OH, and H?TrpTyr?OH.     

Short Oxoproline-Containing Peptides as Potential Pharmacological Means of Hypolipidemic and Antithrombotic Actions

The search and research of pharmacological agents that could combine lipid-lowering and antithrombotic effects on the human organism are one of the most urgent and important tasks of modern biological and medical research. The unique effects of the regulatory peptides of the oxoproline series (5-охо-Pro- His-Pro-NH₂, 5-oxo-Pro-Trp-Pro, and 5-oxo-Pro-Arg-Pro or Pyr-His-Pro-NH₂, Pyr-Trp-Pro, and Pyr- Arg-Pro) synthesized by the methods of classical peptide chemistry have been found in animals with experimental hypercholesterolemia. Repeated intranasal administration of these peptides to animals with developed hypercholesterolemia increased their anticoagulant, fibrinolytic and antiplatelet potential of the blood and simultaneously lowered increased concentrations of total cholesterol, low-density lipoprotein cholesterol, and triglycerides. In addition, they promoted normalization of blood glucose. A week after the last administration of these peptides, the hypocholesterolemic, normoglycemic and anticoagulant effects persisted. The relationship between the structure of the oxoproline-containing peptides and their functional properties is discussed. It is concluded that further studies of oxoproline-containing peptides are promising in the context of development of pharmacological agents, combining the antithrombotic activity with the improvement of lipid metabolism in the body.     

Improved eIF4E Binding Peptides by Phage Display Guided Design: Plasticity of Interacting Surfaces Yield Collective Effects

Eukaryotic initiation factor (eIF)4E is over-expressed in many types of cancer such as breast, head and neck, and lung. A consequence of increased levels of eIF4E is the preferential translation of pro-tumorigenic proteins (e.g. c-Myc and vascular endothelial growth factor) and as a result is regarded as a potential therapeutic target. In this work a novel phage display peptide has been isolated against eIF4E. From the phage sequence two amino acids were delineated which improved binding when substituted into the eIF4G1 sequence. Neither of these substitutions were involved in direct interactions with eIF4E and acted either via optimization of the helical capping motif or restricting the conformational flexibility of the peptide. In contrast, substitutions of the remaining phage derived amino acids into the eIF4G1 sequence disrupted binding of the peptide to eIF4E. Interestingly when some of these disruptive substitutions were combined with key mutations from the phage peptide, they lead to improved affinities. Atomistic computer simulations revealed that the phage and the eIF4G1 derivative peptide sequences differ subtly in their interaction sites on eIF4E. This raises the issue, especially in the context of planar interaction sites such as those exhibited by eIF4E, that given the intricate plasticity of protein surfaces, the construction of structure-activity relationships should account for the possibility of significant movement in the spatial positioning of the peptide binding interface, including significant librational motions of the peptide.