Results for peptides  
Title: Membrane mediated regulation in free peptides of HIV-1 gp41: minimal modulation of the hemifusion phase.
Abstract:
Membrane-mediated structural modulation in two short fragments of the human HIV-1 envelope protein gp41 is demonstrated. Derived from the C-terminal membrane proximal external (MPE) and N-terminal fusion peptide proximal (FPP) regions, these peptides are widely separated in the primary sequence but form tertiary contacts during the intermediate (hemifusion) phase of HIV infection. The structural perturbations observed at the membrane interface offer evidence of rudimentary regulatory mechanisms operating in the free peptides which may be relevant in the biological system. No such regulatory phenomena were observed for the individual peptides in a membrane environment or between the peptides in aqueous solutions. Structure determination is made using a combination of circular and linear dichroism spectroscopy (supported by calorimetric measurements) and molecular dynamics simulations. Specifically, we show that these peptides interact locally without the conformational support of helical heptad repeat regions in native gp41 and that the modulation is not mutual with the FPP peptide operating as a primary regulator of the MPE-FPP interactions in the hemifusion phase.

Sources: PubMed
Keywords: human immunodeficiency virus,simulation, membranes, molecular dynamics,peptides,protein folding,
Title: Design, synthesis, and pharmacological characterization of fluorescent peptides for imaging human V1b vasopressin or oxytocin receptors.
Abstract:
Among the four known vasopressin and oxytocin receptors, the specific localization of the V1b isoform is poorly described because of the lack of selective pharmacological tools. In an attempt to address this need, we decided to design, synthesize, and characterize fluorescent selective V1b analogues. Starting with the selective V1b agonist [deamino-Cys(1),Leu(4),Lys(8)]vasopressin (d[Leu(4),Lys(8)]VP) synthesized earlier, we added blue, green, or red fluorophores to the lysine residue at position 8 either directly or by the use of linkers of different lengths. Among the nine analogues synthesized, two exhibited very promising properties. These are d[Leu(4),Lys(Alexa 647)(8)]VP (3) and d[Leu(4),Lys(11-aminoundecanoyl-Alexa 647)(8)]VP (9). They remained full V1b agonists with nanomolar affinity and specifically decorated the plasma membrane of CHO cells stably transfected with the human V1b receptor. These new selective fluorescent peptides will allow the cellular localization of V1b or OT receptor isoforms in native tissues.

Sources: PubMed
Keywords: receptors,peptides,
Title: Pretreatment of low-abundance peptides on detonation nanodiamond for direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Abstract:
Detonation nanodiamond (dND) was firstly employed as adsorbent for pretreatment of peptides in dilute/contaminated sample solution. Detonation nanodiamond showed high efficiency for isolating and enriching peptides in a wide pH range. Remarkably, good tolerance capability toward salts and detergents could be achieved by using dNDs. Due to the inherent specificities of dNDs, dND-bound peptides could be directly analyzed by MALDI-TOF MS, so as to avoid the elution step and reduce sample loss. This pretreatment method also exhibited a better performance for protein identification compared to solvent evaporation and Ziptip pretreatment approach.

Sources: PubMed
Keywords:  adsorption, mass spectrometry,hydrogen,peptides,
Title: Sequence specific association of tryptic peptides with multiwalled carbon nanotubes: effect of localization of hydrophobic residues.
Abstract:
A model-free approach has been used to study the association of peptides onto multiwalled carbon nanotubes (MWCNT) in aqueous solution at ambient pH to understand the molecular basis of interaction of the peptides with MWCNT. The peptides obtained by tryptic digestion of cytochrome P450cam from P. putida were allowed to interact with MWCNT, and several peptides were found to bind to the nanotube leading to formation of stable homogeneous dispersion of the bionano conjugates of MWCNT. The peptides bound to the MWCNT were separated from the unbound peptides and sequence analyses by tandem MS/MS technique identified the strongly bound peptides as well as the unbound and the weakly bound peptides. The peptide-MWCNT conjugate was further characterized by TEM as well as Raman, FTIR, vis-NIR absorption, and circular dichroism spectroscopy. A model based on the hydrophobicity of residues in the peptides suggested that the amphiphilic peptides with localized hydrophobic residues at the center or at one end of the sequence form stable dispersions of the peptide-MWCNT conjugates.

Sources: PubMed
Keywords: nanotubes,peptides,
Title: Phage display selection of peptides that home to atherosclerotic plaques: IL-4 receptor as a candidate target in atherosclerosis.
Abstract:
Imaging or drug delivery tools for atherosclerosis based on the plaque biology are still insufficient. Here, we attempted to identify peptides that selectively home to atherosclerotic plaques using phage display. A phage library containing random peptides was ex vivo screened for binding to human atheroma tissues. After three to four rounds of selection, the DNA inserts of phage clones wer sequenced. A peptide sequence, CRKRLDRNC, was the most frequently occurring one. Intravenously injected phage displaying the CRKRLDRNC peptide was observed to home to atherosclerotic aortic tissues of low-density lipoprotein receptor-deficient (Ldlr-/-) mice at higher levels than to normal aortic tissues of wild-type mice. Moreover, a fluorescein- or radioisotope-conjugated synthetic CRKRLDRNC peptide, but not a control peptide, homed in vivo to atherosclerotic plaques in Ldlr(-/-) mice, while homing of the peptide to other organs such as brain was minimal. The homing peptide co-localized with endothelial cells, macrophages and smooth muscle cells a mouse and human atherosclerotic plaques. Homology search revealed that the CRKRLDRNC peptide shares a motif of interleukin-receptor (IL-4) that is critical for binding to its receptor. The peptide indeed co-localized with IL-4 receptor (IL-4R) at atherosclerotic plaques. Moreover, the peptide bound to cultured cells expressing IL-4R on the cell surface and the binding was inhibited by the knock-down of IL-4R. These results show that the CRKRLDRNC peptide homes to atherosclerotic plaques through binding to IL-4R as its target and may be a useful tool for selective drug delivery and molecular imaging of atherosclerosis.

Sources: PubMed
Keywords: receptors,dna,peptides,phage display,
Title: Oxetanyl peptides: novel peptidomimetic modules for medicinal chemistry.
Abstract:
The synthesis of novel oxetanyl peptides, where the amide bond is replaced by a non-hydrolyzable oxetanylamine fragment, is reported. This new class of pseudo-dipeptides with the same H-bond donor/acceptor pattern found in proteins expands the repertoire of peptidomimetics.

Sources: PubMed
Keywords:  medicinal chemistry,peptides,peptidomimetics,proteins,
Title: Fighting microbial infections: A lesson from amphibian skin-derived esculentin-1 peptides.
Abstract:
Due to the growing emergence of resistance to commercially available antibiotics/antimycotics in virtually all clinical microbial pathogens, the discovery of alternative anti-infective agents, is greatly needed. Gene-encoded antimicrobial peptides (AMPs) hold promise as novel therapeutics. In particular, amphibian skin is one of the richest storehouses of AMPs, especially that of the genus Rana, with esculentins-1 being among the longest (46 amino acids) AMPs found in nature to date. Here, we report on the recently discovered in vitro and in vivo activities and mechanism of action of two derivatives of the N-terminal part of esculentin-1a and -1b peptides, primarily against two relevant opportunistic microorganisms causing a large number of life-threatening infections worldwide; i.e. the Gram-negative bacterium Pseudomonas aeruginosa and the yeast Candida albicans. Because of distinct advantages compared to several mammalian AMPs, the two selected frog skin AMP-derivatives represent attractive candidates for the development of new antimicrobial compounds with expanded properties, for both human and veterinary medicine.

Sources: PubMed
Keywords: amino acids,antibiotics,peptides,
Title: Diagnostic value of soluble mesothelin-related peptides for malignant mesothelioma: a meta-analysis.
Abstract:
Serum concentrations of soluble mesothelin-related peptides (SMRP) have been reported to be higher in patients with malignant mesothelioma than in healthy subjects and in patients with non-malignant mesothelioma diseases. The aim of the present meta-analysis was to establish the overall diagnostic accuracy of the measurement of SMRPs for diagnosing malignant mesothelioma.

Sources: PubMed
Keywords: glycoproteins,peptides,
Title: Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome.
Abstract:
To study positioning of the polypeptide release factor eRF1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mRNA analogs, derivatives of oligoribonucleotides. The human eRF1 peptides cross-linked to these short mRNAs were identified. Cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the "YxCxxxF loop") in the N domain. Hence, both regions are involved in the recognition of the purines. A cross-linker at the first uridine of the stop codon modifies Val66 near the NIKS loop (positions 61-64), and this region is important for recognition of the first uridine of stop codons. Since the N domain distinct regions of eRF1 are involved in a stop-codon decoding, the eRF1 decoding site is discontinuous and is not of "protein anticodon" type. By molecular modeling, the eRF1 molecule can be fitted to the A site proximal to the P-site-bound tRNA and to a stop codon in mRNA via a large conformational change to one of its three domains. In the simulated eRF1 conformation, the YxCxxxF motif and positions 31-33 are very close to a stop codon, which becomes also proximal to several parts of the C domain. Thus, in the A-site-bound state, the eRF1 conformation significantly differs from those in crystals and solution. The model suggested for eRF1 conformation in the ribosomal A site and cross-linking data are compatible.

Sources: PubMed
Keywords: amino acids,rna, molecular modeling,mrna,mutagenesis,peptides,proteins,
Title: Arginine-rich peptides destabilize the plasma membrane, consistent with a pore formation translocation mechanism of cell penetrating peptides
Abstract:
Recent molecular dynamics simulations (Herce and Garcia, PNAS, 104: 20805 (2007)) have suggested that the arginine-rich HIV Tat peptides might be able to translocate by destabilizing and inducing transient pores in phospholipid bilayers. In this pathway for peptide translocation, arginine residues play a fundamental role not only in the binding of the peptide to the surface of the membrane but also in the destabilization and nucleation of transient pores across the bilayer, despite being charged and highly hydrophilic. Here we present a molecular dynamics simulation of a peptide composed of nine arginines (Arg-9) that shows that this peptide follows the same translocation pathway previously found for the Tat peptide. We test this hypothesis experimentally by measuring ionic currents across phospholipid bilayers and cell membranes through the pores induced by Arg-9 peptides. We find that Arg-9 peptides, in the presence of an electrostatic potential gradient, induce ionic currents across planar phospholipid bilayers, as well as in cultured osteosarcoma cells and human smooth muscle cells freshly isolated from the umbilical artery. Our results suggest that the mechanism of action of Arg-9 peptide involves the creation of transient pores in lipid bilayers and cell membranes.

Sources: Arxivs
Keywords: lipids,biophysics,membranes,artery,peptide nucleic acids,peptides,phospholipids,peptide hormone,peptide mucolytics,
Title: Trypanosoma cruzi: synergistic cytotoxicity of multiple amphipathic anti-microbial peptides to T. cruzi and potential bacterial hosts.
Abstract:
The parasite Trypanasoma cruzi is responsible for Chagas disease and its triatomine vector, Rhodnius prolixus, has a symbiotic relationship with the soil bacterium, Rhodococcus rhodnii. R. rhodnii that was previously genetically engineered to produce the anti-microbial peptide, cecropin A was co-infected with T. cruzi into R. prolixus resulting in clearance of the infectious T. cruzi in 65% of the vectors. Similar anti-microbial peptides have been isolated elsewhere and were studied for differential toxicity against T. cruzi and R. rhodnii. Of the six anti-microbial peptides tested, apidaecin, magainin II, melittin, and cecropin A were deemed potential candidates for the Chagas paratransgenic system as they were capable of killing T.cruzi at concentrations that exhibit little or no toxic effects on R. rhodnii. Subsequent treatments of T. cruzi with these peptides in pair-wise combinations resulted in synergistic killing, indicating that improvement of the 65% parasite clearance seen in previous experiments may be possible utilizing combinations of different anti-microbial peptides.

Sources: PubMed
Keywords: cytotoxicity,chagas disease,peptides,proteins,
Title: Antimicrobial properties and interaction of two Trp-substituted cationic antimicrobial peptides with a lipid bilayer.
Abstract:
Tryptophan (Trp) residues reportedly exhibit a strong membrane-disruptive activity, and this property endows Trp-containing antimicrobial peptides (AMPs) with a unique ability to interact with the surface of bacterial cell membranes, possibly improving antimicrobial properties. In this study, we investigated the influence of Trp residues engineered to have a distinct preference for the interface region of lipid bilayers on antimicrobial activity. We designed two Trp-substituted AMPs (I1WL5W and I4WL5W) by replacing Ile or Leu residues with two Trp residues at different positions in the L-K6 peptide, and determined their antimicrobial activity and mechanism of membrane action. Both I1WL5W and I4WL5W exhibited significantly higher antimicrobial activity and lower cytotoxicity against Gram-negative and Gram-positive bacteria compared with L-K6. The Trp-substituted peptides had a disordered structure in aqueous solution and adopted an α-helical structure in solutions of 50% trifluoroethanol/water and 30 mM SDS. I1WL5W and I4WL5W caused a significant leakage of calcein from liposomes containing membranes that mimicked those of Escherichia coli and Staphylococcus aureus. Scanning electron microscopy analysis suggested that I1WL5W and I4WL5W killed bacteria by disrupting bacterial cell membranes. Furthermore, fluorescence and quenching data from a variety of liposomes, which mimic different cell membranes, indicated that the Trp-substituted peptides could insert into the lipid bilayers and induce blue shifts in the emission spectra of the Trp residues. I1WL5W and I4WL5W were also less susceptible to acrylamide or KI quenchers. The current work may be important for designing novel Trp-containing peptides exhibiting strong antimicrobial abilities by penetrating bacterial membranes.

Sources: PubMed
Keywords:  cytotoxicity,drug discovery, liposomes,electron, membranes,fluorescence,peptides,
Title: Drosophila ALS regulates growth and metabolism through functional interaction with insulin-like peptides.
Abstract:
In metazoans, factors of the insulin family control growth, metabolism, longevity, and fertility in response to environmental cues. In Drosophila, a family of seven insulin-like peptides, called Dilps, activate a common insulin receptor. Some Dilp peptides carry both metabolic and growth functions, raising the possibility that various binding partners specify their functions. Here we identify dALS, the fly ortholog of the vertebrate insulin-like growth factor (IGF)-binding protein acid-labile subunit (ALS), as a Dilp partner that forms a circulating trimeric complex with one molecule of Dilp and one molecule of Imp-L2, an IgG-family molecule distantly related to mammalian IGF-binding proteins (IGFBPs). We further show that dALS antagonizes Dilp function to control animal growth as well as carbohydrate and fat metabolism. These results lead us to propose an evolutionary perspective in which ALS function appeared prior to the separation between metabolic and growth effects that are associated with vertebrate insulin and IGFs.

Sources: PubMed
Keywords:  lead,peptides,
Title: Prediction of linear cationic antimicrobial peptides based on characteristics responsible for their interaction with the membranes
Abstract:
Most available antimicrobial peptides (AMP) prediction methods use common approach for different classes of AMP. Contrary to available approaches, we suggest, that a strategy of prediction should be based on the fact, that there are several kinds of AMP which are vary in mechanisms of action, structure, mode of interaction with membrane etc. According to our suggestion for each kind of AMP a particular approach has to be developed in order to get high efficacy. Consequently in this paper a particular but the biggest class of AMP - linear cationic antimicrobial peptides (LCAP) - has been considered and a newly developed simple method of LCAP prediction described. The aim of this study is the development of a simple method of discrimination of AMP from non-AMP, the efficiency of which will be determined by efficiencies of selected descriptors only and comparison the results of the discrimination procedure with the results obtained by more complicated discriminative methods. As descriptors the physicochemical characteristics responsible for capability of the peptide to interact with an anionic membrane were considered. The following characteristics such as hydrophobicity, amphiphaticity, location of the peptide in relation to membrane, charge, propensity to disordered structure were studied. On the basis of these characteristics a new simple algorithm of prediction is developed and evaluation of efficacies of the characteristics as descriptors performed. The results show that three descriptors: hydrophobic moment, charge and location of the peptide along the membranes can be used as discriminators of LCAPs. For the training set our method gives the same level of accuracy as more complicated machine learning approaches offered as CAMP database service tools. For the test set sensitivity obtained by our method gives even higher value than the one obtained by CAMP prediction tools.

Sources: Arxivs
Keywords: anions,cations,membranes,sensitizers,peptides,
Title: Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis.
Abstract:
Phospho-proteomics relies on methods for efficient purification and sequencing of phosphopeptides from highly complex biological systems using low amounts of starting material. Current methods for phosphopeptide enrichment, e.g., immobilized metal affinity chromatography and titanium dioxide chromatography, provide varying degrees of selectivity and specificity for phosphopeptide enrichment. Furthermore, the number of multiply phosphorylated peptides that are identified in most published studies is rather low. Here the protocol for a new strategy that separates mono-phosphorylated pep-tides from multiply phosphorylated peptides using sequential elution from immobilized metal affinity chromatography is described. The two separate phosphopeptide fractions are subsequently analyzed by mass spectrometric methods optimized for mono-phosphorylated and multiply phosphorylated peptides, respectively, resulting in improved identification of especially multiply phosphorylated peptides from a minimum amount of starting material. The new method increases the coverage of the phosphoproteome significantly.

Sources: PubMed
Keywords: proteomics, mass spectrometry,peptides,
Title: Memory-enhancing effects of silk fibroin-derived peptides in scopolamine-treated mice.
Abstract:
Although enzyme-hydrolyzed silk fibroin has been reported to enhance cognitive function before, it has been still unknown which peptides can improve memory. Here we report that amino acid sequences of three novel peptides were identified from fibroin hydrolysate. Fibroin hydrolysate was obtained by hydrolysis with protease after partial hydrolysis with 5M CaCl2. Synthesized peptides derived from these sequences improved scopolamine-induced memory impairments in mice. We confirmed this hydrolysate had effects that improved learning and memory abilities by performing the Rey-Kim test. From this hydrolysate of silk fibroin, amino acid sequences of eight peptides were identified by LC-MS/MS. Three peptides (GAGAGTGSSGFGPY, GAGAGSGAGSGAGAGSGAGAGY, and SGAGSGAGAGSGAGAGSGA) were synthesized to investigate whether they could improve memory. Passive avoidance test and Morris water maze test were performed, and all peptides showed memory-enhancing abilities on scopolamine-induced memory impairments in mice. In this study, we identified three novel peptides that could improve memory, and that silk fibroin hydrolysate was a mixture of various active peptides that could enhance memory.

Sources: PubMed
Keywords: adverse effects, liquid chromatography, mass spectrometry, metabolism,hydrolases,hydrolysis,peptides,
Title: Designed peptides as model self-assembling nanosystems: characterization and potential biomedical applications.
Abstract:
Synthesis of nanomaterials via 'molecular self-assembly' allows one to define the properties of the nanomaterial by rational design of the individual constituents. Use of peptides for self-assembly offers the ease of design and synthesis, and provides higher biofunctionality and biocompatibility to nanomaterials. Our work focused on the synthesis, characterization and potential biomedical applications of small self-assembled peptide-based nanosystems. We demonstrated that dipeptides containing the conformational restricting residue alpha,beta-dehydrophenylalanine, self-assembled into nanovesicular and nanotubular structures. The nanosystems could encapsulate and release anticancer drugs, showed enhanced stability to proteinase K degradation, a property crucial for them to have a high in vivo half-life, and exhibited no cytotoxicity towards cultured mammalian cells. The dipeptide nanostructures were easily taken up by cells and could evade uptake by reticuloendothelial systems when injected into healthy laboratory animals. Thus, small self-assembling peptides may offer novel scaffolds for the future design of nanostructures with potential applications in the field of drug delivery.

Sources: PubMed
Keywords: cytotoxicity,self-assembly,nanostructures,peptides,
Title: The impact of peptides on lipid membranes.
Abstract:
We review the fundamental strategies used by small peptides to associate with lipid membranes and how the different strategies impact on the structure and dynamics of the lipids. In particular we focus on the binding of amphiphilic peptides by electrostatic and hydrophobic forces, on the anchoring of peptides to the bilayer by acylation and prenylation, and on the incorporation of small peptides that form well-defined channels. The effect of lipid-peptide interactions on the lipids is characterized in terms of lipid acyl-chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation, as well as acyl-chain dynamics. The different situations are illustrated by specific cases for which experimental observations can be interpreted and supplemented by theoretical modeling and simulations. A comparison is made with the effect on lipids of trans-membrane proteins. The various cases are discussed in the context of the possible roles played by lipid-peptide interactions for the biological, physiological, and pharmacological function of peptides.

Sources: PubMed
Keywords:  acylation, lipids, membrane proteins, membranes,peptides,thermodynamics,
Title: Evidence for natriuretic peptides A and B as non-invasive markers in congenital and valvular heart disease.
Abstract:
The aim of this study was to evaluate the diagnostic utility of natriuretic peptides of type A and B as noninvasive markers in the diagnosis and treatment of congenital and valvular heart disease.

Sources: PubMed
Keywords: clinical biochemistry,valvular heart disease (heart valve disease),peptides,
Title: De novo zygotic transcription in wheat (Triticum aestivum L.) includes genes encoding small putative secreted peptides and a protein involved in proteasomal degradation.
Abstract:
Wheat is one of the world's most important crops, and increasing grain yield is a major challenge for the future. Still, our knowledge about the molecular machineries responsible for early post-fertilization events such as zygotic reprogramming, the initial cell-specification events during embryogenesis, and the intercellular communication between the early embryo and the developing endosperm is very limited. Here, we describe the identification of de novo transcribed genes in the wheat zygote. We used wheat ovaries of defined post-fertilization stages to isolate zygotes and early embryos, and identified genes that are specifically induced in these particular stages. Importantly, we observed that some of the zygotic-induced genes encode proteins with similarity to secreted signaling peptides such as TAPETUM DETERMINANT 1 and EGG APPARATUS 1, and to MATH-BTB proteins which are known substrate-binding adaptors for the Cullin3-based ubiquitin E3 ligase. This suggests that both cell-cell signaling and targeted proteasomal degradation may be important molecular events during zygote formation and the progression of early embryogenesis.

Sources: PubMed
Keywords: proteasome, metabolism,peptides,proteins,