Comparison on effect of hydrophobicity on the antibacterial and antifungal activities of α-helical antimicrobial peptides

HPRP-A1, a 15-mer α-helical cationic peptide, was derived from N-terminus of ribosomal protein L1 (RpL1) of Helicobacter pylori. In this study, HPRP-A1 was used as a framework to obtain a series of peptide analogs with different hydrophobicity by single amino acid substitutions in the center of nonpolar face of the amphipathic helix in order to systematically study the effect of hydrophobicity on biological activities of -helical antimicrobial peptides. Hydrophobicity and net charge of peptides played key roles in the biological activities of these peptide analogs; HPRP-A1 and peptide analogs with relative higher hydrophobicity exerted broad spectrum antimicrobial activity against Gram-negative bacteria, Gram-positive bacteria and pathogenic fungi, but also showed stronger hemolytic activity; the change of hydrophobicity and net charge of peptides had similar effects with close trend and extent on antibacterial activities and antifungal activities. This indicated that there were certain correlations between the antibacterial mode of action and the antifungal mode of action of these peptides in this study. The peptides exhibited antimicrobial specificity for bacteria and fungi, which provided potentials to develop new antimicrobial drugs for clinical practices.     

Screened peptides from one-bead one-compound technique extend half-life of peptide drugs in circulation through binding to albumin

Peptide drugs are known for their high biological safety. However, compared with small molecule drugs,peptide drugs are easily oxidized and hydrolyzed as well as short in half-life. Herein, inspired by the long circulation of albumin in blood, we screened albumin binding peptides(ABPs) from a one-bead one-compound(OBOC) peptide library to increase the half-life of peptide drugs. Beads displaying random peptides were screened using fluorescent labeled human serum albumin. Fluorescent beads with s...     

Response of peptide intensity to concentration in ESI–MS-based proteome

High-throughput quantification with label-free methods has received considerable attention in electrospray ionization(ESI)-mass spectrometry(MS),but the manner by which MS signals respond to peptide concentration remains unclear in proteomics.We developed a new mathematical formula to describe the intrinsic log-log relationship between the MS intensity response and peptide concentration in an analytical ESI process.Experimental results showed that the calibration curve is fairly fit to the log-log formula with a linear dynamic range of approximate four to five orders of magnitude.However,we found that the ionization of analytical peptides can be severely suppressed by coexisting matrix peptides,such that the calibration curve can be poorly leveled off on both ends.Our study suggests that the interferences from coexisting matrix peptides should be reduced in the ESI process to use the log-log calibration curve successfully for the high-throughput quantification.     

Screening and Identification of a Targeting Peptide to nGLP-1R from Phage Display Peptide Library

<正>In order to provide the structure information for designing new exendin-4 analogues,a phage display peptide library was screened by targeting the N-terminal extracellular domain of GLP-1R(nGLP-1R).After four rounds of selection,nine sequences were obtained,four of them have higher affinity for nGLP-1R than the others.We chose two of them named X and Y peptides.Isletβ-cell proliferation assay suggested that X and Y peptides didn't have any activity to increase isletβ-cell proliferation.In other words,X and Y peptides were not agonists to GLP-1R.However, the conservative motifs of X and Y peptides provided us useful information to design new exendin-4 analogues.     

Polymeric adsorbents with peptide pendants as artificial receptors for β-Mactam antibiotics by mimicking the binding sites of β-lactamases

A scries of polymeric adsorbents with peptide pendants were designed as the artificial receptors of β-laetarn antibiotics by mimicking the structures of binding site in β-lactamases.Crosslinked poly(N,N-dimethyl acry-lamide) gel as a carrier was prepared by suspension copolyrnerization of N,N-dimethyl acrylamide and N,N-bisacryl-diaminoethane and then functionalized with ethylenediamine after partial hydrolysis.Using solid-phase peptide synthesis with symmetrical anhydride of protected amino acid step by step,various peptide pendants were respectively anchored onto the functionalized carrier.The adsorption properties of these peptide-containing adsorbents for β-lactam antibiotics such as ampicillin and cefotaxime were then studied.The results showed that only those adsorbents in which peptide chains contained more than one lysine residues could obviously adsorb both β-lactams and that static interaction as well as hydrogen bond played an important role during the adsorption     

High yield synthesis of cyclic analogues of antibacterial peptides P-113 by Sortase A-mediated ligation and their conformation studies

P-113 is a fragment of natural occurring peptide Histatin 5 found in human saliva. This peptide exhibited broad spectrum of antibacterial and antifungal biological activities. In this study, bifunctional P-113 peptides 2–5 were designed as Sortase A substrates and synthesized by solid support peptide synthesis,where the N-terminus were equipped with glycine and its analogues, and C-terminus were extended with LPETGGS, respectively. Under Sortase A catalyzed condition, head to tail cyclization products 7–10were afforded in yields from 76% to 93%. The conformation insights of linear peptides 2–5 and cyclic analogues 7–10 in aqueous buffers and in trifluroethanol(TFE) analyzed by circular dichroism(CD)suggested that a-helix structures were produced progressively in hydrophobic environment independent of the cyclization, which displayed the similar behavior as parent peptide P-113.     

Isolation and Characterization of an Antimicrobial Polypeptide from Loach

Hydrobionts formed their special defense systems during evolution. One such system is that of non-specific immunity which comprises a wide variety of peptides with potent antimicrobial activities1. The mechanism of action of most antimicrobial peptides was reported as that a few peptide molecules formed a channel on cell membrane, and the cell was then died of the outflowing of cellular contents. The above mechanism was different from that of antibiotics2, 3. It is a promising area to disc…     

A Peptide Binder of E3 Ligase Adaptor SPOP Disrupts Oncogenic SPOP-Protein Interactions in Kidney Cancer Cells

The E3 ligase adaptor SPOP,overexpressed in the nucleus but frequently dislocated into the cytoplasm in all clear cell Renal Cell Carcinomas(ccRCC),serves as a regulatory hub to promote kidney cancer through the ubiquitination and degradation of multiple downstream cancer proteins.Recently,our identification of a selective small-molecule inhibitor of the SPOP-phosphatase and tensin homolog(PTEN)interaction has demonstrated that the oncogenic SPOP-protein interaction would be a druggable target specific to ccRCC therapy.To our knowledge,this is the first time such a small-molecule inhibitor has been developed.Herein,we have identified a peptide binder for the SPOP-MATH domain that disrupts the oncogenic SPOP-protein interactions in kidney cancer cells.Computational design and biophysical characterization yielded peptide Pep38 that binds to the MATH domain of SPOP and competes on PTEN-binding to SPOP in vitro.The X-ray complex structure reveals that the peptide binder features the following combination:one,a mimic of the native peptide binder and two,an additionalβ-strand motif in sequence,which could contribute to increased binding affinity.In order to improve cellular permeability,we fused Pep38 with the delivery peptide TAT to prepare peptide TAT38,which inhibits the endogenous substrate binding to SPOP and suppresses the proliferation of the ccRCC cells.Our identification of the peptide inhibitors for SPOP-protein interactions provides further validation that the oncogenic SPOP-signaling pathway in ccRCC could be a druggable target specifically applicable to the therapy of kidney cancers.     

Supramolecular Chemistry of Peptide Bundles

Amphiphilic octadecapeptides containing 8～9 leucines in the hydrophobic phase wete syn-thesized and shown to self-associate to form α-helical hexamers. The NMR spectra of molecular com-plexes from such peptides and substrate 1 showed that these hexamers exist as a twisted helical bundlecontaining an annular space in its middle.     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

Using an Inhibitor to Prevent Plasticizer Migration from Polyurethane Matrix to EPDM Based Substrate

The loss of adhesion between the propellant and insulator is one of the most important problems in solid propellant motors due to migration of plasticizer to interface of propellant and insulator. In this work, the polyurethane (PU) binder containing DOP plasticizer was used as a polymeric matrix and β-cyclodextrin (β-CD) was applied as inhibitor agent to prevent plasticizer migration from the PU matrix into the ethylene propylene diene monomer (EPDM) substrate. To increase the compatibility of β-CD and PU matrix, a derivative of β-CD has been synthesized using toluene diisocyanate (β-CD-TDI). The synthesized derivative was characterized by MALDI-MS and FTIR-ATR analyses. FTIR-ATR results confirmed the formation of bonding between β-CD and the polymeric network while the MALDIMS results showed that the synthesized derivative contained two β-CD and 7 TDI molecules bonded to β-CD. Investigation of the mechanical properties of PU modified by β-CD-TDI showed a decrease in tensile strength and an increase in elongation at break with increasing β-CD-TDI content. DMTA results showed a decrement in crosslinking density by increasing the β-CD-TDI content. Also, to investigate plasticizer migration, extraction of the DOP plasticizer from samples was performed using dichloromethane solvent and its concentration was measured by gas chromatography. The results of migration evaluation after four months showed that using β-CD as an inhibitor agent in the PU binder could prevent the migration of plasticizer to EPDM substrate.     

STUDIES ON THE PORE FORMATION MECHANISM OF β-CRYSTALLINE POLYPROPYLENE UNDER STRETCHING*

The pore formation mechanism of,β-crystalline polypropylene under stretching was investigated. The porosity of the samples increases rapidly with stretching, having a maximum at draw ratios around 2 and then decreases monotonically. An abrupt formation process of initial micropores at very low draw ratios was evidenced by in situ SAXS measurements. At the same time the phase transition from ,β-crystal to α-crystal proceeds slowly in the whole deformation process up to large draw ratios around 5. Comparative studies of α- and ,β-crystalline polypropylene samples before stretching indicate that in addition to difference in crystal forms the α- and β-crystalline polypropylene samples exhibit quite different morphological features. There are a lot of interfaces in ,β-crystalline polypropylene samples, which may have a lower density value and can be easily etched by argon ions and penetrated by small molecules. It was concluded from these experimental facts that the pore formation and crystal transition are two independent phenomena during the deformation of β-crystalline polypropylene samples, and phase transition from ,β-crystal to α-crystal could hardly be the origin of pore formation. A defect initiation mechanism was proposed to understand the pore formation behavior of β-crystalline polypropylenes.     

Synthesis of β–Amino Acid Derivatives

In recent years, β-amino acids and their derivatives have attracted considerable attention due to their occurrence in biologically active natural products, such as dolastatins, cyclohexylnorstatine and Taxol. β–Amino acids also find application in the synthesis of β–lactams, piperidines, indolizidines. Moreover, the peptides consisting of β–amino acids, the so-called β–peptides, have been extensively studied recently. Consequently, considerable efforts have been directed to the synthe…     

Isolation and identification of phosphorylated lysine peptides by retention time difference combining dimethyl labeling strategy

Protein phosphorylation plays essential roles in various biological procedures. Despite the well-established enrichment strategies for O-phosphoproteomics, the intrinsic acid lability of N–P phosphoramidate bond(phosphorylation of histidine, arginine and lysine) has impaired the progress of N-phosphoproteomics. Herein, we reported a retention time difference combining dimethyl labeling(ReDD) strategy for the isolation and identification of phosphorylated lysine(pLys) peptides. By such a method, pLys peptide could be isolated under 100000-fold interference of non-phosphorylated peptides. Furthermore, ReDD strategy was applied to map pLys sites from E. coli samples, leading to the identification of 11 pLys sites, among which K26p that originating from autonomous glycyl radical cofactor was validated both in mass spectrometry and HPLC co-elution experiments. Furthermore, 112 pLys sites from 100 proteins were identified in HeLa cells. All these results demonstrate that ReDD could provide a first glimpse into Lys phosphorylation, and could be an important step toward the global perspective on protein phosphorylation.     

Computer simulation on kinetics of primary process in photosynthesis of algae (V) --Excitation energy transfer in phycoerythrocyanins

Excitation energy transfer in phycoerythrocyanins (PEC) was studied by use of computer simulation. The results observed from the simulation are as follows: (i) The α84 is a more efficient sensitizing chromophore than β155 and donates the excitation energy into β84 and β155 while it scarcely emits fluorescence itself, (ii) Only the 1α84 →2β84 is the sub-picosecond process in a PEC trimer, therefore it is readily to obtain the time constant from fs-level time-resolved spectral measurement. (iii) The β84 and β155 chromophores in PEC behave quite differently from those in C-PC because of the changes in α84. It is observed that 1β156→6β155 is the dominant pathway linking two trimers and both of the chromophores possess much higher fluorescence fractions, and about 80% of the total fluorescence is emitted from the β84 chromophore. (iv) A far less mean number of transfer times is observed through the fast-transfer pairs in PEC compared with that in C-PC because of slow transfer rate for the path     

Aβ-binding molecules: Possible application as imaging probes and as anti-aggregation agents

As amyloid β (Aβ) is at the centre of pathogenesis of Alzheimer's disease (AD), Aβ aggregate-specific probes for in vivo studies of Aβ are potentially important for the early diagnosis and the assessment of new treatment strategies in the AD brain by noninvasive imaging. Several series of compounds derived from Congo red (CR) and Thioflavin T (ThT) have been evaluated as potential probes for the Aβ imaging. They include a diversity of core structures contributing to their affinities to Aβ. Small-molecule inhibi- tors were known to inhibit the formation of Aβ oligomers and fibrils. This inhibition has to be performed in such a way that these inhibitors bind to Aβ in the binding channel where Aβ-binding probes should sit. Therefore, several of them were used as novel core structures to develop Aβ probes, with their de- rivatives exhibiting good Aβ affinities. This approach will facilitate the design of a variety of candidates for Aβ probe molecules and anti-aggregation-therapeutic drugs. Moreover, the finding of Aβ probes with diverse core structures recognized by binding sites on Aβs will likely provide a promising per- spective for the design of 99mTc-labeled probe-derived molecules.     

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.     

具有咖啡酰基和没食子酰基的β-二酮酸及喹噁啉酮类HIV整合酶抑制剂的设计合成及其对Cu2+的选择性识别

An efficient procedure for the synthesis of caffeoyl-and galloyl-containing β-diketoacid derivatives linked byarylamide was reported by,in the key step,dissolving the corresponding phenyl methyl ketone in THF/DME in thepresence of NaOMe as base and dimethyl oxalate as oxalylation reagent,and then separating the sodium ketoe-nolate ester.The resulting β-diketoacids underwent further condensation reaction with o-phenylenediamine to gen-erate quinoxalone derivatives in good yield,rather than 2-benzimidazol.The preliminary ion binding properties ofquinoxalone derivatives were also investigated.UV-Vis spectra showed that these compounds could selectively rec-ognize Cu~(2 )ion in ethanol and form a 1∶2 complex.     

Analysis of Peptide Ligand Binding to FGFR1

Simulating annealing algorithm was used in docking computation to predict a selected peptide VYMSPF(P2) binding site on the ectodomain of FGFR1.The peptide is located on the hydrophobic surface of the receptor,which is critical for FGF binding.The synthesized peptide can effectively inhibit the mitogenic activity of afGF,and has a potential to become a therapeutic agent as an aFGF antagonist.     

Using PVP/SDS Complex as a Probe to Study the Inclusion Complex of β-cyclodextrin with SDS in Aqueous Solution

PVP/SDS complex was applied as a probe to study the interaction between β-cyclodextrin （β-CD） and sodium dodecyl sulfate （SDS） in aqueous solution. It has been found that a critical concentration, namely cs, exists in the relative viscosity of solution containing PVP/SDS complex versus β-CD concentration plot. As the β-CD concentration is less than cs, the relative viscosity of solution decreases sharply by adding β-CD into solution successively. On the other hand, as the β-CD concentration is greater than cs, the relative viscosity of solution increases gradually by adding β-CD into solution. The decrease of the relative viscosity of solution containing PVP/SDS in the presence of β-CD is just due to the inclusion complex of β-CD with the guest molecule SDS. And, this inclusion interaction takes down SDS from the PVP chains in solution. The ratio of the host molecule β-CD to the guest molecule SDS can be calculated from Cs. In our experiment the inclusion ratio of β-CD to SDS is 1/1. The further experimental results indicate that cs is associated with SDS but free from PVP in PVP/SDS complex. However, the inclusion ratio of β-CD to SDS has proved to be independent of either SDS or PVP in PVP/SDS complex.