Studies of Site Specific DNA Binding of Small Peptides by Competitive Assays with Hoechst 33258

With a view to finding out precisely how small peptides recognize a particular binding site of DNA, we have accomplished DNA binding studies of two peptides, H-Tyr-Arg-OH (YR) and H-Gly-Gly-His-OH (GGH) by using measurements in comparison with the binding between DNA and Hoechst 33258. The inhibition mode by YR and GGH to DNA binding of Hoechst 33258 was analyzed by Lineweaver-Burk plot which shows the plot of typical competitive inhibition at concentration of Hoechst 33258 from 3.66 ( 10-9 mol / L to 1.09 ( 10-8 mol / L. And it is concluded that YR binds to DNA in its minor groove (AT rich regions) with a binding constant K = 1.02 ( 108 (mol / L)-1. The GGH(s specificity is reduced at high concentration because it can also bind GC base pair.

Peptide nucleic acid (PNA) binding-mediated gene regulation

Peptide nucleic acids (PNAs) are synthetic oligonucleotides with chemically modified backbones. PNAs can bind to both DNA and RNA targets in a sequence-specific manner to form PNA/DNA and PNA/RNA duplex structures. When bound to double-stranded DNA (dsDNA) targets, the PNA molecule replaces one DNA strand in the duplex by strand invasion to form a PNA/DNA/PNA [or (PNA)2/DNA] triplex structure and the displaced DNA strand exists as a singlestranded D-loop. PNA has been used in many studies as research tools for gene regulation and gene targeting. The Dloops generated from the PNA binding have also been demonstrated for its potential in initiating transcription and inducing gene expression. PNA provides a powerful tool to study the mechanism of transcription and an innovative strategy to regulate target gene expression. An understanding of the PNA-mediated gene regulation will have important clinical implications in treatment of many human diseases including genetic, cancerous, and age-related diseases.

Cyclic heptapeptides with metal binding properties isolated from the fungus Cadophora malorum from Antarctic soil

The Antarctic fungus Cadophora malorum produces previously undescribed cyclic heptapeptides(cadophorin A and B)containing an anthranilic acid residue.The planar structure of these peptides was determined by high-resolution mass spectrometry combined with extensive 1D and 2D NMR spectroscopy.The absolute configuration of the amino acids was determined by Marfey’s method,with HPLC analysis of FDVA(Nα-(2,4-dinitro-5-fluorphenyl)-l-valinamide)derivatives making use of a PFP column.Remarkably,cadophorin 2 possesses both the uncommon d-Ile and d-allo-Ile in its structure.The peptides have metal binding properties as shown by LCMS with post column addition of metal salt solutions.These results were supported by DFT calculations.

Identifying peptides that specifically bind to MDA-MB-468 breast cancer cells

Objective To use phage display technique to screen for small polypeptides that specifically bind to MDA-MB-468 cells.Methods A random heptapeptide phage display library was used for in vitro screening against target MDA-MB-468 cells.SC1180 cells were used for subtractive selection.High-affinity phage DNA was extracted,and peptides were sequenced.Results(1)The original library capacity of the polypeptide library was 2×10^13 pfu/mL,and phage titer was determined over 4 rounds.The average library capacity was 1.8×10^13 pfu/mL.(2)Subtractive screening showed that the phage library volume of each round was 1.8×10^12 pfu/mL,and that there was an enrichment effect in each subsequent round.Screening was stopped after the fourth round.(3)PCR results showed that the size of 39 products(78.0%)and 11 products(22%),were 300 bp and 258 bp,respectively.Thirty positive phages were selected for DNA extraction and sequencing,and the corresponding amino acid sequence was LMTRXSK.The sequence had no homology with known genes or proteins.Conclusion Using the phage display technique,we identified that the short polypeptide,LMTRXSK,specifically binds MDA-MB-468 human breast cancer cells.

The novel amyloid-beta peptide aptamer inhibits intracellular amyloid-beta peptide toxicity

Amyloid β peptide binding alcohol dehydrogenase （ABAD） decoy peptide （DP） can competitively antagonize binding of amyloid β peptide to ABAD and inhibit the cytotoxic effects of amyloid β peptide. Based on peptide aptamers, the present study inserted ABAD-DP into the disulfide bond of human thioredoxin （TRX） using molecular cloning technique to construct a fusion gene that can express the TRX1-ABAD-DP-TRX2 aptamer. Moreover, adeno-associated virus was used to allow its stable expression. Immunofluorescent staining revealed the co-expression of the transduced fusion gene TRX1-ABAD-DP-TRX2 and amyloid β peptide in NIH-3T3 cells, indicating that the TRXl-ABAD-DP-TRX2 aptamer can bind amyloid β peptide within cells. In addition, cell morphology and MTT results suggested that TRX1-ABAD-DP-TRX2 attenuated amyloid β peptide-induced SH-SY5Y cell injury and improved cell viability. These findings confirmed the possibility of constructing TRX-based peptide aptamer using ABAD-DP. Moreover, TRXl-ABAD-DP-TRX2 inhibited the cytotoxic effect of amyloid β peptide.

The calcium-binding activity of fish scale protein hydrolysates

The calcium-binding activity of tilapia scale protein hydrolysates sequentially hydrolyzed by trypsin, flavor enzyme and pepsin were investigated. The hydrolysates were divided into four fractions using G-15 gel chromatography, and the F3 fraction has the higher calcium-binding activity of 196.3 mg/g. The UV-vis and the Fourier transform infrared spectroscopy (FTIR) demonstrate that the amino nitrogen atoms and the oxygen atoms belonging to the carboxylate groups are the primary binding sites for Ca2+. The X-ray diffraction and scanning electron microscopy (SEM) confirmed the reaction between the peptde and calcium. The results obtained indicated that this fish scale protein hydroly-sates have potential as functional foods for calcium-supplementation.

The Covalent Binding of Genistein to the Non-prosthetic-heme-moiety of Bovine Lactoperoxidase Leads to Enzymatic Inactivation

Objective Genistein, a major soy isoflavone metabolite （SIF）, inactivates oxidation activity of bovine lactoperoxidase （LPO）. Modification of the heme moiety of LPO by nitrogen-containing compounds has been shown to inactivate LPO. In contrast, SIF mediated inactivation of LPO does not involve a heme modification and the mechanism of SIF inhibition is poorly understood. Methods After inactivation of LPO by genistein in the presence of H202, trypsin-digested LPO peptide fragments were collected and analyzed by MALDI-TOF-MS to characterize the chemical binding of genistein（s） to LPO. Results The heme moiety of LPO was not modified by genistein. A covalent binding study showed that 3H-genistein bound to LPO with a ratio of ~12 to 1. After HPLC analysis and peak collection, trypsin-digested peptide fragments were analyzed by MALDI-TOF-MS. The 3H-genistein co-eluted peptide fragments （RT=24 min） were putatively identified as 1991VGYLDEEGVLDQNR214 with two bound genistein molecules or a genistein dimer （2 259 Da）, 486TPDNIDIWlGGNAEPMVER504 with two bound genistein molecules or a genistein dimer （2 663 Da）, and 161ARWLPAEYEDGLALPFGWTQR182 with three bound genistein molecules or a genistein trimer （3 060 Da）. The fragment with a mass of 2 792 Da （RT=36 min） was identified as 132CDENSPYR139 with three genistein molecules or a genistein trimer. Conclusions The results suggest that LPO was inactivated by irreversible covalent binding of genistein or genistein polymers to particular peptide fragments constituting regions of the outward domain. No genistein interaction with the prosthetic heme moiety of LPO was observed.

Metallo-β-Lactamases:A Major Threat to Human Health

Antibiotic resistance is one of the most significant challenges facing global healthcare. Since the 1940s, antibiotics have been used to fight infections, initially with penicillin and subsequently with various derivatives including cephalosporins, carbapenams and monobactams. A common characteristic of these antibiotics is the four-memberedβ-lactam ring. Alarmingly, in recent years an increasing number of bacteria have become resistant to these antibiotics. A major strategy employed by these pathogens is to use Zn(II)-dependent enzymes, the metallo-β-lactamases (MBLs), which hydrolyse theβ-lactam ring. Clinically useful MBL inhibitors are not yet available. Consequently, MBLs remain a major threat to human health. In this review biochemical properties of MBLs are discussed, focusing in particular on the interactions between the enzymes and the functionally essential metal ions. The precise role(s) of these metal ions is still debated and may differ between different MBLs. However, since they are required for catalysis, their binding site may present an alternative target for inhibitor design.

Photo-induced crosslinked and anti-PD-L1 peptide incorporated liposomes to promote PD-L1 multivalent binding for effective immune checkpoint blockade therapy

Immune checkpoint blockade(ICB)therapy targeting PD-L1 via monoclonal antibody(m Ab)has shown extensive clinical benefits in the diverse types of advanced malignancies.However,most patients are completely refractory to ICB therapy owing to the PD-L1 recycling mechanism.Herein,we propose photo-induced crosslinked and anti-PD-L1 peptide incorporated liposomes(immune checkpoint blockade liposomes;ICB-LPs)to promote PD-L1 multivalent binding for inducing lysosomal degradation of PD-L1 in tumor cells.The ICB-LPs are prepared by formulation of DC_(8,9)PC with photo-polymerized diacetylenic moiety,1,2-dipalmitoylphosphatidylcholine(DPPC)and anti-PD-L1peptide(D-form NYSKPTDRQYHF)-conjugated DSPE-PEG_(2k)(anti-PD-L1-DSPE-PEG_(2k))in a molar ratio of 45:45:10,followed by cross-linking of liposomal bilayer upon UV irradiation.The 10 mol% antiPD-L1-DSPE-PEG_(2k)incorporated ICB-LPs have a nano-sized lipid bilayer structure with an average diameter of 137.7±1.04 nm,showing a high stability in serum condition.Importantly,the ICB-LPs efficiently promote the multivalent binding with PD-L1 on the tumor cell membrane,which are endocytosed with aim to deliver PD-L1 to the lysosomes,wherein the durable PD-L1 degradation is observed for72 h,in contrast to anti PD-L1 m Abs showing the rapid PD-L1 recycling within 9 h.The in vitro coculture experiments with CD8^(+)T cells show that ICB-LPs effectively enhance the T cell-mediated antitumor immune responses against tumor cells by blocking the PD-L1/PD-1 axis.When ICB-LPs are intravenously injected into colon tumor-bearing mice,they efficiently accumulate within the targeted tumor tissues via both passive and active tumor targeting,inducing a potent T cell-mediated antitumor immune response by effective and durable PD-L1 degradation.Collectively,this study demonstrates the superior antitumor efficacy of crosslinked and anti-PD-L1 peptide incorporated liposome formulation that promotes PD-L1 multivalent binding for trafficking of PD-L1 toward the lysosomes instead of the recycling endosomes.

Fluorescence Resonance Energy Transfer Competitive Binding Assay for Secretin Receptor （Class B-GPCR）

Human secretin is responsible for carrying a number of physiological functions including energy and water homeostasis, thus making secretin receptor a promising target for drug development. For GPCRs （G protein-coupled receptors）, radioactive ligands are usually used in conventional binding assays to characterize the binding affinities of the ligands. An alternative non-hazardous fluorescence based binding assay is lucrative over the radio-ligand assays. Here, we have developed a FRET （fluorescence resonance energy transfer） competitive binding assay for human secretin receptor. The receptor gene sequence is cloned in the SNAP （single nucleotide amplified polymorphisms） tag-plasmid and expressed in CHO （chinese hamster ovary）-K1 cells. Its expression and function is confirmed with immunofluorescence localization and receptor activation. The receptor and the ligand are labeled with fluorescent donor （Tb） and acceptor （Alexa488）. FRET signals are produced when the labeled ligand is bound to the receptor and the same drop when it is displaced by the test compounds. The saturation concentration of the receptor labeling is 100 nM, and the ligand Kd value is 500 nM. At these concentrations, the IC50 of unlabeled secretin is 1.63 4- 3.55 nM. Additionally, few class-B ligands are screened and hold good correlation with traditional radio-ligand assay. Henceforth, this FRET binding assay can be efficiently used as a primary screening tool for peptide analogs.

Binding characteristics of pancreatic polypeptide receptors on rat hepatic membranes

目的：研究大鼠肝膜胰多肽受体的结合特性．方法：在控制条件下，用１２５Ｉ标记的胰多肽进行胰多肽受体的结合特性研究．结果：制备了适用于进行配体和受体相互作用研究的１２５Ｉ标记的猪胰多肽和鸭胰多肽．１２５Ｉ猪胰多肽与大鼠肝膜胰多肽受体结合依赖于时间和温度，而这一专一结合能被未标记的猪胰多肽以剂量关系所抑制．鸭胰多肽只有在高浓度下才显示出部分抑制作用．Ｓｃａｔｃｈａｒｄ作图分析表明大鼠肝膜存在两种胰多肽的结合位点，高亲和结合位点和低亲和结合位点．它们的结合解离常数Ｋｄ分别为５４ｎｍｏｌ·Ｌ－１和１５８ｎｍｏｌ·Ｌ－１．结论：大鼠肝膜存在胰多肽的专一结合受体。

A resistin binding peptide selected by phage display inhibits 3T3-L1 preadipocyte differentiation

Background Resistin, a newly discovered cysteine-rich hormone secreted mainly by adipose tissues, has been proposed to form a biochemical link between obesity and type 2 diabetes. However, the resistin receptor has not yet been identified. This study aimed to identify resistin binding proteins/receptor. Methods Three cDNA fragments with the same 11 bp 5＇ sequence were found by screening a cDNA phage display library of rat multiple tissues. As the reading frames of the same 11 bp 5＇ sequence were interrupted by a TGA stop codon, plaque lift assay was consequently used to prove the readthrough phenomenon. The stop codon in the same 11 bp 5＇ sequence was replaced by tryptophan, and the binding activity of the coded peptide [AWIL, which was designated as resistin binding peptide （RBP）] with resistin was identified by the confocal microscopy technique and the affinity chromatography experiment, pDual GC-resistin and pDual GC-resistin binding peptide were co-transfected into 3T3-L1 cells to confirm the function of resistin binding peptide. Results Three cDNA fragments with the same 11 bp 5＇ sequence were found. The TGA stop codon in reading frames of the same 11 bp 5＇ sequence was proved to be readthroughed. The binding activity of RBP with resistin was consequently identified. The expression of the resistin binding peptide in 3T3-L1 preadipocytes expressing pDual G-C-resistin significantly inhibited the adipogenic differentiation. Conclusion RBP could effectively rescue the promoted differentiation of resistin overxepressed 3T3-L1 preadipocyte.

Analysis of the binding sites with NL-101 to amino acids and peptides by HPLC/MS/MS

The binding between NL-101, a novel nitrogen mustard anti-cancer drug, with amino acids and peptides has been investigated by high performance liquid chromatography electrospray tandem mass spectrometry(HPLC/ESI-MS/MS). This study offers supporting data of the interaction among drug and amino acids and peptides, which could potentially explain the cytotoxic and mutagenic effects of the drug. Collision-induced dissociation(CID) experiment demonstrated that under the same collision energy, the amino group combined with NL-101 adducts are sensitive and often produce more fragment ions; the carboxyl group combined with NL-101 adducts are hard to break and display fewer fragment ions. In addition, when other group(like sulfhydryl group) of amino acids binds to NL-101, CID spectra show different fragmentation pattern. These differences could display structural information about the drug adducts and be utilized as location of the authentic binding sites.

Molecular modeling on Zn(II) binding modes of Alzheimer's amyloid β-peptide in insoluble aggregates and soluble complexes

Aggregation of the amyloid b-peptide (A b) into insoluble fibrils is a key pathologi-cal event in Alzheimers disease. Zn(II) ion induces significant Ab aggregation at nearly physio-logical concentrations in vitro. In order to explore the induce mechanism, the possible binding modes of Zn(II) in Ab peptide are studied by molecular modeling method. First, the Ab species containing 1,2,4 and 12 peptides are established respectively. And next a Zn(II) ion is manually hold the different sits of the Ab species based on the experimental data and subsequently the coordinate atom and number are assigned. Finally, the optimum binding site is found by the system energy minimization. Modeling results show that in soluble Zn(II) complex, Nt of imidazole ring of His14, O of carbonyl of main-chain, and two O of water occupy the four ligand positions of the tetrahedral complex; in the aggregation of Ab, the His13(Nt)-Zn(II)-His14(Nt) bridges are formed by Zn(II) cross-linking action. Therefore, the possible Zn(II) binding mode obtained by the studies will be helpful to reveal the form mechanism of pathogenic aggregates in brain.

Peptide 68-88 of apocytochromec plays a crucial role in its insertion into membrane and binding to mitochondria

Apocytochrome c (Apocyt. c) is the precursor of cytochrome c. It is synthesized in the cytosol and posttranslationally imported into mitochondria. In order to determine the crucial se-quence in apocyt. c translocation, deleted mutant and chemically synthesized peptides with differ-ent length were used. Obtained results showed that sequence 68-88 of apocyt. c plays a critical role in its insertion into membrane and binding to mitochondria.

Development of a universal phosphorylated peptide-binding protein for simultaneous assay of kinases

This study describes the development of a universal phosphorylated peptide-binding protein designed to simultaneously detect serine, threonine and tyrosine kinases. The Escherichia

Selective inhibition of resistant bacterial pathogens using a β-lactamase-activatable antimicrobial peptide with significantly reduced cytotoxicity

The expression ofβ-lactamase,particularly metallo-β-lactamase(MBL)in bacteria has caused significant resistance to clinically importantβ-lactam antibiotics,including life-saving carbapenems.Antimicrobial peptides(AMPs)have emerged as promising therapeutic agents to combat antibiotic resistance.However,the cytotoxic AMPs has been one of the major concerns for their applications in clinical practice.Herein,we report a novel cephalosporin-caged AMP,which shows significantly reduced cytotoxicity,hemolytic activity,and antibacterial activity but turns highly active against bacteria upon specific hydrolysis by the antimicrobial resistance-causativeβ-lactamase.Further investigations demonstrate thisβ-lactamaseactivatable AMP selectively inactivates resistant bacterial pathogens over susceptible bacteria.This strategy should be applicable to other AMPs as a potential solution for the treatment of infectious diseases caused byβ-lactamase-expressing pathogenic bacteria.

Effect of covalent-binding modes of osteogenic-related peptides with artificial carriers on their biological activities in vivo

Covalent binding between bioactive substances and materials in different ways can significantly improve the bone inductivity and biological activity of bone repair materials.However,there is a lack of systematic understanding of how these binding modes affect biological activities of the active substances.In this study,four kinds of functionalized Multi-walled carbon nanotubes(MWCNTs)were prepared,ensuring the same grafting rate of different functional groups.Subsequently,two kinds of osteogenic-related peptides,bone morphogenetic protein-2 mimicking peptides and osteogenic growth mimicking peptides,were covalently bound to functionalized MWCNTs,ensuring the same molar mass of peptides bound to different functionalized MWCNTs in this process.Then the same amount of functionalized MWC-NTs/Peptides composites were introduced into the scaffolds,and through the ectopic osteogenesis model in rats and calvarial defect model in rabbits,ectopic osteogenesis and bone repair ability of the composites were analyzed.Furthermore,the effects of different covalent binding modes on peptide-induced osteogenesis and bone repair were studied.The results showed that the negative influencing trend of different covalent binding modes of osteogenic-related peptides with artificial carriers on their biological activities was in the order as follows:amide binding(carboxyl)>silane coupling>dopamine bind-ing>amide binding(amino),whose mechanism might be mainly that the covalent binding of peptides with different functional groups resulted in different charges.We believe that the results of this study have important guiding significance for the research and development of bone repair materials covalently bound with bioactive substances.

Principles of amino-acid–ribonucleotide interaction revealed by binding affinities between homogeneous oligopeptides and singlestranded RNA molecules

We have determined the binding strengths between ribonucleotides of adenine(A),guanine(G),uracil(U),and cytosine(C)in homogeneous single-stranded ribonucleic acids(ssRNAs)and homo-decapeptides consisting of 20 common amino acids.We use a bead-based fluorescence assay for these measurements in which decapeptides are immobilized on the bead surface and ssRNAs are in solutions.The results provide a molecular basis for analyzing selectivity,specificity,and polymorphisms of amino-acid–ribonucleotide interactions.Comparative analyses of the distribution of the binding energies reveal unique binding strength patterns assignable to each pair of amino acid and ribonucleotide originating from the chemical structures.Pronounced favorable(such as Arg–G)and unfavorable(such as Met–U)binding interactions can be identified in selected groups of amino acid and ribonucleotide pairs that could provide basis to elucidate energetics of amino-acid–ribonucleotide interactions.Such interaction selectivity,specificity,and polymorphism manifest the contributions from RNA backbone,RNA bases,as well as main chain and side chain of the amino acids.Such characteristics in peptide–RNA interactions might be helpful for understanding the mechanism of protein–RNA specific recognition and the design of RNA nano-delivery systems based on peptides and their derivatives.

金属抗菌肽SIF_(4)对大肠杆菌拓扑异构酶活性及胞内核酸合成的影响

为系统阐明金属抗菌肽SIF_(4)基于DNA拓扑异构酶靶点的非细胞质膜抑菌机理,以大肠杆菌为模式菌株,研究了金属抗菌肽SIF_(4)与基因组DNA的结合方式、对DNA拓扑异构酶I/II活性以及胞内核酸生物合成的影响机理。研究发现,金属抗菌肽SIF_(4)可能以类似溴化乙锭嵌插方式与基因组DNA结合,对拓扑异构酶I有较强抑制活性,但对拓扑异构酶II影响较小,可通过影响DNA负超螺旋解链和RNA聚合酶结合催化RNA转录过程发挥抑菌活性。研究还发现,经金属抗菌肽SIF_(4)处理12 h后,大肠杆菌胞内总DNA和总RNA生物合成量均受到不同程度的抑制,且呈现良好的量-效关系,1/2最小抑菌浓度(minimal inhibitory concentration,MIC)组与对照组(0 MIC)相比,胞内DNA和RNA生物量差异不显著(P>0.05),MIC和2 MIC组与对照组相比,胞内DNA和RNA生物量差异显著(P<0.05)。实验结果可为金抗肽SIF_(4)在食源性大肠杆菌生物防控中的应用提供理论支持。