Thermoresponsive dendronized copolymers for protein recognitions based on biotin-avidin interaction

Thermoresponsive biotinylated dendronized copolymers carrying dendritic oligoethylene glycol（OEG）pendants were prepared via free radical polymerization,and their protein recognitions based on biotin-avidin interaction investigated.Both first（PG1） and second generation（PG2） dendronized copolymers were designed to examine possible thickness effects on the interaction between biotin and avidin.Inherited from the outstanding thermoresponsive properties from OEG dendrons,these biotinylated cylindrical copolymers show characteristic thermoresponsive behavior which provides an envelope to capture avidin through switching temperatures above or below their phase transition temperatures（T_（cp）s）.Thus,the recognition of polymer-supported biotin with avidin was investigated with UV/vis spectroscopy and dynamic laser light scattering.In contrast to the case for PG1,the increased thickness for copolymer PG2 hinders partially and inhibits the recognition of biotin moieties with avidin either below or above its T_（cp）.This demonstrates the significant architecture effects from dendronized polymers on the biotin moieties to shift onto periphery of the collapsed aggregates,which should be a prerequisite for protein recognition.These kinds of novel thermoresponsive copolymers may pave a way for the interesting biological applications in areas such as reversible activity control of enzyme or proteins,and for controlled delivery of drugs or genes.

Protein surface recognition of the novel tetra-carboxylphenyl calix[4]arene to cytochrome c

The interaction of the novel tetra-carboxylphenyl calix[4]arene （TCPC） with the bovine heart cytochrome c （Cc） was first investigated by fluorescence spectroscopy and molecular modeling methods. The formation of a stable 1：1 complex was monitored by fluorescence titration, and its binding constant is 1.916 ×10^7 L mol^-1. Molecular modeling reveals the recognition mechanism of TCPC to the Cc surface, that is, the electrostatic interaction drives TCPC to the Cc surface, and the van der Waals interaction orientates TCPC parallel to the cleft of Cc.

Identification,Phylogeny and Expressional Profiles of Peptidoglycan Recognition Protein(PGRP)Gene Family in Sinonovacula constricta

Peptidoglycan recognition protein(PGRP)plays a vital role in invertebrate innate immunity system as a specific pattern recognition receptor for peptidoglycan.Bivalves possess various PGRP systems for self-defense;however,it has not been characterized in razor clam Sinonovacula constricta.In this study,eight PGRP coding sequences were identified and analyzed from S.constricta genome,which are designated as ScPGRP-S1,ScPGRP-S2,ScPGRP-S3,ScPGRP-S4,ScPGRP-S5,ScPGRP-S6,ScPGRP-S7,ScPGRP-S8.The results of molecular evolutionary analyses showed that all eight ScPGRP genes were highly conserved and exhi-bited a typical PGRP/amidase_2 domain as PGRP genes in other mollusks.Moreover,the presence of signal peptides was predicted in ScPGRP-S2,ScPGRP-S3 and ScPRP-S6,while a transmembrane structure only existed in ScPGRP-S6.Notably,a tertiary struc-ture analysis indicated that no disulfide bond was observed in ScPGRP-S5 and ScPGRP-S7.The mRNA transcripts analysis of ScPGRPs revealed that the high expression patterns of ScPGRP-S1 and ScPGRP-S4 were found in mantle,adductor muscle and foot,while those of ScPGRP-S2,ScPGRP-S3 and ScPGRP-S6 were observed in hepatopancreas.Furthermore,the temporal expression profiles of ScPGRPs in the hepatopancreas were analyzed by qPCR<https://www.sciencedirect.com/topics/immunology-and-microbiology/real-time-polymerase-chain-reaction>after Gram-negative Vibrio parahaemolyticus and Gram-positive Staphylococcus aureus challenges.The mRNA expressions of ScPGRP-S2,ScPGRP-S3 and ScPGRP-S6 could be induced by V.pa-rahaemolyticus and S.aureus.Overall,our findings indicated that ScPGRPs were involved in the immune defense against invaders,which constituted a comprehensive understanding of the potential role of PGRP genes in S.constricta.

Site-specific incorporation of reduction-controlled guest amino acids into proteins for cucurbituril recognition

Protein recognition using host-guest recognition approach is of great interest but has been limited mainly to the protein N-terminal residues.Here,we site-specific incorporated two novel non-canonical amino acids containing supramolecular guest motifs into protein via an expanded genetic code.Through Staudinger reduction reactions,the encoded unnatural residues on protein becoming activated and can be specifically recognized by cucurbit[7]uril(CB[7])and cucurbit[8]uril(CB[8]).We demonstrated that enzyme containing guest amino acid incorporated near the active site can be reversibly regulated by CB[7]recognition,and CB[8]recognition induces protein dimerization.These amino acids will make useful addition to the supramolecular toolbox for protein targeting using molecular recognition approaches.

Antiviral function of peptidoglycan recognition protein in Spodoptera exigua(Lepidoptera:Noctuidae)

Peptidoglycan recognition proteins(PGRPs)are a class of molecules that play a critical role in insect immunity.Understanding the function of PGRPs is important to improve the efficiency of microbial insecticides.In this study,we investigated the role of PGRP-LB(a long type PGRP)in insect immunity against viruses using Spodoptera exigua and Spodoptera exigua multiple nucleopolyhedrovirus(SeMNPV)as an insect-virus model.We cloned and identified a PGRP-LB gene from S.exigua;the gene consisted of 7 exons that encoded a polypeptide of 234 amino acids with a signal peptide and a typical amidase domain.Expression analysis revealed that the abundance of SePGRP-LB transcripts in the fat body was greater than in other tissues.Overexpression of SePGRP-LB resulted in a significant decrease of 49%in the rate of SeMNPV-infected cells.In addition,the multiplication of SeMNPV was significantly decreased:a decrease of 79%in the production of occlusion-derived virion(ODV),and a maximum decrease of 50%in the production of budded virion(BV).In contrast,silencing of SePGRP-LB expression by RNA interference resulted in a significant 1.65-fold increase in the rate of SeMNPV-infected cells,a significant 0.54-fold increase in ODV production,a maximum 1.57-fold increase in BV production,and the larval survival dropped to 21%.Our findings show that SePGRP-LB has an antiviral function against SeMNPV,and therefore this gene may provide a target for lepidopteran pest control using virus insecticides.

Comparative analysis of peptidoglycan recognition proteins in endoparasitoid wasp Microplitis mediator

Peptidoglycan recognition proteins （PGRPs） are a family of innate immune receptors that specifically recognize peptidoglycans （PGNs） on the surface of a number of pathogens. Here, we have identified and characterized six PGRPs from endoparasitoid wasp, Microplitis mediator （MmePGRPs）. To understand the roles of PGRPs in parasitoid wasps, we analyzed their evolutionary relationship and orthology, expression profiles during different developmental stages, and transcriptional expression following infection with Gram-positive and -negative bacteria and a fungus. MmePGRP-S1 was significantly induced in response to pathogenic infection. This prompted us to evaluate the effects of RNA interference mediated gene specific knockdown ofMmePGRP-S1. The knockdown of MmePGRP-S1 （iMmePGRP-S1） dramatically affected wasps＇ survival following challenge by Micrococcus luteus, indicating the involvement of this particular PGRP in immune responses against Gram-positive bacteria. This action is likely to be mediated by the Toll pathway, but the mechanism remains to be determined. MmePGRP-S 1 does not play a significant role in anti-fungal immunity as indicated by the survival rate of iMmePGRP-S wasps. This study provides a comprehensive characterization of PGRPs in the economically important hymenopteran species M. mediator.

Characterization of a β-1,3-glucan recognition protein from the beet armyworm, Spodoptera exigua （Insecta： Lepidoptera： Noctuidae）

The β-1,3-glucan recognition protein gene from Spodoptera exigua （SeβGRP） was cloned and characterized. The cDNA of this gene is 1？644 nucleotides in length and the predicted polypeptide is 491 amino acids （aa） in length, with a calculated molecular mass of 54.8 kDa. The first 22 aa encode a predicted secretion signal peptide. A BLAST search, multiple sequence alignment, and phylogenetic analysis of the aa sequence of SeβGRP revealed that this protein is most similar to the β-1,3-glucan recognition protein （βGRP） family of pattern recognition proteins. Using reverse-transcription polymerase chain reaction, we detected the presence of SeβGRP transcripts in the egg, larval, pupal, and adult stages of S. exigua. In addition, the SeβGRP transcript was expressed in all the tissues examined including the brain, hemocytes, fat body, intestine, and cuticle. There were no changes in SeβGRP mRNA levels in larvae infected with ultraviolet （UV）-killed Escherichia coli DH5α compared with the control larvae inoculated with the water; however, SeβGRP mRNA levels were markedly elevated 4–8 h after infection and slightly induced 12–24 h after infection in larvae injected with UV-killed Fusarium oxysporum. This may be because β-1,3-glucan is the main component of the cell wall of F. oxysporum, but not E. coli DH5α.

Conformation-dependent recognition of mutant HTT proteins by selective autophagy

With the support by the National Natural Science Foundation of China,a study led by Prof.Lu Boxun(鲁伯埙)from Fudan University demonstrates that a toxic mutant HTT species is resistant to selective autophagy,revealing the fundamental mechanism of Huntington’s Disease.The study was published

Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned se- quences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitu- tion matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9.

A Statistical Analysis of Protein-Protein Interaction with Knowledge-Based Potential at Residue Level

Protein protein recognition is an important step in biological processes, which still largely remains elusive. The inter residue contact potential, CP ij , describes the propensity of contact between two types of residue. In this study, several different CP ij variants were examined with the objective of discriminating the binding potential of surface pairs. Using solvent mediated inter molecule contact potential (SM IMCP ij ), an evaluation model was deduced and tested. Using the evaluation model it was found that the SM IMCP ij gives a better performance than either residue mediated IMCP ij (RM IMCP ij ) or folding residue contact potential (FCP ij ). The results suggest that the evaluation model provides a fast, effective, and discriminative method for the evaluation of proposed binding interfaces.

A splice variant of PGRP-LC required for expression of antimicrobial peptides in Anopheles gambiae

Members of the peptidoglycan recognition protein （PGRP） family play essential roles in different manifestations of immune responses in insects. PGRP-LC, one of seven members of this family in the malaria vector Anopheles gambiae produced several spliced variants. Here we show that PGRP-LC, and not other members of the PGRP family nor the six members of the Gram-negative binding protein families, is required for the expression of antimicrobial peptide genes （such as CEC1 and GAM1） under the control of the Imd-Rel2 pathway in an A. gambiae cell line, 4a3A. PGRP-LC produces many splice variants that can be classified into three sub-groups （LC1, LC2 and LC3）, based on the carboxyl terminal sequences. RNA interference against one LC1 sub-group resulted in dramatic reduction of CEC1 and GAM1. Over-expression of LCla and to a lesser extent LC3a （a member of the LC1 and LC3 sub-group, respectively） in the 4a3A cell line enhances the expression of CEC1 and GAM1. These results demonstrate that the LC1-subgroup splice variants are essential for the expression of CEC1 and GAM1 in A. gambiae cell line.

Functional characterization of PGRP-LC1 of Anopheles gambiae through deletion and RNA interference

Peptidoglycan recognition proteins （PGRP） play an important role in innate immunity in insects through the activation of the Imd pathway, which has been shown to be required in the antibacterial response in insects and in the limitation of the number of Plasmodium berghei oocysts developing in mosquito midgut. The LCI gene of the PRGP family in Anopheles gambiae produces many products through alternative splicing. In this work, we demonstrate that PGRP-LC1a alone is sufficient to activate the Imd pathway in the A. gambiae L3-5 cell line through a combination of terminal or internal deletions, and RNA interference against endogenous PGRP-LC products. In the absence of endogenous PGRP-LC proteins, the integrity of the cytoplasmic domain is necessary for LCla function, while that of the extracellular domain is not. Moreover, the shorter the extracellular domain, the higher the activity for LC1 a. However, the removal of either the cytoplasmic or the extracellular PGRP-binding domain has little impact on the activity of LC 1 a in the presence of endogenous PGRP-LC proteins.