Showing papers on "Peptide sequence published in 2018"
TL;DR: It is discovered that the broadly expressed RNA-binding protein TIS11B forms a membraneless organelle, called TIS granule, that enriches membrane protein-encoding mRNAs with multiple AU-rich elements, thus allowing increased surface expression and functional diversity of proteins, including CD47 and PD-L1.
216 citations
TL;DR: This tutorial review aims to provide the reader with the latest developments in NCL- and EPL-based ligation technologies as well as illustrated examples of using these methods, together with synthetic logic, to access proteins and modified proteins for biological study.
Abstract: Native chemical ligation (NCL) provides a highly efficient and robust means to chemoselectively link unprotected peptide and protein segments to generate proteins. The ability to incorporate non-proteinogenic amino acids (e.g.d-amino acids or fluorescent labels) and post-translational modifications into proteins by stitching together peptide fragments has driven extremely important developments in peptide and protein science over the past 20 years. Extensions of the original NCL concept (including the development of thiol- and selenol-derived amino acids and desulfurisation and deselenisation methods), improved access to peptide thioesters, and the use of the methodology in combination with recombinantly expressed polypeptide fragments (termed Expressed Protein Ligation, EPL) have helped to further expand the utility of the methodology. Over the past five years, there has been a dramatic increase in the number of proteins that have been accessed by total chemical synthesis and semi-synthesis, including a large range of modified proteins; new records have also been set with regards to the size of proteins that can now be accessed via ligation chemistry. Together these efforts have not only contributed to a better understanding of protein structure and function, but have also driven innovations in protein science. In this tutorial review, we aim to provide the reader with the latest developments in NCL- and EPL-based ligation technologies as well as illustrated examples of using these methods, together with synthetic logic, to access proteins and modified proteins for biological study.
183 citations
TL;DR: A computational algorithm is developed that starts with peptides naturally occurring in plants and optimizes this starting material to yield new variants which are highly distinct from the parent peptide, which could be used to design effective peptide antibiotics.
Abstract: Plants are extensively used in traditional medicine, and several plant antimicrobial peptides have been described as potential alternatives to conventional antibiotics. However, after more than four decades of research no plant antimicrobial peptide is currently used for treating bacterial infections, due to their length, post-translational modifications or high dose requirement for a therapeutic effect . Here we report the design of antimicrobial peptides derived from a guava glycine-rich peptide using a genetic algorithm. This approach yields guavanin peptides, arginine-rich α-helical peptides that possess an unusual hydrophobic counterpart mainly composed of tyrosine residues. Guavanin 2 is characterized as a prototype peptide in terms of structure and activity. Nuclear magnetic resonance analysis indicates that the peptide adopts an α-helical structure in hydrophobic environments. Guavanin 2 is bactericidal at low concentrations, causing membrane disruption and triggering hyperpolarization. This computational approach for the exploration of natural products could be used to design effective peptide antibiotics.
163 citations
TL;DR: This study provides a feasible approach to isolate calcium-binding peptides and to clarify the possible binding mechanism of calcium and peptide.
103 citations
TL;DR: A two‐layer SVM‐based ensemble model with fine‐grain optimized parameters was developed, and correctly identified two very recently validated T6SE proteins, which represent challenging prediction targets because they significantly differed from previously known T6 SEs in terms of their sequence similarity and cellular function.
Abstract: Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data. Results: We extracted a wide range of features from T6SE protein sequences and comprehensively analyzed the prediction performance of these features through unsupervised and supervised learning. By integrating these features, we subsequently developed a two-layer SVM-based ensemble model with fine-grain optimized parameters, to identify potential T6SEs. We further validated the predictive model using an independent dataset, which showed that the proposed model achieved an impressive performance in terms of ACC (0.943), F-value (0.946), MCC (0.892) and AUC (0.976). To demonstrate applicability, we employed this method to correctly identify two very recently validated T6SE proteins, which represent challenging prediction targets because they significantly differed from previously known T6SEs in terms of their sequence similarity and cellular function. Furthermore, a genome-wide prediction across 12 bacterial species, involving in total 54 212 protein sequences, was carried out to distinguish 94 putative T6SE candidates. We envisage both this information and our publicly accessible web server will facilitate future discoveries of novel T6SEs. Availability and implementation: http://bastion6.erc.monash.edu/. Supplementary information: Supplementary data are available at Bioinformatics online.
92 citations
TL;DR: It is found that the PPII peptide is a non-typical binder that can only interact effectively with its cognate SH3 domain when it is integrated into the full-length c-Src kinase protein; stripping the peptide from the protein would considerably impair SH3 affinity by increasing entropy penalty upon the domain–peptide binding, suggesting that the protein context plays an essential role in the SBP’s biological function.
Abstract: Proto-oncogene non-receptor tyrosine protein kinase c-Src has been involved in the development, progression and metastasis of a variety of human cancers. This protein contains two self-binding peptide (SBP) sites separately between the SH3 domain and polyproline-II (PPII) helix and between the SH2 domain and C-terminal phosphorylatable tail (CTPT), which are potential targets of anticancer drugs to regulate the kinase activity. Here, we described an integrated protocol to systematically investigate the structural basis, energetic property and dynamics behaviour of PPII binding to SH3, and to rationally design potent peptide ligands to target the SBP site of SH3-PPII interaction. Our study found that the PPII peptide is a non-typical binder that can only interact effectively with its cognate SH3 domain when it is integrated into the full-length c-Src kinase protein; stripping the peptide from the protein would considerably impair SH3 affinity by increasing entropy penalty upon the domain-peptide binding, suggesting that the protein context plays an essential role in the SBP's biological function. Next, we identified that the PPII peptide binds to SH3 domain in a class II manner and, on this basis, we derived a series of modified versions of the wild-type PPII peptide using a structure-based rational strategy. These modified peptide mutants have been structurally optimized with respect to their molecular flexibility and interaction potency with SH3 domain, in order to minimize indirect entropy penalty and to maximize direct binding enthalpy simultaneously. Consequently, several rationally designed peptides were obtained, including PPIIm2 (TSKPQTPGRA), PPIIm5 (KPPTPPRA), PPIIm6 (FPPPPPRA) and PPIIm7 (YPPLPPRA), which exhibit a moderately or considerably increased affinity (Kd = 72, 34, 15 and 5.7 μM, respectively) relative to the wild-type PPII (TSKPQTQGLA) (Kd = 160 μM). These peptides can be used as lead molecular entities to further develop new anticancer therapeutics to regulate c-Src kinase activity by targeting the SBP site of SH3-PPII interaction.
85 citations
TL;DR: Molecular dynamic simulation showed the conformation of peptide was markedly varied, and the distance between calcium ion and Gln and Ile residues was changing all the time, however, the distance around carboxyl oxygen of arginine residues was not changed significantly, and Identified peptide can be used as a novel calcium supplement.
83 citations
TL;DR: A multifunctional peptide is utilized to present an interface that supports the very specific recruitment of targets from serum that is readily extended to a broad range of targets for which an affinity sequence can be generated.
Abstract: The construction of sensitive and selective biosensors capable of detecting specific targets in complex biological samples remains a challenge highly relevant to a range of sensor/diagnostic applications. Herein, we have utilized a multifunctional peptide to present an interface that supports the very specific recruitment of targets from serum. The novel peptide sequence designed contains an anchoring domain (CPPPP-), an antifouling domain (-NQNQNQNQDHWRGWVA), and a human immunoglobulin G (IgG) recognition domain (-HWRGWVA), and the whole peptide was designed to be antifouling. These were integrated into polyaniline nanowire arrays in supporting the quantification of IgG (with a limit of detection of 0.26 ng mL–1) in neat serum and real clinical samples. The strategy of utilizing multisegment peptide films to underpin highly selective target recruitment is, of course, readily extended to a broad range of targets for which an affinity sequence can be generated.
80 citations
TL;DR: The structure of the human CLC-1 channel is determined, finding subtle differences in glutamate gate conformation, internal pore diameter and Cl− affinity distinguish CLC channels and transporters.
Abstract: CLC channels mediate passive Cl- conduction, while CLC transporters mediate active Cl- transport coupled to H+ transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC transporters seems undetectable by amino acid sequence. To understand why they are different functionally we determined the structure of the human CLC-1 channel. Its 'glutamate gate' residue, known to mediate proton transfer in CLC transporters, adopts a location in the structure that appears to preclude it from its transport function. Furthermore, smaller side chains produce a wider pore near the intracellular surface, potentially reducing a kinetic barrier for Cl- conduction. When the corresponding residues are mutated in a transporter, it is converted to a channel. Finally, Cl- at key sites in the pore appear to interact with reduced affinity compared to transporters. Thus, subtle differences in glutamate gate conformation, internal pore diameter and Cl- affinity distinguish CLC channels and transporters.
77 citations
TL;DR: The genome-guided discovery of bacterial pathways that posttranslationally create β-amino acid–containing products is reported, and it is shown that the β-Amino acids result from an unusual protein splicing process involving backbone carbon-carbon bond cleavage and net excision of tyramine.
Abstract: Current textbook knowledge holds that the structural scope of ribosomal biosynthesis is based exclusively on α-amino acid backbone topology. Here we report the genome-guided discovery of bacterial pathways that posttranslationally create β-amino acid–containing products. The transformation is widespread in bacteria and is catalyzed by an enzyme belonging to a previously uncharacterized radical S -adenosylmethionine family. We show that the β-amino acids result from an unusual protein splicing process involving backbone carbon-carbon bond cleavage and net excision of tyramine. The reaction can be used to incorporate diverse and multiple β-amino acids into genetically encoded precursors in Escherichia coli . In addition to enlarging the set of basic amino acid components, the excision generates keto functions that are useful as orthogonal reaction sites for chemical diversification.
75 citations
TL;DR: It is proposed that PUX10 is involved in a protein degradation pathway at LDs, mediating an interaction between polyubiquitinated proteins targeted for degradation and downstream effectors such as CDC48.
Abstract: The number of known proteins associated with plant lipid droplets (LDs) is small compared with other organelles. Many aspects of LD biosynthesis and degradation are unknown, and identifying and characterizing candidate LD proteins could help elucidate these processes. Here, we analyzed the proteome of LD-enriched fractions isolated from tobacco (Nicotiana tabacum) pollen tubes. Proteins that were highly enriched in comparison with the total or cytosolic fraction were further tested for LD localization via transient expression in pollen tubes. One of these proteins, PLANT UBX DOMAIN-CONTAINING PROTEIN10 (PUX10), is a member of the plant UBX domain-containing (PUX) protein family. This protein localizes to LDs via a unique hydrophobic polypeptide sequence and can recruit the AAA-type ATPase CELL DIVISION CYCLE48 (CDC48) protein via its UBX domain. PUX10 is conserved in Arabidopsis thaliana and expressed in embryos, pollen tubes, and seedlings. In pux10 knockout mutants in Arabidopsis, LD size is significantly increased. Proteomic analysis of pux10 mutants revealed a delayed degradation of known LD proteins, some of which possessed ubiquitination sites. We propose that PUX10 is involved in a protein degradation pathway at LDs, mediating an interaction between polyubiquitinated proteins targeted for degradation and downstream effectors such as CDC48.
TL;DR: An unbiased, multistep ADP‐ribosylome data analysis workflow is established that led to the identification of tyrosine as a novel ARTD1/PARP1‐dependent in vivo ADPr‐acceptor amino acid.
Abstract: Despite recent mass spectrometry (MS)-based breakthroughs, comprehensive ADP-ribose (ADPr)-acceptor amino acid identification and ADPr-site localization remain challenging. Here, we report the establishment of an unbiased, multistep ADP-ribosylome data analysis workflow that led to the identification of tyrosine as a novel ARTD1/PARP1-dependent in vivo ADPr-acceptor amino acid. MS analyses of in vitro ADP-ribosylated proteins confirmed tyrosine as an ADPr-acceptor amino acid in RPS3A (Y155) and HPF1 (Y238) and demonstrated that trans-modification of RPS3A is dependent on HPF1. We provide an ADPr-site Localization Spectra Database (ADPr-LSD), which contains 288 high-quality ADPr-modified peptide spectra, to serve as ADPr spectral references for correct ADPr-site localizations.
TL;DR: The results show that biochemical function can be implemented in small and simple proteins, and intriguingly suggest that the P-loop emerged as a polynucleotide binder and catalysis of phosphoryl transfer evolved later upon acquisition of higher sequence and structural complexity.
Abstract: Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.
TL;DR: This study presents the crystal structure of human PTH1R in complex with a peptide agonist at 2.5-A resolution, allowing to delineate the agonist binding mode for this receptor and revealing molecular details within conserved structural motifs that are critical for class B receptor function.
Abstract: Parathyroid hormone 1 receptor (PTH1R) is a class B multidomain G-protein-coupled receptor (GPCR) that controls calcium homeostasis. Two endogenous peptide ligands, parathyroid hormone (PTH) and parathyroid hormone-related protein (PTHrP), activate the receptor, and their analogs teriparatide and abaloparatide are used in the clinic to increase bone formation as an effective yet costly treatment for osteoporosis. Activation of PTH1R involves binding of the peptide ligand to the receptor extracellular domain (ECD) and transmembrane domain (TMD), a hallmark of class B GPCRs. Here, we present the crystal structure of human PTH1R in complex with a peptide agonist at 2.5-A resolution, allowing us to delineate the agonist binding mode for this receptor and revealing molecular details within conserved structural motifs that are critical for class B receptor function. Thus, this study provides structural insight into the function of PTH1R and extends our understanding of this therapeutically important class of GPCRs.
TL;DR: This work is the first to categorize the structures of INS peptides and relate these structures to the functions of all 40 INS peptide ligands in vivo and will promote the study of insulin function on development, metabolism, and aging-related diseases.
TL;DR: A novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent control of the steady-state protein level and inducible accumulation of target proteins.
Abstract: Most of the current methods for controlling the formation rate of a key protein or enzyme in cell factories rely on the manipulation of target genes within the pathway. In this article, we present a novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent control of the steady-state protein level and inducible accumulation of target proteins. The FENIX device is based on the constitutive, proteasome-dependent degradation of the target polypeptide by tagging with a short synthetic, hybrid NIa/SsrA amino acid sequence in the C-terminal domain. Protein production is triggered via addition of an orthogonal inducer (i.e., 3-methylbenzoate) to the culture medium. The system was benchmarked in Escherichia coli by tagging two fluorescent proteins (GFP and mCherry), and further exploited to completely uncouple poly(3-hydroxybutyrate) (PHB) accumulation from bacterial growth. By tagging PhaA (3-ketoacyl-CoA thiolase, first step of the route), a dynamic metab...
TL;DR: A computational-experimental framework for the discovery of novel cryptic antimicrobial peptides (AMPs) was described, which showed no toxicity toward human cells and exhibited anti-infective activity in vivo, reducing by up to 4 orders of magnitude the bacterial load in a mouse skin infection model.
Abstract: Novel approaches are needed to combat antibiotic resistance. Here, we describe a computational-experimental framework for the discovery of novel cryptic antimicrobial peptides (AMPs). The computational platform, based on previously validated antimicrobial scoring functions, indicated the activation peptide of pepsin A, the main human stomach protease, and its N- and C-terminal halves as antimicrobial peptides. The three peptides from pepsinogen A3 isoform were prepared in a recombinant form using a fusion carrier specifically developed to express toxic peptides in Escherichia coli. Recombinant pepsinogen A3-derived peptides proved to be wide-spectrum antimicrobial agents with MIC values in the range 1.56-50 μM (1.56-12.5 μM for the whole activation peptide). Moreover, the activation peptide was bactericidal at pH 3.5 for relevant foodborne pathogens, suggesting that this new class of previously unexplored AMPs may contribute to microbial surveillance within the human stomach. The peptides showed no toxicity toward human cells and exhibited anti-infective activity in vivo, reducing by up to 4 orders of magnitude the bacterial load in a mouse skin infection model. These peptides thus represent a promising new class of antibiotics. We envision that computationally guided data mining approaches such as the one described here will lead to the discovery of antibiotics from previously unexplored sources.
TL;DR: In this paper, Amino acid composition, structure, and proper positioning of amino acid in a peptide are closely related to its antioxidant activity and the authors identified novel antioxidant peptides from fraction CPH2-III.
TL;DR: Four umami peptides were separated and purified by ultrafiltration, gel filtration chromatography, and identified by ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS), the amino acid sequences of four peptides are Val-Pro-Tyr (VPY), Thr-Ala-tyr (TAY), Ala- ala-pro-T Tyr (AAPY) and Gly-Phe-Pro (GFP).
TL;DR: Data suggest that SAPHM may be considered as potential candidate for future applications in non-aqueous peptide biocatalysis because it possesses an elevated organic solvent resistance and catalytic efficiency higher than those of Alcalase and Thermolysin.
TL;DR: Results support the application of the peptide for neuroprotection and present a low cytotoxicity and suppressed menadione‐induced redox imbalance when tested with fibroblast in culture.
TL;DR: A user‐friendly protein–peptide docking server, MDockPeP, which globally docks the all‐atom, flexible peptide to the protein receptor and evaluates the produced modes with a statistical potential‐based scoring function, ITScorePeP.
Abstract: Protein-peptide interactions play a crucial role in a variety of cellular processes. The protein-peptide complex structure is a key to understand the mechanisms underlying protein-peptide interactions and is critical for peptide therapeutic development. We present a user-friendly protein-peptide docking server, MDockPeP. Starting from a peptide sequence and a protein receptor structure, the MDockPeP Server globally docks the all-atom, flexible peptide to the protein receptor. The produced modes are then evaluated with a statistical potential-based scoring function, ITScorePeP. This method was systematically validated using the peptiDB benchmarking database. At least one near-native peptide binding mode was ranked among top 10 (or top 500) in 59% (85%) of the bound cases, and in 40.6% (71.9%) of the challenging unbound cases. The server can be used for both protein-peptide complex structure prediction and initial-stage sampling of the protein-peptide binding modes for other docking or simulation methods. MDockPeP Server is freely available at http://zougrouptoolkit.missouri.edu/mdockpep. © 2018 Wiley Periodicals, Inc.
TL;DR: The map-based cloning of the causal gene OsPELOTA is reported, indicating that the rice PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway.
Abstract: We previously reported a spotted-leaf mutant pelota (originally termed HM47) in rice displaying arrested growth and enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae. Here, we report the map-based cloning of the causal gene OsPELOTA (originally termed splHM47 ). We identified a single base substitution from T to A at position 556 in the coding sequence of OsPELOTA, effectively mutating phenylalanine to isoleucine at position 186 in the translated protein sequence. Both functional complementation and over-expression could rescue the spotted-leaf phenotype. OsPELOTA, a paralogue to eukaryotic release factor 1 (eRF1), shows high sequence similarity to Drosophila Pelota and also localizes to the endoplasmic reticulum and plasma membrane. OsPELOTA is constitutively expressed in roots, leaves, sheaths, stems, and panicles. Elevated levels of salicylic acid and decreased level of jasmonate were detected in the pelota mutant. RNA-seq analysis confirmed that genes responding to salicylic acid were upregulated in the mutant. Our results indicate that the rice PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway.
TL;DR: It is shown that the acetyltransferase colocalized with the albusnodin gene cluster is required for the biosynthesis of this lasso peptide.
TL;DR: A systematic study of the effect of polyethylene glycol (PEG)-based spacer length on the performance of such biosensors in order to gain a deeper understanding of their role and optimise a peptide-based electrochemical sensor.
Abstract: Peptide-based electrochemical biosensors typically consist of a short peptide sequence, labelled with a redox reporter and modified with a thiol-containing moiety to allow immobilisation onto a gold electrode surface. A spacer is often introduced between the thiol group and the peptide with the aim of promoting enzyme accessibility as well as conferring flexibility onto the probe. Herein we report a systematic study of the effect of polyethylene glycol (PEG)-based spacer length on the performance of such biosensors in order to gain a deeper understanding of their role and optimise a peptide-based electrochemical sensor. Thus, a specific peptide endowed with varying PEG spacers (PEG-4, PEG-6, PEG-8 and PEG-12) were synthesised and interrogated by the addition of both a target enzyme (trypsin) and BSA in order to evaluate their analytical performance. An alkyl-based spacer was also assessed in order to compare the effect of the nature of the spacer. All of the proposed probes supported efficient protease detection; however, PEG-6 provided enhanced anti-fouling properties, which highlights the vital role of the spacer in the design of peptide-based probes.
TL;DR: The aim of this paper is to review the biochemical peculiarities that can improve the nutraceutical use of peptides and report the involvement of amino acid sequence, N- and C-terminal groups, and internal chemical modifications of peptide.
TL;DR: This review aims at summarizing conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures and concludes with a summary of current challenges faced and an outlook on potential future directions.
Abstract: Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as “the protein folding problem,” has been a grand chall...
TL;DR: The results showed that the dipeptide purified from jellyfish gonad protein hydrolysates can be used as functional food material and is helpful in the study of antioxidant and inhibition of ACE.
Abstract: The gonad of jellyfish (Rhopilema esculentum Kishinouye), containing high protein content with a rich amino acid composition, is suitable for the preparation of bioactive peptides. Jellyfish gonad was hydrolysed with neutral protease to obtain jellyfish gonad protein hydrolysate (JGPH), which was then purified sequentially by ultrafiltration, gel filtration chromatography, and RP-HPLC. The peptides were characterized with HPLC-MS/MS. One peptide with amino acid sequence Ser-Tyr (SY) was identified and synthesized, which showed good ACE inhibitory and antioxidant activity. The IC50 of this peptide on DPPH, ·OH, super oxygen anion scavenging activities, and ACE inhibitory activity are 84.623 μM, 1177.632 μM, 456.663 μM, and 1164.179 μM, respectively. The anchor in the binding site of SY and ACE C-domain (ACE-C) was obtained by molecular simulations. The results showed that the dipeptide purified from jellyfish gonad protein hydrolysates can be used as functional food material and is helpful in the study of antioxidant and inhibition of ACE.
TL;DR: The results indicated the specific binding between TNT and peptide TNTHCDR3, which was testified by six kinds of TNT analogues.
Abstract: In this study, 2,4,6-trinitrotoluene (TNT) binding peptide was synthesized and screened for TNT specific detection using surface plasmon resonance (SPR) sensor. The TNT binding peptide was rational design and synthesized through amino acid sequence from complementarity determining region (CDR) in the anti-TNT monoclonal antibody, which was produced from hybridoma cell using TNP-KLH conjugate as antigen. Three TNT binding peptide sequences were obtained from the heavy chain of CDR1 named TNTHCDR1, TNTHCDR2 from CDR2 and TNTHCDR3 from CDR3 of anti-TNT antibody. Screening process of three candidate peptides were carried out by using the SPR sensor with direct determination, which the peptide was directly immobilized on the sensor chip CM7 surface through amine coupling reaction. The results demonstrated that peptide TNTHCDR3 was determined as TNT binding peptide and no non-specific binding was observed. The selectivity of TNT binding peptide TNTHCDR3 was also testified by six kinds of TNT analogues. The results indicated the specific binding between TNT and peptide TNTHCDR3.
TL;DR: In this article, mutated peptides and a homologous series of peptides were designed and prepared, based on the original peptide sequence of an antioxidant peptide from Pinctada fucata meat (PFMAP), to better understand the structural relationships, including primary structure, spatial conformation and activity.