Peptide Pairs Research Articles

The quantum chemical causality of pMHC-TCR biological avidity: Peptide atomic coordination data and the electronic state of agonist N termini.

The quantum state of functional avidity of the synapse formed between a peptide-Major Histocompatibility Complex (pMHC) and a T cell receptor (TCR) is a subject not previously touched upon. Here we present atomic pair correlation meta-data based on crystalized tertiary structures of the Tax (HTLV-1) peptide along with three artificially altered variants, all of which were presented by the (Class I) HLA-A201 protein in complexation with the human (CD8+) A6TCR. The meta-data reveal the existence of a direct relationship between pMHC-TCR functional avidity (agonist/antagonist) and peptide pair distribution function (PDF). In this context, antagonist peptides are consistently under-coordinated in respect to Tax. Moreover, Density Functional Theory (DFT) datasets in the BLYP/TZ2P level of theory resulting from relaxation of the H species on peptide tertiary structures reveal that the coordination requirement of agonist peptides is also expressed as a physical observable of the protonation state of their N termini: agonistic peptides are always found to retain a stable ammonium (NH3+) terminal group while antagonist peptides are not.

Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry

In pathogenic Gram-negative bacteria, interactions among membrane proteins are key mediators of host cell attachment, invasion, pathogenesis, and antibiotic resistance. Membrane protein interactions are highly dependent upon local properties and environment, warranting direct measurements on native protein complex structures as they exist in cells. Here we apply invivo chemical cross-linking mass spectrometry, to reveal the first large-scale protein interaction network in Pseudomonas aeruginosa, an opportunistic human pathogen, by covalently linking interacting protein partners, thereby fixing protein complexes invivo. A total of 626 cross-linked peptide pairs, including previously unknown interactions of many membrane proteins, are reported. These pairs not only define the existence of these interactions in cells but also provide linkage constraints for complex structure predictions. Structures of three membrane proteins, namely, SecD-SecF, OprF, and OprI are predicted using invivo cross-linked sites. These findings improve understanding of membrane protein interactions and structures in cells.

Proteome-wide analysis of mutant p53 targets in breast cancer identifies new levels of gain-of-function that influence PARP, PCNA, and MCM4

The gain-of-function mutant p53 (mtp53) transcriptome has been studied, but, to date, no detailed analysis of the mtp53-associated proteome has been described. We coupled cell fractionation with stable isotope labeling with amino acids in cell culture (SILAC) and inducible knockdown of endogenous mtp53 to determine the mtp53-driven proteome. Our fractionation data highlight the underappreciated biology that missense mtp53 proteins R273H, R280K, and L194F are tightly associated with chromatin. Using SILAC coupled to tandem MS, we identified that R273H mtp53 expression in MDA-MB-468 breast cancer cells up- and down-regulated multiple proteins and metabolic pathways. Here we provide the data set obtained from sequencing 73,154 peptide pairs that then corresponded to 3,010 proteins detected under reciprocal labeling conditions. Importantly, the high impact regulated targets included the previously identified transcriptionally regulated mevalonate pathway proteins but also identified two new levels of mtp53 protein regulation for nontranscriptional targets. Interestingly, mtp53 depletion profoundly influenced poly(ADP ribose) polymerase 1 (PARP1) localization, with increased cytoplasmic and decreased chromatin-associated protein. An enzymatic PARP shift occurred with high mtp53 expression, resulting in increased poly-ADP-ribosylated proteins in the nucleus. Mtp53 increased the level of proliferating cell nuclear antigen (PCNA) and minichromosome maintenance 4 (MCM4) proteins without changing the amount of pcna and mcm4 transcripts. Pathway enrichment analysis ranked the DNA replication pathway above the cholesterol biosynthesis pathway as a R273H mtp53 activated proteomic target. Knowledge of the proteome diversity driven by mtp53 suggests that DNA replication and repair pathways are major targets of mtp53 and highlights consideration of combination chemotherapeutic strategies targeting cholesterol biosynthesis and PARP inhibition.

An Enhanced In Vivo Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Model for Quantification of Drug Metabolism Enzymes *

Many of the enzymes involved in xenobiotic metabolism are maintained at a low basal level and are only synthesized in response to activation of upstream sensor/effector proteins. This induction can have implications in a variety of contexts, particularly during the study of the pharmacokinetics, pharmacodynamics, and drug–drug interaction profile of a candidate therapeutic compound. Previously, we combined in vivo SILAC material with a targeted high resolution single ion monitoring (tHR/SIM) LC-MS/MS approach for quantification of 197 peptide pairs, representing 51 drug metabolism enzymes (DME), in mouse liver. However, as important enzymes (for example, cytochromes P450 (Cyp) of the 1a and 2b subfamilies) are maintained at low or undetectable levels in the liver of unstimulated metabolically labeled mice, quantification of these proteins was unreliable. In the present study, we induced DME expression in labeled mice through synchronous ligand-mediated activation of multiple upstream nuclear receptors, thereby enhancing signals for proteins including Cyps 1a, 2a, 2b, 2c, and 3a. With this enhancement, 115 unique, lysine-containing, Cyp-derived peptides were detected in the liver of a single animal, as opposed to 56 in a pooled sample from three uninduced animals. A total of 386 peptide pairs were quantified by tHR/SIM, representing 68 Phase I, 30 Phase II, and eight control proteins. This method was employed to quantify changes in DME expression in the hepatic cytochrome P450 reductase null (HRN) mouse. We observed compensatory induction of several enzymes, including Cyps 2b10, 2c29, 2c37, 2c54, 2c55, 2e1, 3a11, and 3a13, carboxylesterase (Ces) 2a, and glutathione S-transferases (Gst) m2 and m3, along with down-regulation of hydroxysteroid dehydrogenases (Hsd) 11b1 and 17b6. Using DME-enhanced in vivo SILAC material with tHR/SIM, therefore, permits the robust analysis of multiple DME of importance to xenobiotic metabolism, with improved utility for the study of drug pharmacokinetics, pharmacodynamics, and of chemically treated and genetically modified mouse models.

Intact stable isotope labeled plasma proteins from the SILAC-labeled HepG2 secretome.

The plasma proteome remains an attractive biospecimen for MS-based biomarker discovery studies. The success of these efforts relies on the continued development of quantitative MS-based proteomics approaches. Herein we report the use of the SILAC-labeled HepG2 secretome as a source for stable isotope labeled plasma proteins for quantitative LC-MS/MS measurements. The HepG2 liver cancer cell line secretes the major plasma proteins including serum albumin, apolipoproteins, protease inhibitors, coagulation factors, and transporters that represent some of the most abundant proteins in plasma. The SILAC-labeled HepG2 secretome was collected, spiked into human plasma (1:1 total protein), and then processed for LC-MS/MS analysis. A total of 62 and 56 plasma proteins were quantified (heavy:light (H/L) peptide pairs) from undepleted and depleted (serum albumin and IgG), respectively, with log2 H/L = ± 6. Major plasma proteins quantified included albumin, apolipoproteins (e.g., APOA1, APOA2, APOA4, APOB, APOC3, APOE, APOH, and APOM), protease inhibitors (e.g., A2M and SERPINs), coagulation factors (e.g., Factor V, Factor X, fibrinogen), and transport proteins (e.g., TTR). The average log2 H/L values for shared plasma proteins in both undepleted and depleted plasma samples were 0.43 and 0.44, respectively. This work further expands the SILAC strategy into MS-based biomarker discovery of clinical biospecimens.

Identifying t-cell epitopes of the VP1 capsid protein of human rhinovirus

Background The newly identified HRV-C has been linked to more severe symptoms of asthma and an increased risk of prior and subsequent hospital admission. Our research team has recently reported that despite their sequence dissimilarity, the HRV-A and HRV-C species have a high degree of antibody cross-reactivity and the HRV-C specific antibody response is low (Iwasaki et al., 2013). This study aims to identify species-specific and cross-reactive T-cell epitopes for the HRV-A and HRV-C species. Methods In total, 110 overlapping synthetic peptides of HRV-A (genotype HRV-34) and HRV-C (genotype QPM) were purchased from Mimotopes (Vic, Australia) covering the entire VP1 protein of both genotypes. T-cell proliferation was measured by 3 H-thymidine incorporation. Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of 20 adults from the general population of Perth (WA), with no evidence of current respiratory illness. The PBMCs were cultured in AIM-V media with the individual peptides of HRV-A and HRV-C in triplicate. PHA and PPD were included as positive controls and negative controls contained only media. 3 H-thymidine incorporation was measured after a 6-day culture and a stimulation index of greater than 2 (calculated by the mean of wells containing antigen divided by the mean of the negative control wells) was considered a positive lymphoproliferative response. Variation on replicate cultures was lower than 20%. Results We have identified four species-specific peptides for HRV-QPM and three for HRV-34 that triggered T-cell proliferation in more than 50% of the tested subjects. Four pairs of cross-reactive peptides were identified for HRV-A and HRV-C that stimulated the cells of more than 40% of the subjects tested. Conclusions To our knowledge, this is the first study to map T-cell epitopes in a genotype of HRV-C and also the first to map the entire HRV VP1 protein. Future HLA typing and in silico studies for other HRV-A and HRV-C genotypes based on the reactive peptides will be conducted. These findings will help to identify differences in the immune recognition of the two most prevalent HRV species and are valuable tools for future vaccine development.

Separate and overlapping specificities in rheumatoid arthritis antibodies binding to citrulline- and homocitrulline-containing peptides related to type I and II collagen telopeptides.

IntroductionOur objective was to find out if there are antibodies binding to homocitrulline-containing type I and II collagen carboxyterminal telopeptides in sera of patients with rheumatoid arthritis (RA), and if these antibodies cross-react with citrulline and homocitrulline in the same peptide sequence.MethodsA total of 72 RA and 72 control sera were analyzed for binding using enzyme-linked immunosorbent assay to citrulline- or homocitrulline-containing type I and II collagen carboxyterminal telopeptides, as well as to cyclic citrullinated peptide (CCP) and to mutated citrullinated vimentin (MCV). Specificities of the antibodies were tested using inhibition-ELISA.ResultsOf the RA sera, 39 (54%) and 41 (57%) were positive for binding to CCP and MCV, respectively. Further, 34 (47%) and 30 (42%) of the patients had specific antibodies binding to and being inhibited by citrulline-containing type I collagen telopeptides and by citrulline-containing type II collagen carboxyterminal telopeptides, respectively. The corresponding figures regarding homocitrulline-containing type I and homocitrulline-containing type II collagen telopeptides were 16 (22%) and 14 (19%). Most of the patients, who were seropositive for citrullinated peptides, showed binding in multiple assays. A total of 10 (14%) RA patients were positive for all the tested peptide pairs, while 28 (39%) of them had antibodies that contained overlapping specifities between citrulline and homocitrulline in the same peptide sequence.ConclusionsAntibodies to both citrulline and homocitrulline containing type I and II collagen telopeptides can be found in sera of RA patients. These antibodies are not constant from one RA patient to another, but contain separate or overlapping specificities within the same peptide sequence varying between individuals. Our results suggest some relationship between citrulline and homocitrulline-recognizing antibodies, since homocitrulline antibodies exist mainly in individuals seropositive to anti-CCP and anti-MCV.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-014-0515-z) contains supplementary material, which is available to authorized users.

Screening for Potential HLA-DRB1-Restricted T-Cell Epitopes in Factor VIII Using Peptide Microarrays

Therapeutic factor VIII (FVIII) infusions provoke CD4 T-cell proliferation and cytokine secretion leading to neutralizing anti-FVIII antibodies (inhibitors) in a substantial fraction of hemophilia A patients, leading to bleeding that is difficult to control. T-cell stimulation occurs when FVIII peptides bind to HLA-DRB1 proteins and are presented on the surface of antigen presenting cells, followed by T-cell recognition of these peptide-HLA-DRB1 complexes. Our laboratory is interested in identifying immunodominant, HLA-restricted T-cell epitopes in FVIII, in order to identify and then modify these immunological “hotspots” that cause inhibitors to develop. We have previously mapped several immunodominant HLA-restricted T-cell epitopes in FVIII recognized by the immune systems of inhibitor subjects, using HLA-DRB1 tetramers loaded with 20-mer FVIII peptides. However, because FVIII is such a large protein (>2,000 amino acid residues), methods more efficient than systematic mapping using overlapping peptides spanning its sequence would be useful. This study focuses on the binding of FVIII peptides to recombinant extracellular domains of 10 HLA-DRB1 proteins, which together represent HLA-DRB1 alleles found in >50% of the U.S population. PepStarTM (JPT Peptide Technologies) microarrays containing triplicate sets of FVIII peptides immobilized on glass slides via a flexible linker were incubated with HLA-DRB1 proteins at several dilutions, followed by incubation with a fluorescent-labeled antibody that recognizes the peptide-bound conformations of HLA-DRB1 proteins, and the slides were washed and read on a microarray scanner. The intensities of fluorescent signals from the triplicate sets of spots were quantified and also displayed as heat maps. Fluorescent signals ranged from background levels (indicating no binding) up to the detector saturation range. Between 20-40% of the FVIII peptides produced fluorescent signals indicating peptide binding to each of the HLA-DRB1 proteins tested, including positive control peptides containing FVIII and non-FVIII epitopes with known HLA-DRB1 restriction. The percentage of apparently high-affinity binding interactions was much lower. T-cell epitopes are generally 10-14 amino acid residues long. Therefore, strong signals from pairs of 20-mer peptides with a 12-residue overlapping sequence localized the FVIII sequence fitting into the HLA-DRB1 binding groove to the overlapping region, while disparate signals from other pairs of overlapping sequences localized the HLA-DRB1 binding sequence to the non-overlapping regions. For subsets of the FVIII peptides, the signal strengths were compared to (a) affinities (IC50 values) derived from quantitative, competition peptide-HLA-DRB1 binding assays, and (b) results of computer prediction algorithms MHCPanII and Propred. Peptides that bound strongly to one or more HLA-DRB1 protein were prioritized for further testing. This microarray-based screening procedure is an efficient method to generate manageable lists of potential T-cell epitopes in large antigenic proteins such as FVIII, where systematic epitope mapping using HLA-DRB1 tetramers loaded with peptides spanning the entire sequence is not feasible, due to both the high cost of such experiments and the blood volumes that can reasonably be requested from patient volunteers. DisclosuresNo relevant conflicts of interest to declare.

Catalytically Relevant Electrostatic Interactions of Cytochrome P450c17 (CYP17A1) and Cytochrome b5

Two acidic residues, Glu-48 and Glu-49, of cytochrome b5 (b5) are essential for stimulating the 17,20-lyase activity of cytochrome P450c17 (CYP17A1). Substitution of Ala, Gly, Cys, or Gln for these two glutamic acid residues abrogated all capacity to stimulate 17,20-lyase activity. Mutations E49D and E48D/E49D retained 23 and 38% of wild-type activity, respectively. Using the zero-length cross-linker ethyl-3-(3-dimethylaminopropyl)carbodiimide, we obtained cross-linked heterodimers of b5 and CYP17A1, wild-type, or mutations R347K and R358K. In sharp contrast, the b5 double mutation E48G/E49G did not form cross-linked complexes with wild-type CYP17A1. Mass spectrometric analysis of the CYP17A1-b5 complexes identified two cross-linked peptide pairs as follows: CYP17A1-WT: (84)EVLIKK(89)-b5: (53)EQAGGDATENFEDVGHSTDAR(73) and CYP17A1-R347K: (341)TPTISDKNR(349)-b5: (40)FLEEHPGGEEVLR(52). Using these two sites of interaction and Glu-48/Glu-49 in b5 as constraints, protein docking calculations based on the crystal structures of the two proteins yielded a structural model of the CYP17A1-b5 complex. The appositional surfaces include Lys-88, Arg-347, and Arg-358/Arg-449 of CYP17A1, which interact with Glu-61, Glu-42, and Glu-48/Glu-49 of b5, respectively. Our data reveal the structural basis of the electrostatic interactions between these two proteins, which is critical for 17,20-lyase activity and androgen biosynthesis.

Automated immunoassays for the autoantibodies to carbamylated or citrullinated telopeptides of type I and II collagens.

The aim of the study was to describe automated immunoassays for autoantibodies to homocitrulline or citrulline containing telopeptides of type I and II collagen in various disease categories in an early arthritis series. Serum samples were collected from 142 patients over 16 years of age with newly diagnosed inflammatory joint disease. All samples were analyzed with an automated inhibition chemiluminescence immunoassay (CLIA) using four different peptide pairs, each consisting of a biotinylated antigen and an inhibiting peptide. Assays were performed with an IDS-iSYS analyzer. Autoantibodies binding to homocitrulline and citrulline containing C-telopeptides of type I (HTELO-I, TELO-I) and type II collagens (HTELO-II, TELO-II) were analyzed. The mean ratio of HTELO-I inhibition in seropositive and seronegative rheumatoid arthritis (RA) was 3.07 (95% CI 1.41-11.60), p=0.003, and in seropositive and seronegative undifferentiated arthritis (UA) 4.90 (1.85-14.49), p<0.001. The respective mean ratios in seropositive and seronegative RA and UA were in TELO-I 8.72 (3.68-58.01), p<0.001 and 3.13 (1.49-6.16), p=0.008, in HTELO-II 7.57 (3.18-56.60), p<0.001 and 2.97 (1.23-6.69), p=0.037, and in TELO-II 3.01 (1.30-9.51), p=0.002 and 3.64 (1.86-7.65), p=0.008. In reactive arthritis, ankylosing spondylitis, psoriatic arthritis and unspecified spondyloarthritis the inhibition levels were similar to those observed in seronegative RA or UA. Autoantibodies binding to homocitrulline or citrulline containing telopeptides of type I and II collagen did not differ significantly. They were highest among patients with seropositive disease and they differentiated seropositive and seronegative arthritis.

XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry.

BackgroundChemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, and to the overall low-abundance of cross-link species in the background of linear peptides. Cross-linkers non-specific at one end, such as photo-inducible diazirines, may complicate the analysis further. In this report, we design and validate a novel cross-linked peptide mapping algorithm (XLPM) and compare it to StavroX, which is currently one of the best algorithms in this class.ResultsWe have designed a novel cross-link search algorithm -XLPM - and implemented it both as an online tool and as a downloadable archive of scripts. We designed a filter based on an observation that observation of a b-ion implies observation of a complimentary y-ion with high probability (b-y filter). We validated the b-y filter on the set of linear peptides from NIST library, and demonstrate that it is an effective way to find high-quality mass spectra. Next, we generated cross-linked data from an ssDNA binding protein, Rim1with a specific cross-linker disuccinimidyl suberate, and a semi-specific cross-linker NHS-Diazirine, followed by analysis of the cross-linked products by nanoLC-LTQ-Orbitrap mass spectrometry. The cross-linked data were searched by XLPM and StavroX and the performance of the two algorithms was compared. The cross-links were mapped to the X-ray structure of Rim1 tetramer. Analysis of the mixture of NHS-Diazirine cross-linked 15N and 14N-labeled Rim1 tetramers yielded 15N-labeled to 14N-labeled cross-linked peptide pairs, corresponding to C-terminus-to-N-terminus cross-linking, demonstrating interaction between different two Rim1 tetramers. Both XLPM and StavroX were successful in identification of this interaction, with XLPM leading to a better annotation of higher-charged fragments. We also put forward a new method of estimating specificity and sensitivity of identification of a cross-linked residue in the case of a non-specific cross-linker.ConclusionsThe novel cross-link mapping algorithm, XLPM, considerably improves the speed and accuracy of the analysis compared to other methods. The quality selection filter based on b-to-y ions ratio proved to be an effective way to select high quality cross-linked spectra.

Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions.

Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein–protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein–protein interactions within whole animals.

A Simple Carbamidomethylation-Based Isotope Labeling Method for Quantitative Shotgun Proteomics

In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as a complementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of all cysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA- 13 C2, D2), denoted as CM and iCCM, respectively, leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantifica- tion, 6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, and alpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. The resulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimental results, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional noniso- baric labeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative varia- tions in the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developed iCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study

Coiled Coil Peptides and Polymer–Peptide Conjugates: Synthesis, Self-Assembly, Characterization and Potential in Drug Delivery Systems

Coiled coils are a common structural motif in many natural proteins that can also be utilized in the design and preparation of drug delivery systems for the noncovalent connection of two macromolecules. In this work, two different pairs of peptides forming coiled coil hetero-oligomers were designed, synthesized, and characterized. While the peptide sequences (VAALEKE)4 and (VAALKEK)4 predominantly form coiled coil heterodimers with randomly orientated peptide chains, (IAALESE)2-IAALESKIAALESE and IAALKSKIAALKSE-(IAALKSK)2 tend to form higher hetero-oligomers with an antiparallel orientation of their peptide chains. The associative behavior of these peptides was studied in aqueous solutions using circular dichroism spectroscopy, size-exclusion chromatography, isothermal titration calorimetry and sedimentation analyses. The orientation of the peptide chains in the coiled coil heterodimers was assessed using fluorescence spectroscopy with fluorescence resonance energy transfer labels attached to the ends of the peptides. The formation of the heterodimer can be used as a general method for the selective noncovalent conjugation of a specific targeting moiety with various drug carrier systems; this process involves simple self-assembly in a physiological solution before drug administration. The preparation of targeted macromolecular therapeutics consisting of a synthetic polymer drug carrier and a recombinant protein targeting ligand is discussed.

Identification of New Citrulline‐Specific Autoantibodies, Which Bind to Human Arthritic Cartilage, by Mass Spectrometric Analysis of Citrullinated Type II Collagen

To investigate type II collagen (CII) as a joint-specific target of the anti-citrullinated protein antibody (ACPA) response in rheumatoid arthritis (RA). Potential citrullinated neoepitopes were identified by high-resolution tandem mass spectrometry (MS/MS) of in vitro peptidylarginine deiminase 2 (PAD-2)-treated CII, and the relationship between citrullination and CII conformation was investigated by circular dichroism and conformation-dependent antibodies. Based on the MS analyses, synthetic peptides were designed and analyzed for serum IgG reactivity in the Epidemiological Investigation of RA (EIRA) case-control cohort of 1,949 RA patients and 278 healthy controls. Peptide-specific antibodies were purified from RA patient serum and used to stain RA cartilage specimens. We described the conformation-dependent citrullination pattern of CII after PAD-2 treatment at room temperature and 37°C and showed that CII could be citrullinated in its native triple-helical conformation. Screening of Arg and Cit pairs of synthetic peptides revealed new citrullinated B cell epitopes on CII. Antibodies directed to 2 proximal epitopes close to the C-terminus of the CII triple helix were recognized by autoantibodies in 21% and 17% of RA patients, respectively. Affinity-purified antibodies from RA sera directed to these 2 epitopes, but not antibodies directed to citrullinated α-enolase peptide 1, bound to RA cartilage. These findings suggest that cartilage-directed anticitrulline immunity contributes to the induction of joint inflammation in RA.

A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database

A high molecular weight fraction of a HeLa cell nuclear extract containing nearly 1100 identified proteins was cross-linked with bis(succinimidyl)-3-azidomethyl glutarate (BAMG). The azido group in cross-linked peptides can be reduced to an amine group. Reduction enables isolation of cross-linked peptides by diagonal strong cation exchange chromatography. Collision-induced dissociation (CID) of reduced cross-linked peptides shows abundant cleavage of the cross-link amide bonds, along with the cleavage of peptide bonds of the composing peptide pair. A defined relationship exists between the sum of the masses of a pair of cleavage products and the mass of the parent compound. This relationship enables accurate mass determination of the two composing peptides. With this knowledge, the identity of the pair of peptides in a cross-link is revealed at an extremely low false discovery rate by peptide fragment fingerprinting with MS1MS2 data from the entire human sequence databases with a conventional search engine for peptide identification. Our approach resulted in identification of 229 intraprotein and 18 interprotein cross-links. Mapping protein-protein interactions in complex samples like digests of in vitro cross-linked extracts, by interrogation of entire species specific sequence database with tandem mass spectrometric data may yield repositories of cross-linked peptides. Results will reveal interactions between proteins, the identity of which may lead to new hypotheses about molecular mechanisms and regulations of biological function, or new targets for drug development. In this paper we describe a new analytical strategy that improves existing approaches of cross-link mapping in complex samples. The cross-linker that we have designed and synthesized for our approach is membrane permeable. This opens avenues for in vivo cross-linking for better understanding of dynamic protein complex topologies involved in many biological processes.

Interaction-dependent Native Chemical Ligation and Enzyme Reconstitution for Detection of Peptide–Peptide Interaction

Abstract A new detection method for ligand–protein interactions was constructed using interaction-dependent native chemical ligation and enzyme reconstitution (IDNCL-ER) by employing ribonuclease S. Using a coiled-coil peptide pair as a model of ligand–protein interactions, we determined that IDNCL-ER can work well to detect the peptide–peptide interactions by enzymatic activity.

Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry

Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS) of plasma that has been depleted of abundant proteins and fractionated at the peptide level into six to eight fractions is a proven method for quantifying proteins present at low nanogram-per-milliliter levels. A drawback of fraction-MRM is the increased analysis time due to the generation of multiple fractions per biological sample. We now report that the use of heated, long, fused silica columns (>30 cm) packed with 1.9 μm of packing material can reduce or eliminate the need for fractionation prior to LC-MRM-MS without a significant loss of sensitivity or precision relative to fraction-MRM. We empirically determined the optimal column length, temperature, gradient duration, and sample load for such assays and used these conditions to study detection sensitivity and assay precision. In addition to increased peak capacity, longer columns packed with smaller beads tolerated a 4- to 6-fold increase in analyte load without a loss of robustness or reproducibility. The longer columns also provided a 4-fold improvement in median limit-of-quantitation values with increased assay precision relative to the standard 12 cm columns packed with 3 μm material. Overall, the optimized chromatography provided an approximately 3-fold increase in analysis throughput with excellent robustness and less than a 2-fold reduction in quantitative sensitivity relative to fraction-MRM. The value of the system for increased multiplexing was demonstrated by the ability to configure an 800-plex MRM-MS assay, run in a single analysis, comprising 2400 transitions with retention time scheduling to monitor 400 unlabeled and heavy labeled peptide pairs.

Degranulation of basophilic leukemia cells on branched-chain peptide array with an OVA–DNP double epitope

Simple method for identification of heterovalent allergen epitopes was constructed to reflect the allergic reaction initiated by the cross-linking of the IgE receptors. The peptide array-based degranulation assay that enables interaction between solid support-bound peptide pairs and IgE sensitized basophilic leukemia cells was developed. Using lysine side chains, a chicken egg white ovalbumin (OVA) epitope and a dinitrophenol (DNP) modified amino acid was synthesized in the branched-chain peptide array. The basophilic leukemia cells sensitized with anti-OVA IgE and anti-DNP IgE induced degranulation directly on the branched-chain peptide array. The OVA–DNP double peptide disk caused the release of 37.5% of β-hexosaminidase whereas the DNP-only peptide disk caused the release by 20.9%. These results show that the double epitope branched-chain peptide array can induce degranulation, and would represent a suitable model for screening the heterovalent epitope pairs of allergens.

Characterization of the Raptor/4E-BP1 Interaction by Chemical Cross-linking Coupled with Mass Spectrometry Analysis

mTORC1 plays critical roles in the regulation of protein synthesis, growth, and proliferation in response to nutrients, growth factors, and energy conditions. One of the substrates of mTORC1 is 4E-BP1, whose phosphorylation by mTORC1 reverses its inhibitory action on eIF4E, resulting in the promotion of protein synthesis. Raptor in mTOR complex 1 is believed to recruit 4E-BP1, facilitating phosphorylation of 4E-BP1 by the kinase mTOR. We applied chemical cross-linking coupled with mass spectrometry analysis to gain insight into interactions between mTORC1 and 4E-BP1. Using the cross-linking reagent bis[sulfosuccinimidyl] suberate, we showed that Raptor can be cross-linked with 4E-BP1. Mass spectrometric analysis of cross-linked Raptor-4E-BP1 led to the identification of several cross-linked peptide pairs. Compilation of these peptides revealed that the most N-terminal Raptor N-terminal conserved domain (in particular residues from 89 to 180) of Raptor is the major site of interaction with 4E-BP1. On 4E-BP1, we found that cross-links with Raptor were clustered in the central region (amino acid residues 56-72) we call RCR (Raptor cross-linking region). Intramolecular cross-links of Raptor suggest the presence of two structured regions of Raptor: one in the N-terminal region and the other in the C-terminal region. In support of the idea that the Raptor N-terminal conserved domain and the 4E-BP1 central region are closely located, we found that peptides that encompass the RCR of 4E-BP1 inhibit cross-linking and interaction of 4E-BP1 with Raptor. Furthermore, mutations of residues in the RCR decrease the ability of 4E-BP1 to serve as a substrate for mTORC1 in vitro and in vivo.