Tryptic Cleavage Research Articles

A Highly Efficient Multifunctional Tandem Affinity Purification Approach Applicable to Diverse Organisms

Determining the localization, binding partners, and secondary modifications of individual proteins is crucial for understanding protein function. Several tags have been constructed for protein localization or purification under either native or denaturing conditions, but few tags permit all three simultaneously. Here, we describe a multifunctional tandem affinity purification (MAP) method that is both highly efficient and enables protein visualization. The MAP tag utilizes affinity tags inserted into an exposed surface loop of mVenus offering two advantages: (1) mVenus fluorescence can be used for protein localization or FACS-based selection of cell lines; and (2) spatial separation of the affinity tags from the protein results in high recovery and reduced variability between proteins. MAP purification was highly efficient in multiple organisms for all proteins tested. As a test case, MAP combined with liquid chromatography-tandem MS identified known and new candidate binding partners and modifications of the kinase Plk1. Thus the MAP tag is a new powerful tool for determining protein modification, localization, and interactions.

Soil proteomics: An assessment of its potential for archaeological site interpretation

In this work, two sets of experiments were carried out to assess the potential of soil proteomics for archaeological site interpretation. First, we examined the effects of various protein isolation reagents and soil constituents on peptide mass fingerprinting (PMF) of soil-like materials spiked with bovine serum albumin (BSA). In a subsequent case study, we assessed the relative age of soils from an ancient clay floor of a Roman farmhouse using amino acid racemization and then applied MALDI-TOF–MS–MS to detect and identify biomarkers for human occupation. The results from the first experiments indicate that BSA isolation efficiencies are hampered by the presence of clays and reactive organic matter (glucose), whereas these effects are, to some extent, reversed by the presence of humic acids. We also show that specific regions of the BSA molecule (the out most α-helical regions of domain 2 and 3) are more susceptible to isolation than other regions and this suggest that soil proteins can be only partly isolated. Soil–protein interactions were also found to inhibit tryptic cleavage of BSA, resulting in an enhanced specificity of BSA peptides. Our results further stress the importance of multiple or sequential protein isolation protocols with a focus on citrate and hydrofluoric acid. Results from the case study indicate that the ancient floor samples contain degraded and most likely aged proteinaceous matter, probably of keratinaceous origin.

Phosphorylated serine and threonine residues of PAR2 C‐terminus regulate Beta arrestin 1/2 recruitment and signaling

Protease activated receptor 2 (PAR2) is activated by tryptic cleavage of the N terminus, to trigger signaling by the classic Gq pathway. Following receptor activation scaffolding molecules Beta arrestin 1/2 bind to C terminus of the receptor to terminate G protein signaling and promote internalization. Simultaneously, this triggers Beta arrestin 1/2 dependent effects like chemotaxis through membrane ERK1/2 activation and cofilin dephosphorylation and PI3kinase activation. The exact role of PAR2 C‐tail phosphorylation in arrestin recruitment and the subsequent downstream effects remain unclear. Bioluminescence Resonance Energy Transfer (BRET) assays using inhibitors of the Gq pathway showed that arrestin recruitment to PAR2 can take place independently of initial Gq signaling. Using PAR2WT, PAR2S363/6A (Protein kinase C mutant) and PAR20P (phosphorylation null mutant) we observed that, Beta arrestin 1/2 recruitment rates are significantly attenuated in absence of PKC mediated C‐tail phosphorylation. Beta arrestin 1/2 recruitment to PAR20P was completely abolished. While PAR2WT promote robust cofilin activation and chemotaxis, PAR2S363/6A and PAR20P fail to do so. Thus, although Beta arrestin 1/2 recruitment to PAR2 C tail can take place in absence of initial Gq signaling, the C‐tail needs to be phosphorylated, to ensure stable association of Beta arrestin 1/2 with PAR2 C‐tails.

Phosphorylation of serine residues in the N-terminus modulates the activity of ACA8, a plasma membrane Ca2+-ATPase of Arabidopsis thaliana

ACA8 is a plasma membrane-localized isoform of calmodulin (CaM)-regulated Ca2+-ATPase of Arabidopsis thaliana. Several phosphopeptides corresponding to portions of the regulatory N-terminus of ACA8 have been identified in phospho-proteomic studies. To mimic phosphorylation of the ACA8 N-terminus, each of the serines found to be phosphorylated in those studies (Ser19, Ser22, Ser27, Ser29, Ser57, and Ser99) has been mutated to aspartate. Mutants have been expressed in Saccharomyces cerevisiae and characterized: mutants S19D and S57D—and to a lesser extent also mutants S22D and S27D—are deregulated, as shown by their low activation by CaM and by tryptic cleavage of the N-terminus. The His-tagged N-termini of wild-type and mutant ACA8 (6His-1M-I116) were expressed in Escherichia coli, affinity-purified, and used to analyse the kinetics of CaM binding by surface plasmon resonance. All the analysed mutations affect the kinetics of interaction with CaM to some extent: in most cases, the altered kinetics result in marginal changes in affinity, with the exception of mutants S57D (KD ∼10-fold higher than wild-type ACA8) and S99D (KD about half that of wild-type ACA8). The ACA8 N-terminus is phosphorylated in vitro by two isoforms of A. thaliana calcium-dependent protein kinase (CPK1 and CPK16); phosphorylation of mutant 6His-1M-I116 peptides shows that CPK16 is able to phosphorylate the ACA8 N-terminus at Ser19 and at Ser22. The possible physiological implications of the subtle modulation of ACA8 activity by phosphorylation of its N-terminus are discussed.

The Interaction between the First Transmembrane Domain and the Thumb of ASIC1a Is Critical for Its N-Glycosylation and Trafficking

Acid-sensing ion channel-1a (ASIC1a), the primary proton receptor in the brain, contributes to multiple diseases including stroke, epilepsy and multiple sclerosis. Thus, a better understanding of its biogenesis will provide important insights into the regulation of ASIC1a in diseases. Interestingly, ASIC1a contains a large, yet well organized ectodomain, which suggests the hypothesis that correct formation of domain-domain interactions at the extracellular side is a key regulatory step for ASIC1a maturation and trafficking. We tested this hypothesis here by focusing on the interaction between the first transmembrane domain (TM1) and the thumb of ASIC1a, an interaction known to be critical in channel gating. We mutated Tyr71 and Trp287, two key residues involved in the TM1-thumb interaction in mouse ASIC1a, and found that both Y71G and W287G decreased synaptic targeting and surface expression of ASIC1a. These defects were likely due to altered folding; both mutants showed increased resistance to tryptic cleavage, suggesting a change in conformation. Moreover, both mutants lacked the maturation of N-linked glycans through mid to late Golgi. These data suggest that disrupting the interaction between TM1 and thumb alters ASIC1a folding, impedes its glycosylation and reduces its trafficking. Moreover, reducing the culture temperature, an approach commonly used to facilitate protein folding, increased ASIC1a glycosylation, surface expression, current density and slowed the rate of desensitization. These results suggest that correct folding of extracellular ectodomain plays a critical role in ASIC1a biogenesis and function.

UPLC-MS/MS Method for the Identification of Recombinant Human Erythropoietin Analogues in Horse Plasma and Urine

Recombinant human erythropoietin (rhEPO) analogues are known to have been used in horse sports for their assumed performance enhancing properties. Recently, several authors have published liquid chromatographic-tandem mass spectrometric (LC-MS/MS) methods for confirming the presence of rhEPO analogues in horse plasma. In the current study, an improved LC-MS/MS confirmatory procedure for rhEPO, darbepoetin (DPO) and continuous erythropoietin receptor activator (CERA) in horse plasma was developed and validated. The method was also adapted for and applied to urine samples for the first time. Similar to previously published plasma assays, the methods utilise size exclusion and immunoaffinity extraction prior to tryptic cleavage, enzymatic deglycosylation and LC-MS/MS analysis of the resulting signature tryptic peptides (rhEPO/CERA T5, rhEPO/CERA/DPO T6 and DPO T9). However, the novel application of UPLC chromatography significantly improves the run time of the method compared to nano- or micro-LC and its robustness compared to nano-LC. Furthermore, recombinant canine EPO was found to serve as an effective internal standard, thus allowing confidence in interpretation of the success/failure of every step in the procedure. Limits of detection for confirming the presence of rhEPO, CERA and DPO in plasma were 0.1, 0.25 and 0.05 ng mL−1, respectively, which were equal to or lower than limits achieved using previously published LC-MS/MS based methods. Limits of detection for confirming the presence of rhEPO, CERA and DPO in urine were 0.05, 0.15 and 0.025 ng mL−1 and the analysis of urine samples collected from horses administered rhEPO (Eprex™) or DPO (Aranesp™) demonstrated the use of this matrix as a suitable alternative in situations where plasma is not available.

Measurement of the total proANP product in mammals by processing independent analysis

The cellular processing of natriuretic propeptides is attenuated in heart disease, resulting in release of a mixture of unprocessed precursor, partially processed fragments, and the bioactive hormone. Here, we report a species-independent method for quantification of pro-atrial natriuretic peptide (proANP) and its products irrespective of variable post-translational processing. The processing-independent assay (PIA) was developed raising mono-specific antibodies against the C-terminus of sequence 1–16 in proANP. The assay procedure included plasma extraction followed by tryptic cleavage, which releases the assay epitope from the N-terminal region. The PIA was tested in elderly patients with symptoms of heart failure (n = 450), in pigs with acute myocardial infarction (n = 21), and in normal dogs and dogs with heart failure (n = 77). The epitope specificity permitted reliable measurement in man, dog, cat and pig. In human plasma, the PIA correlated well with an established proANP analysis (r = 0.86, P < 0.0001) but with a 5.5-fold difference in plasma level ( P < 0.0001). In pigs, the PIA measured 9.2-fold higher concentrations compared to a human assay (804 versus 87 pmol/L, P < 0.0001). The basal proANP concentration was 396 pmol/L in dogs: a dramatic increase was seen in canine heart failure. Our new processing- and species-independent proANP assay allows for the measurement of the total proANP product, irrespective of changes in post-translational maturation. We suggest that this tool should be used for comparative studies between human patients and porcine and canine models of human cardiac disease.

Non-small cell lung cancer (NSCLC), analysis of healthy, non-smoking, and smoking patients by MALDI imaging mass spectrometry: Proteomic updating perspective.

e21147 Background: Imaging MALDI Mass spectrometry (IMS) was applied to study tumor tissue of NSCLC subtypes adenocarcinoma (ADK). After a previous comparison of healthy (H) and tumor tissues (TT) on slides from frozen biopsies, our objective was : i) to execute an IMS analysis comparing the mass finger print proteome (MFPP) of smoking (S) versus non smoking (NS) patients from formalin-fixed paraffin-embedded tissue microarrays (TMA) followed by a tryptic treatment ii) to apply a large group of statistical methods iii) validate these proteomic. Methods: Specific profiling of tumor proteome by in situ imaging mass spectrometry was performed with a Maldi Tof-Tof apparatus (ULTRAFLEX III Bruker-De).(H) and (TT) cohort were frozen (40 patients). All tissues were controlled and the stages determined by the pathologist diagnosis. TMA were obtained by slides from paraffin blocks with 33 patients. After removal of paraffin and in situ tryptic digestion we analyzed proteic fragments (800 spectrums/group). Results: we observed that the proteome of the two classes (H) and (TT) start to be different only from the stage IB to IV tested. This was confirmed the PCA analysis. The simple and hierarchical clustering corresponding confirm these two distinct classes of proteome and permit to select groups of masses oriented to biomarkers. This was similar the same for TMA, but the proteome of these stages, with IMS, was not the same in the 2 classes (S) and (NS). In each condition were analyzed the under and upper expression to select potential biomarkers. Conclusions: Then main interest of our study is to characterize the proteome of each class analyzed indeed in the under expressed m/z group from the ratio (NS)/(S) we have found 4 tryptic fragments of 1320, 1793, 1838 and 2704 which could be candidates to correspond to fragments of tryptic cleavage in silico of glypican 5 justly under expressed and associated to lung cancer in never smokers (Yafei Li and al. Lancet 2010).

Liquid chromatography/tandem mass spectrometry based targeted proteomics quantification of P‐glycoprotein in various biological samples

P-Glycoprotein (P-gp/ABCB1) is expressed in membrane barriers to exclude pharmacological substrates from cells, and therefore influences the ADME/Tox properties and efficacy of therapeutics. In the present study, a liquid chromatography/tandem mass spectrometry (LC/MS/MS)-mediated targeted proteomics was developed to quantitate P-gp protein. With the aid of in silico predictive tools, a unique 9-mer tryptic peptide of P-gp protein was synthesized (with the stable isotope labeled (SIL) peptide as internal standard) and applied for quantitative LC/MS/MS method development. For LC/MS/MS quantification, the N-glycosylation of the peptide, polymorphism and transmembrane region was intended to be excluded during the peptide selection. The lower limit of quantification was established to be 0.025 nM with the linearity of the standard curve ranging to 20 nM of P-gp signature peptides in the matrix digested surrogate bovine serum albumin. The digestion efficiency, both the accuracy (relative error) and the precision (coefficient of variation) of the method, was verified by using the synthetic quantification peptide and the synthetic surrogate substrate peptide that mimics the sequence of tryptic peptide and associated flanking tryptic cleavage sites at the N- and C-terminals. By applying the method developed, the absolute amounts of human, dog and mouse P-gp (Mdr1a) were quantified in various biological samples. LC/MS/MS-mediated P-gp quantification was achieved as a highly sensitive, selective and reproducible assay and could be directly applicable to many current research needs related to P-gp.

Quantitative analysis of erythropoietin in human plasma by tandem mass spectrometry

The extended use of protein drugs in therapeutics has created the need for their quantification in human plasma. A methodology using the therapeutic protein itself as internal standard for quantitative analysis by multiple reaction monitoring (MRM) has been designed and applied to epoetin beta, a recombinant human erythropoietin (rhEPO). After depletion of major proteins, plasma samples were desalted and enriched in rhEPO by reversed phase liquid chromatography prior to tryptic cleavage. Differential isotopic labeling of peptides was performed by derivatization with 2-methoxy-4,5-dehydro-imidazole. A light version (four hydrogen atoms) of this reagent was used for plasma peptides. Tryptic peptides obtained from pure rhEPO were derivatized with a heavy version (four deuterium atoms) of the same reagent and used as internal standards. Two rhEPO tryptic peptides with three MRM transitions per peptide were selected for quantification. This strategy provided a quantification limit close to 50 amol of epoetin beta per microliter of plasma (equivalent to 1.7 ng/mL), i.e., well below the expected therapeutic concentrations in plasma (around 100-500 amol/μL).

Sequence Elucidation of an Unknown Cyclic Peptide of High Doping Potential by ETD and CID Tandem Mass Spectrometry

Identification of an unknown substance without any information remains a daunting challenge despite advances in chemistry and mass spectrometry. However, an unknown cyclic peptide in a sample with very limited volume seized at a Pennsylvania racetrack has been successfully identified. The unknown sample was determined by accurate mass measurements to contain a small unknown peptide as the major component. Collision-induced dissociation (CID) of the unknown peptide revealed the presence of Lys (not Gln, by accurate mass), Phe, and Arg residues, and absence of any y-type product ion. The latter, together with the tryptic digestion results of the unusual deamidation and absence of any tryptic cleavage, suggests a cyclic structure for the peptide. Electron-transfer dissociation (ETD) of the unknown peptide indicated the presence of Gln (not Lys, by the unusual deamidation), Phe, and Arg residues and their connectivity. After all the results were pieced together, a cyclic tetrapeptide, cyclo[Arg-Lys-N(C(6)H(9))Gln-Phe], is proposed for the unknown peptide. Observations of different amino acid residues from CID and ETD experiments for the peptide were interpreted by a fragmentation pathway proposed, as was preferential CID loss of a Lys residue from the peptide. ETD was used for the first time in sequencing of a cyclic peptide; product ions resulting from ETD of the peptide identified were categorized into two types and named pseudo-b and pseudo-z ions that are important for sequencing of cyclic peptides. The ETD product ions were interpreted by fragmentation pathways proposed. Additionally, multi-stage CID mass spectrometry cannot provide complete sequence information for cyclic peptides containing adjacent Arg and Lys residues. The identified cyclic peptide has not been documented in the literature, its pharmacological effects are unknown, but it might be a "designer" drug with athletic performance-enhancing effects.

Human Phenotypically Distinct TGFBI Corneal Dystrophies Are Linked to the Stability of the Fourth FAS1 Domain of TGFBIp

Mutations in the human TGFBI gene encoding TGFBIp have been linked to protein deposits in the cornea leading to visual impairment. The protein consists of an N-terminal Cys-rich EMI domain and four consecutive fasciclin 1 (FAS1) domains. We have compared the stabilities of wild-type (WT) human TGFBIp and six mutants known to produce phenotypically distinct deposits in the cornea. Amino acid substitutions in the first FAS1 (FAS1-1) domain (R124H, R124L, and R124C) did not alter the stability. However, substitutions within the fourth FAS1 (FAS1-4) domain (A546T, R555Q, and R555W) affected the overall stability of intact TGFBIp revealing the following stability ranking R555W>WT>R555Q>A546T. Significantly, the stability ranking of the isolated FAS1-4 domains mirrored the behavior of the intact protein. In addition, it was linked to the aggregation propensity as the least stable mutant (A546T) forms amyloid fibrils while the more stable variants generate non-amyloid amorphous deposits in vivo. Significantly, the data suggested that both an increase and a decrease in the stability of FAS1-4 may unleash a disease mechanism. In contrast, amino acid substitutions in FAS1-1 did not affect the stability of the intact TGFBIp suggesting that molecular the mechanism of disease differs depending on the FAS1 domain carrying the mutation.

A Novel Proteomics Approach to Identify SUMOylated Proteins and Their Modification Sites in Human Cells

The small ubiquitin-related modifier (SUMO) is a small group of proteins that are reversibly attached to protein substrates to modify their functions. The large scale identification of protein SUMOylation and their modification sites in mammalian cells represents a significant challenge because of the relatively small number of in vivo substrates and the dynamic nature of this modification. We report here a novel proteomics approach to selectively enrich and identify SUMO conjugates from human cells. We stably expressed different SUMO paralogs in HEK293 cells, each containing a His(6) tag and a strategically located tryptic cleavage site at the C terminus to facilitate the recovery and identification of SUMOylated peptides by affinity enrichment and mass spectrometry. Tryptic peptides with short SUMO remnants offer significant advantages in large scale SUMOylome experiments including the generation of paralog-specific fragment ions following CID and ETD activation, and the identification of modified peptides using conventional database search engines such as Mascot. We identified 205 unique protein substrates together with 17 precise SUMOylation sites present in 12 SUMO protein conjugates including three new sites (Lys-380, Lys-400, and Lys-497) on the protein promyelocytic leukemia. Label-free quantitative proteomics analyses on purified nuclear extracts from untreated and arsenic trioxide-treated cells revealed that all identified SUMOylated sites of promyelocytic leukemia were differentially SUMOylated upon stimulation.

Effects of a Disulfide Crosslink (XL) on the Trypsin Cleavage Pattern of Rabbit Cardiac Tropomyosin (TM)

A specific tryptic cleavage site at R133 with a subsequent site at R182 in Tm (1-284) was identified by Pato, et al, 1981. Ueno reported (1984) that a disulfide XL at C190 increased the rate of cleavage at higher temperatures (35o-40o). Here we redetermined the affect of the XL on the cleavage pattern at 26o, where Tm is >95% helical, and at 40o, where the middle region of Tm is unfolded. We used SDS-gels, N-terminal sequencing, and MALDI, to identify the products of cleavage. We found that the rate of Tm cleavage at R133 was unaffected by the crosslink at 26oC, but was slightly increased at 40oC. XL cleavage intermediates containing one cleaved and one uncleaved chain were observed. At 26o, cleavage of XL Tm at R133 produced a 51K XL heterodimer, (134-284/1-284), and a 35K XL homodimer, (134-284)2. At longer times, a second cleavage site at R168, produced a smaller 27K XL homodimer (169-284)2. At 40o, The XL increased the cleavage rate at K168 to produce a 47K XL heterodimer (169-284/1-284) and the 51K XL heterodimer. A shorter 31K XL heterodimer, (169-284/134-284) was also produced. The homodimer, (169-284)2 was also present early . The 35K homodimer seen at 26o was not produced. This study detected cleavage intermediates that could not be seen for uncrosslinked Tm. A new cleavage at K168 was seen which dominated at 40o. Cleavage at R183 after the initial cleavage at R133, (Pato et al, 1981), was not observed. This shows that: 1) both chains are not cleaved simultaneously; 2) locally unstable regions near R133 and R168 exhibit increased flexibility especially at physiological temperatures. Supported by NIH HL 22461-29 and an ARRA student summer grant. to D.Y.

A QUICK Screen for Lrrk2 Interaction Partners – Leucine-rich Repeat Kinase 2 is Involved in Actin Cytoskeleton Dynamics

Mutations in human leucine-rich repeat kinase 2 (Lrrk2), a protein of yet unknown function, are linked to Parkinson's disease caused by degeneration of midbrain dopaminergic neurons. The protein comprises several domains including a GTPase and a kinase domain both affected by several pathogenic mutations. To elucidate the molecular interaction network of endogenous Lrrk2 under stoichiometric constraints, we applied QUICK (quantitative immunoprecipitation combined with knockdown) in NIH3T3 cells. The identified interactome reveals actin isoforms as well as actin-associated proteins involved in actin filament assembly, organization, rearrangement, and maintenance, suggesting that the biological function of Lrrk2 is linked to cytoskeletal dynamics. In fact, we demonstrate Lrrk2 de novo binding to F-actin and its ability to modulate its assembly in vitro. When tested in intact cells, knockdown of Lrrk2 causes morphological alterations in NIH3T3 cells. In developing dopaminergic midbrain primary neurons, Lrrk2 knockdown results in shortened neurite processes, indicating a physiological role of Lrrk2 in cytoskeletal organization and dynamics of dopaminergic neurons. Hence, our results demonstrate that molecular interactions as well as the physiological function of Lrrk2 are closely related to the organization of the actin-based cytoskeleton, a crucial feature of neuronal development and neuron function.

Mechanisms of the Plurality of Scorpaena Porcus L. Serum Albumin

The proteins, which bind albuminspecific dye Evans blue, are revealed in the low-molecular protein fraction of the blood serum from Scorpaena porcus L. and identified as serum albumin. They were represented by three bands in 2D-SDS-PAAG. MALDI-TOF-analysis revealed the fundamental similarity of the mass spec-trum of the fragments of tryptic cleavage of proteins with molecular weight 73 and 76 kDa. The role of du-plications and intragenic reconstructions in the creation of the plurality of scorpaena albumins is discussed.

Alternative methods for verifying the results of the mass spectrometric identification of peptides in shotgun proteomics

Database search is the most popular approach used for the identification of peptides in contemporary shotgun proteomics; it utilizes only mass spectrometric data. In this work, we introduce three criteria for the verification of peptide identification; these are based on the analysis of data orthogonal to tandem mass spectra. The first one utilizes chromatographic retention times of peptides. The development of such approaches has been hindered by the relatively low accuracy of retention time prediction algorithms. In this work, we suggest the use of two independent models of the liquid chromatography of peptides, which increase the reliability of the results. The second criterion utilizes the mean number of missed tryptic cleavages per peptide. The third one results from the analysis of the difference between theoretical and experimentally measured peptide masses. The proposed criteria were applied to the tandem mass spectra of tryptic peptides from rat kidney tissue, which were processed by the Mascot search engine. All the criteria showed that Mascot significantly overestimated the reliability of an identification. This conclusion was supported by the PeptideProphet algorithm.

Rapid and efficient glycoprotein identification through microwave‐assisted enzymatic digestion

Identification of protein glycosylation sites is analytically challenging due to the diverse glycan structures associated with a glycoprotein. Mass spectrometry (MS)-based identification and characterization of glycoproteins has been achieved predominantly with the bottom-up approach, which typically involves the enzymatic cleavage of proteins to peptides prior to LC/MS or LC/MS/MS analysis. However, the process can be challenging due to the structural variations and steric hindrance imposed by the attached glycans. Alternatives to conventional heating protocols, that increase the rate of enzymatic cleavage of glycoproteins, may aid in addressing these challenges. An enzymatic digestion of a glycoprotein can be accelerated and made more efficient through microwave-assisted digestion. In this paper, a systematic study was conducted to explore the efficiency of microwave-assisted enzymatic (trypsin) digestion (MAED) of glycoproteins as compared with the conventional method. In addition, the optimum experimental parameters for the digestion such as temperature, reaction time, and microwave radiation power were investigated. It was determined that efficient tryptic digestion of glycoproteins was attained in 15 min, allowing comparable if not better sequence coverage through LC/MS/MS analysis. Optimum tryptic cleavage was achieved at 45°C irrespective of the size and complexity of the glycoprotein. Moreover, MAED allowed the detection and identification of more peptides and subsequently higher sequence coverage for all model glycoprotein. MAED also did not appear to prompt a loss or partial cleavage of the glycan moieties attached to the peptide backbones.

Crystallization and preliminary X-ray crystallographic analysis of a full-length active form of the Cry4Ba toxin fromBacillus thuringiensis

To obtain a complete structure of the Bacillus thuringiensis Cry4Ba mosquito-larvicidal protein, a 65 kDa functional form of the Cry4Ba-R203Q mutant toxin was generated for crystallization by eliminating the tryptic cleavage site at Arg203. The 65 kDa trypsin-resistant fragment was purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the rhombohedral space group R32, with unit-cell parameters a = b = 184.62, c = 187.36 A. Diffraction data were collected to at least 2.07 A resolution using synchrotron radiation and gave a data set with an overall R(merge) of 9.1% and a completeness of 99.9%. Preliminary analysis indicated that the asymmetric unit contained one molecule of the active full-length mutant, with a V(M) coefficient and solvent content of 4.33 A(3) Da(-1) and 71%, respectively.

Identifying protease cleavage sites by label‐free mass spectrometry

Methodsa method for identifying the cleavage sites for proteases in complex proteomes is described. The method makes use of a computer program called MS‐Cleave. The utility of the approach is demonstrated by determining of the cleavage sites in a set of recombinant Escherichia coli proteins generated by two matrix metalloproteinases (MMPs), MMP‐9 and MMP25. MS‐Cleave analyzes LC‐MS/MS data of standard samples with no additional chemical labels, processes them through a stringent peptide identification procedure, filters out tryptic cleavages and terminal trimming products. Each cleavage site is given a score based on the cleavage efficiency.ResultsTwenty‐two E. coli proteins were subjected to proteolysis by either MMP‐9 or MMP‐25. The cleaved samples were combined and analyzed by LC‐MS/MS. The cleavage sites are validated by comparison with the known substrate specificity of the two proteases which were defined with a substrate phage display library.ConclusionMS‐Cleave analysis is a reliable and convenient approach for the identification of protease cleavage sites without the use of additional chemical tags. The method is applicable for any standard proteomics facility.This work was supported by NIH 5U54RR020843‐05 grant to JWS, NIH 5R01RR016522‐05 and 1‐P41‐RR024851‐01 grants and Howard Hughes Medical Institute Professor Award to PP.