Can ultrasonic energy efficiently speed 18O‐labeling of proteins?

We report in this work on the robustness of ultrasonic energy as a tool to speed the isotopic labeling of proteins using the ¹⁸O‐decoupling procedure. The first part of the decoupling procedure, comprising protein denaturation, reduction, alkylation and digestion, is done in 8 min under the effects of an ultrasonic field whilst the second part, the isotopic labeling, was assayed with and without the use of ultrasonic energy. Our results clearly demonstrate that the ¹⁸O‐isotopic labeling in a decoupling procedure cannot be accelerated using an ultrasonic field.     

Regulatory elements and functional implication for the formation of dimeric visinin‐like protein‐1

Size exclusion chromatographic analyses showed that Ca²⁺‐free VILIP‐1 contained both monomeric and dimeric forms, while no appreciable dimerization was noted with Ca²⁺‐free VILIP‐3. Swapping of EF‐hands 3 and 4 of VILIP‐1 with those of VILIP‐3 caused the inability of the resulting chimeric protein to form dimeric protein. Nonreducing SDS‐PAGE analyses revealed that most of the dimeric VILIP‐1 was noncovalently bound together. Reduced glutathione (GSH)/oxidized glutathione (GSSG) treatment notably enhanced the formation of disulfide‐linked VILIP‐1 dimer, while Ca²⁺ and Mg²⁺ enhanced disulfide dimerization of VILIP‐1 marginally in the presence of thiol compounds. Cys‐187 at the C‐terminus of VILIP‐1 contributed greatly to form S‐S‐crosslinked dimer as revealed by mutagenesis studies. The ability of GSH/GSSG‐treated VILIP‐1 to activate guanylyl cyclase B was reduced by substituting Cys‐187 with Ala. Together with disulfide dimer of VILIP‐1 detected in rat brain extracts, our data may imply the functional contribution of disulfide dimer to the interaction of VILIP‐1 with its physiological target(s). Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Protein recovery and identification from the gulf killifish, Fundulus grandis: comparing snap-frozen and RNAlater® preserved tissues

Reliable proteomic analysis of biological tissues requires sampling approaches that preserve proteins as close to their in vivo state as possible. In the current study, the patterns of protein abundance in one‐dimensional (1‐D) gels were assessed for five tissues of the gulf killifish, Fundulus grandis, following snap‐freezing tissues in liquid nitrogen or immersion of fresh tissues in RNAlater^®. In liver and heart, the protein profiles in 1‐D gels were better preserved by snap‐freezing, while in gill, the 1‐D protein profile was better preserved by immersion in RNAlater^®. In skeletal muscle and brain, the two approaches yielded similar patterns of protein abundance. LC‐MS/MS analyses and database searching resulted in the identification of 17 proteins in liver and 12 proteins in gill. Identified proteins include enzymes of energy metabolism, structural proteins, and proteins serving other biological functions. These protein identifications for a species without a sequenced genome demonstrate the utility of F. grandis as a model organism for environmental proteomic studies in vertebrates.     

Human Dickkopf-1 (huDKK1) protein: characterization of glycosylation and determination of disulfide linkages in the two cysteine-rich domains

Human Dickkopf‐1 (huDKK1), an inhibitor of the canonical Wnt‐signaling pathway that has been implicated in bone metabolism and other diseases, was expressed in engineered Chinese hamster ovary cells and purified. HuDKK1 is biologically active in a TCF/lef‐luciferase reporter gene assay and is able to bind LRP6 coreceptor. In SDS‐PAGE, huDKK1 exhibits molecular weights of 27–28 K and 30 K at ～ 1:9 ratio. By MALDI‐MS analysis, the observed molecular weights of 27.4K and 29.5K indicate that the low molecular weight form may contain O‐linked glycans while the high molecular weight form contains both N‐ and O‐linked glycans. LC‐MS/MS peptide mapping indicates that ～ 92% of huDKK1 is glycosylated at Asn²²⁵ with three N‐linked glycans composed of two biantennary forms with 1 and 2 sialic acid (23% and 60%, respectively), and one triantennary structure with 2 sialic acids (9%). HuDKK1 contains two O‐linked glycans, GalNAc (sialic acid)‐Gal‐sialic acid (65%) and GalNAc‐Gal[sialic acid] (30%), attached at Ser 30 as confirmed by β‐elimination and targeted LC‐MS/MS. The 10 intramolecular disulfide bonds at the N‐ and C‐terminal cysteine‐rich domains were elucidated by analyses including multiple proteolytic digestions, isolation and characterization of disulfide‐containing peptides, and secondary digestion and characterization of selected disulfide‐containing peptides. The five disulfide bonds within the huDKK1 N‐terminal domain are unique to the DKK family proteins; there are no exact matches in disulfide positioning when compared to other known disulfide clusters. The five disulfide bonds assigned in the C‐terminal domain show the expected homology with those found in colipase and other reported disulfide clusters.     

Trichloroacetic acid‐induced protein precipitation involves the reversible association of a stable partially structured intermediate

Sample preparation for proteomic analysis involves precipitation of protein using 2,2,2‐trichloroacetic acid (TCA). In this study, we examine the mechanism of the TCA‐induced protein precipitation reaction. TCA‐induced protein precipitation curves are U‐shaped and the shape of the curve is observed to be independent of the physicochemical properties of proteins. TCA is significantly less effective in precipitating unfolded states of proteins. Results of the 1‐anilino‐8‐napthalene sulfonate (ANS) and size‐exclusion chromatography, obtained using acidic fibroblast growth factor (aFGF), show that a stable “molten globule‐like” partially structured intermediate accumulates maximally in 5% (w/v) of trichloroacetate. Urea‐induced unfolding and limited proteolytic digestion data reveal that the partially structured intermediate is significantly less stable than the native conformation. ¹H‐¹⁵N chemical shift perturbation data obtained using NMR spectroscopy indicate that interactions stabilizing the β‐strands at the N‐ and C‐ terminal ends (of aFGF) are disrupted in the trichloroacetate‐induced “MG‐like” state. The results of the study clearly demonstrate that TCA‐induced protein precipitation occurs due to the reversible association of the “MG‐like” partially structured intermediate state(s). In our opinion, the findings of this study provide useful clues toward development of efficient protocols for the isolation and analysis of the entire proteome.     

Identification of differentially expressed proteins by treatment with PUGNAc in 3T3‐L1 adipocytes through analysis of ATP‐binding proteome

O‐GlcNAc (2‐acetamino‐2‐deoxy‐β‐D‐glucopyranose), an important modification for cellular processes, is catalyzed by O‐GlcNAc transferase and O‐GlcNAcase. O‐(2‐acetamido‐2‐deoxy‐D‐glucopyranosylidene) amino‐N‐phenylcarbamate (PUGNAc) is a nonselective inhibitor of O‐GlcNAcase, which increases the level of protein O‐GlcNAcylation and is known to induce insulin‐resistance in adipose cells due to uncharacterized targets of this inhibitor. In this study, using ATP affinity chromatography, we applied a targeted proteomic approach for identification of proteins induced by treatment with PUGNAc. For optimization of proteomic methods using ATP affinity chromatography, comparison of two cell lines (3T3‐L1 adipocytes and C2C12 myotubes) and two different digestion steps was performed using four different structures of immobilized ATP‐bound resins. Using this approach, based on DNA sequence homologies, we found that the identified proteins covered almost half of ATP‐binding protein families classified by PROSITE. The optimized ATP affinity chromatography approach was applied for identification of proteins that were differentially expressed in 3T3‐L1 adipocytes following treatment with PUGNAc. For label‐free quantitation, a gel‐assisted method was used for digestion of the eluted proteins, and analysis was performed using two different MS modes, data‐independent (671 proteins identified) and data‐dependent (533 proteins identified) analyses. Among identified proteins, 261 proteins belong to nucleotide‐binding proteins and we focused on some nucleotide‐binding proteins, ubiquitin‐activation enzyme 1 (E1), Hsp70, vasolin‐containing protein (Vcp), and Hsp90, involved in ubiquitin‐proteasome degradation and insulin signaling pathways. In addition, we found that treatment with PUGNAc resulted in increased ubiquitination of proteins in a time‐dependent manner, and a decrease in both the amount of Akt and the level of phosphorylation of Akt, a key component in insulin signaling, through downregulation of Hsp90. In this study, based on a targeted proteomic approach using ATP affinity chromatography, we found four proteins related to ubiquitination and insulin signaling pathways that were induced by treatment with PUGNAc. This result would provide insight into understanding functions of PUGNAc in 3T3‐L1 cells.     

Covalent structure and some pharmacological features of native and cleaved α‐KTx12−1, a four disulfide‐bridged toxin from Tityus serrulatus venom

A toxin with four disulfide bridges from Tityus serrulatus venom was able to compete with ¹²⁵I‐kaliotoxin on rat brain synaptosomal preparations, with an IC₅₀ of 46 nM . The obtained amino acid sequence and molecular mass are identical to the previously described butantoxin. Enzymatic cleavages in the native peptide followed by mass spectrometry peptide mapping analysis were used to determine the disulfide bridge pattern of α‐KTx_12?1. Also, after the cleavage of the first six N‐terminal residues, including the unusual disulfide bridge which forms an N‐terminus ring, the potency of the cleaved peptide was found to decrease about 100 fold compared with the native protein. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.     

Chemical treatment of Escherichia coli: 3. Selective extraction of a recombinant protein from cytoplasmic inclusion bodies in intact cells

In previous parts of this study we developed procedures for the high‐efficiency chemical extraction of soluble and insoluble protein from intact Escherichia coli cells. Although high yields were obtained, extraction of recombinant protein directly from cytoplasmic inclusion bodies led to low product purity due to coextraction of soluble contaminants. In this work, a two‐stage procedure for the selective extraction of recombinant protein at high efficiency and high purity is reported. In the first stage, inclusion‐body stability is promoted by the addition of 15 mM 2‐hydroxyethyldisulfide (2‐HEDS), also known as oxidized β‐mercaptoethanol, to the permeabilization buffer (6 M urea + 3 mM ethylenediaminetetraacetate [EDTA]). 2‐HEDS is an oxidizing agent believed to promote disulfide bond formation, rendering the inclusion body resistant to solubilization in 6 M urea. Contaminating proteins are separated from the inclusion‐body fraction by centrifugation. In the second stage, disulfide bonds are readily eliminated by including reducing agent (20 mM dithiothreitol [DTT]) into the permeabilization buffer. Extraction using this selective two‐stage process yielded an 81% (w/w) recovery of the recombinant protein Long‐R³‐IGF‐I from inclusion bodies located in the cytoplasm of intact E. coli, at a purity of 46% (w/w). This was comparable to that achieved by conventional extraction (mechanical disruption followed by centrifugation and solubilization). A pilot‐scale procedure was also demonstrated using a stirred reactor and diafiltration. This is the first reported study that achieves both high extraction efficiency and selectivity by the chemical treatment of cytoplasmic inclusion bodies in intact bacterial cells. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 62: 455–460, 1999.     

Quantitative evaluation of refolding conditions for a disulfide-bond-containing protein using a concise ¹⁸O-labeling technique

A concise method was developed for quantifying native disulfide‐bond formation in proteins using isotopically labeled internal standards, which were easily prepared with proteolytic ¹⁸O‐labeling. As the method has much higher throughput to estimate the amounts of fragments possessing native disulfide arrangements by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) than the conventional high performance liquid chromatography (HPLC) analyses, it allows many different experimental conditions to be assessed in a short time. The method was applied to refolding experiments of a recombinant neuregulin 1‐β1 EGF‐like motif (NRG1‐β1), and the optimum conditions for preparing native NRG1‐β1 were obtained by quantitative comparisons. Protein disulfide isomerase (PDI) was most effective at the reduced/oxidized glutathione ratio of 2:1 for refolding the denatured sample NRG1‐β1 with the native disulfide bonds.     

Expanding the mouse embryonic stem cell proteome: Combining three proteomic approaches

The current study used three different proteomic strategies, which differed by their extent of intact protein separation, to examine the proteome of a pluripotent mouse embryonic stem cell line, R1. Proteins from whole‐cell lysates were subjected either to 2‐D‐LC, or 1‐DE, or were unfractionated prior to enzymatic digestion and subsequent analysis by MS. The results yielded 1895 identified non‐redundant proteins and, for 128 of these, the specific isoform could be determined based on detection of an isoform‐specific peptide. When compared with two previously published proteomic studies that used the same cell line, the current study reveals 612 new proteins.     

Structural and functional characterization of CcmG from Pseudomonas aeruginosa,a key component of the bacterial cytochrome c maturation apparatus

The cytochrome c maturation process is carried out in the bacterial periplasm, where some specialized thiol‐disulfide oxidoreductases work in close synergy for the correct reduction of oxidized apocytochrome before covalent heme attachment. We present a structural and functional characterization of the soluble periplasmic domain of CcmG from the opportunistic pathogen P. aeruginosa (Pa‐CcmG), a component of the protein machinery involved in cyt c maturation in gram‐negative bacteria. X‐ray crystallography reveals that Pa‐CcmG is a TRX‐like protein; high‐resolution crystal structures show that the oxidized and the reduced forms of the enzyme are identical except for the active‐site disulfide. The standard redox potential was calculated to be E^0′ = ?0.213 V at pH 7.0; the pK_a of the active site thiols were pK_a = 6.13 ± 0.05 for the N‐terminal Cys74 and pK_a = 10.5 ± 0.17 for the C‐terminal Cys77. Experiments were carried out to characterize and isolate the mixed disulfide complex between Pa‐CcmG and Pa‐CcmH (the other redox active component of System I in P. aeruginosa). Our data indicate that the target disulfide of this TRX‐like protein is not the intramolecular disulfide of oxidized Pa‐CcmH, but the intermolecular disulfide formed between Cys28 of Pa‐CcmH and DTNB used for the in vitro experiments. This observation suggests that, in vivo, the physiological substrate of Pa‐CcmG may be the mixed‐disulfide complex between Pa‐CcmH and apo‐cyt. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Adrenomedullin disulfide bond mimetics uncover structural requirements for AM1 receptor activation

Adrenomedullin (ADM) is a vasoactive peptide hormone of 52 amino acids and belongs to the calcitonin peptide superfamily. Its vasodilative effects are mediated by the interaction with the calcitonin receptor‐like receptor (CLR), a class B G protein‐coupled receptor (GPCR), associated with the receptor activity modifying protein 2 (RAMP2) and functionally described as AM‐1 receptor (AM₁R). A disulfide‐bonded ring structure consisting of six amino acids between Cys¹⁶ and Cys²¹ has been shown to be a key motif for receptor activation. However, the specific structural requirements remain to be elucidated. To investigate the influence of ring size and position of additional functional groups that replace the native disulfide bond, we generated ADM analogs containing thioether, thioacetal, alkane, and lactam bonds between amino acids 16 and 21 by Fmoc/t‐Bu solid phase peptide synthesis. Activity studies of the ADM disulfide bond mimetics (DSBM) revealed a strong impact of structural parameters. Interestingly, an increased ring size was tolerated but the activity of lactam‐based mimetics depended on its position within the bridging structure. Furthermore, we found the thioacetal as well as the thioether‐based mimetics to be well accepted with full AM₁R activity. While a reduced selectivity over the calcitonin gene‐related peptide receptor (CGRPR) was observed for the thioethers, the thioacetal was able to retain a wild–type‐like selectivity profile. The carbon analog in contrast displayed weak antagonistic properties. These results provide insight into the structural requirements for AM₁R activation as well as new possibilities for the development of metabolically stabilized analogs for therapeutic applications of ADM.     

In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis

Site‐specific chemical cross‐linking in combination with mass spectrometry analysis has emerged as a powerful proteomic approach for studying the three‐dimensional structure of protein complexes and in mapping protein–protein interactions (PPIs). Building on the success of MS analysis of in vitro cross‐linked proteins, which has been widely used to investigate specific interactions of bait proteins and their targets in various organisms, we report a workflow for in vivo chemical cross‐linking and MS analysis in a multicellular eukaryote. This approach optimizes the in vivo protein cross‐linking conditions in Arabidopsis thaliana, establishes a MudPIT procedure for the enrichment of cross‐linked peptides, and develops an integrated software program, exhaustive cross‐linked peptides identification tool (ECL), to identify the MS spectra of in planta chemical cross‐linked peptides. In total, two pairs of in vivo cross‐linked peptides of high confidence have been identified from two independent biological replicates. This work demarks the beginning of an alternative proteomic approach in the study of in vivo protein tertiary structure and PPIs in multicellular eukaryotes.     

Exploring skyline for both MSE‐based label‐free proteomics and HRMS quantitation of small molecules

The MS^E (where MS^E is low energy (MS) and elevated energy (E) mode of acquisition) acquisition method commercialized by Waters on its Q‐TOF instruments is regarded as a unique data‐independent fragmentation approach that improves the accuracy and dynamic range of label‐free proteomic quantitation. Due to its special format, MS^E acquisition files cannot be independently analyzed with most widely used open‐source proteomic software specialized for processing data‐dependent acquisition files. In this study, we established a workflow integrating Skyline, a popular and versatile peptide‐centric quantitation program, and a statistical tool DiffProt to fulfill MS^E‐based proteomic quantitation. Comparison with the vendor software package for analyzing targeted phosphopeptides and global proteomic datasets reveals distinct advantages of Skyline in MS^E data mining, including sensitive peak detection, flexible peptide filtering, and transparent step‐by‐step workflow. Moreover, we developed a new procedure such that Skyline MS1 filtering was extended to small molecule quantitation for the first time. This new utility of Skyline was examined in a protein–ligand interaction experiment to identify multiple chemical compounds specifically bound to NDM‐1 (where NDM is New Delhi metallo‐β‐lactamase 1), an antibiotics‐resistance target. Further improvement of the current weaknesses in Skyline MS1 filtering is expected to enhance the reliability of this powerful program in full scan‐based quantitation of both peptides and small molecules.     

Late‐onset retinal degeneration pathology due to mutations in CTRP5 is mediated through HTRA1

Late‐onset retinal degeneration (L‐ORD) is an autosomal dominant macular degeneration characterized by the formation of sub‐retinal pigment epithelium (RPE) deposits and neuroretinal atrophy. L‐ORD results from mutations in the C1q‐tumor necrosis factor‐5 protein (CTRP5), encoded by the CTRP5/C1QTNF5 gene. To understand the mechanism underlying L‐ORD pathology, we used a human cDNA library yeast two‐hybrid screen to identify interacting partners of CTRP5. Additionally, we analyzed the Bruch's membrane/choroid (BM‐Ch) from wild‐type (Wt), heterozygous S163R Ctrp5 mutation knock‐in (Ctrp5^S163R/wt), and homozygous knock‐in (Ctrp5^S163R/S163R) mice using mass spectrometry. Both approaches showed an association between CTRP5 and HTRA1 via its C‐terminal PDZ‐binding motif, stimulation of the HTRA1 protease activity by CTRP5, and CTRP5 serving as an HTRA1 substrate. The S163R‐CTRP5 protein also binds to HTRA1 but is resistant to HTRA1‐mediated cleavage. Immunohistochemistry and proteomic analysis showed significant accumulation of CTRP5 and HTRA1 in BM‐Ch of Ctrp5^S163R/S163R and Ctrp5^S163R/wt mice compared with Wt. Additional extracellular matrix (ECM) components that are HTRA1 substrates also accumulated in these mice. These results implicate HTRA1 and its interaction with CTRP5 in L‐ORD pathology.     

Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets

Cross‐strand disulfides bridge two cysteines in a registered pair of antiparallel β‐strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross‐strand disulfides. Seventy‐six cross‐strand disulfides were found of which 75 and 1 occurred at non‐hydrogen‐bonded (NHB) and hydrogen‐bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T _m . All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG ⁰ = ?3.3 to ?6.7 kcal/mol). The data demonstrate that introduction of cross‐strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Actin,gelsolin and filamin‐A are dynamic actors in the cytoskeleton remodelling contributing to the blood brain barrier phenotype

The brain vascular endothelium operates as a dynamic regulatory interface to maintain the cell environment of the nervous system. In the vicinity of astrocytes, brain endothelial cells develop characteristic features conferring a strong cellular impermeability which limits the penetration of various compounds. The aim of our study was to determine by differential proteomic analysis the changes occurring in bovine brain capillary endothelial cells (BBCEC) differentiated in co‐culture with astrocytes compared with endothelial cells cultured alone. In order to obtain reproducible and meaningful protein profiles of in vitro blood–brain barrier models, three sample preparation procedures were carried out to provide the first 2‐D comparative proteomic study of BBCEC. Our study highlights advantages and drawbacks of each procedure. The cellular proteins prepared from mechanical scraping of collagen‐seeded BBCEC were strongly contaminated by serum proteins. Enzymatic dissociation of BBCEC by trypsin or collagenase solved this problem. A comparative 2‐DE profile study of collagenase‐harvested BBCEC revealed that cytoskeleton‐related proteins (actin, gelsolin and filamin‐A) show the most significant quantitative changes in the Triton soluble protein fraction from BBCEC that exhibit characteristics closest to the in vivo situation.     

Disulfide–bridging PEGylation during refolding for the more efficient production of modified proteins

Proteins that are modified by chemical conjugation require at least two separate purification processes. First the bulk protein is purified, and then after chemical conjugation, a second purification process is required to obtain the modified protein. In an effort to develop new enabling technologies to integrate bioprocessing and protein modification, we describe the use of disulfide‐bridging conjugation to conduct PEGylation during protein refolding. Preliminary experiments using a PEG‐mono‐sulfone reagent with partially unfolded leptin and unfolded RNAse T1 indicated that the cysteine thiols underwent disulfide‐bridging conjugation to give the PEGylated proteins. Interferon‐β1b (IFN‐β1b) was then expressed in E.coli as inclusion bodies and found to undergo disulfide bridging‐conjugation during refolding. The PEG‐IFN‐β1b was isolated by ion‐exchange chromatography and displayed in vitro biological activity. In the absence of the PEGylation reagent, IFN‐β1b refolding was less efficient and yielded protein aggregates. No PEGylation was observed if the cysteines on IFN‐β1b were first modified with iodoacetamide prior to refolding. Our results demonstrate that the simultaneous refolding and disulfide bridging PEGylation of proteins could be a useful strategy in the development of affordable modified protein therapeutics.