Higher TRIP-1 level explains diminished collagen contraction ability of fetal versus adult fibroblasts.

Acute lung injury involving extremely immature lungs often heals without excessive fibrosis unlike later in gestation and in adults. Several factors may be involved, but fibroblast contraction of collagen has been linked to the level of wound fibrosis. To assess whether human lung fibroblasts of fetal versus adult origin differ in ability to contract collagen and define the molecular underpinnings, we performed three-dimensional collagen contraction assay, analyzed their differential mRNA profile, specifically for transforming growth factor-beta (TGF-beta) signaling pathway and extracellular matrix components, studied the cell response to TGF-beta in culture, and used two-dimensional gel electrophoresis followed by mass spectrometry to identify differences in their overall proteomes. Human lung fetal fibroblasts contracted the collagen matrix less than the adults. Smooth muscle actin expression did not differ. TGF-beta stimulation resulted in greater Smad3 phosphorylation in fetal compared with adults. mRNA and proteomic profiling reveal a number of TGF-beta pathways, ECM components, and cytoskeletal regulatory molecules are differentially expressed between the cell types. Of note is TGF-beta receptor interacting protein 1 (TRIP-1), which we show inhibits fibroblast collagen contraction and is higher in fetal than adult fibroblasts. We conclude that human lung fetal fibroblasts are less able to contract collagen than adult lung fibroblasts. The diminished ability is not due to impediment of Smad3 activation but rather, at least in part, due to their higher level of TRIP-1 expression. TRIP-1 is a novel modulator of fibroblast collagen contraction.

The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution.

The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein-protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data revealed that a four-domain isoform of Eap is a monomer in solution. In vitro proteolysis and solution small angle X-ray scattering studies both indicate that Eap adopts an extended conformation in solution, where the linkers connecting sequential EAP modules are solvent exposed. Construction of a low-resolution model of full-length Eap using a combination of ab initio deconvolution of the SAXS data and rigid body modeling of the EAP domain crystal structure suggests that full-length Eap may present several unique concave surfaces capable of participating in ligand binding. These results also raise the possibility that such surfaces may be held together by additional interactions between adjacent EAP modules. This hypothesis is supported by a comparative Raman spectroscopic analysis of full-length Eap and a stoichiometric solution of the individual EAP modules, which indicates the presence of additional secondary structure and a greater extent of hydrogen/deuterium exchange protection in full-length Eap. Our results provide the first insight into the solution structure of full-length Eap and an experimental basis for interpreting the EAP domain crystal structures within the context of the full-length molecule. They also lay a foundation for future studies into the structural and molecular bases of Eap-mediated protein-protein interactions with its many ligands.

Association of specific proteolytic processing of bone sialoprotein and bone acidic glycoprotein-75 with mineralization within biomineralization foci.

Mineral crystal nucleation in UMR 106-01 osteoblastic cultures occurs within 15-25-microm extracellular vesicle-containing biomineralization foci (BMF) structures. We show here that BAG-75 and BSP, biomarkers for these foci, are specifically enriched in laser capture microscope-isolated mineralized BMF as compared with the total cell layer. Unexpectedly, fragments of each protein (45-50 kDa in apparent size) were also enriched within captured BMF. When a series of inhibitors against different protease classes were screened, serine protease inhibitor 4-(2-aminoethyl)benzenesulfonylfluoride HCl (AEBSF) was the only one that completely blocked mineral nucleation within BMF in UMR cultures. AEBSF appeared to act on an osteoblast-derived protease at a late differentiation stage in this culture model just prior to mineral deposition. Similarly, mineralization of bone nodules in primary mouse calvarial osteoblastic cultures was completely blocked by AEBSF. Cleavage of BAG-75 and BSP was also inhibited at the minimum dosage of AEBSF sufficient to completely block mineralization of BMF. Two-dimensional SDS-PAGE comparisons of AEBSF-treated and untreated UMR cultures showed that fragmentation/activation of a limited number of other mineralization-related proteins was also blocked. Taken together, our results indicate for the first time that cleavage of BAG-75 and BSP by an AEBSF-sensitive, osteoblast-derived serine protease is associated with mineral crystal nucleation in BMF and suggest that such proteolytic events are a permissive step for mineralization to proceed.

Virtual polymorphism: finding divergent peptide matches in mass spectrometry data.

The prevailing method of analyzing tandem-MS data for protein identification involves the comparison of peptide molecular weight and fragmentation data to theoretically predicted values, based on known protein sequences in databases. This is generally effective since proteins from most species under study are in the database or have sufficient homology to allow significant matching. We have encountered difficulties identifying proteins from fungal species Alternaria alternata due to significant interspecies protein sequence differences (divergence) and its absence from the database. This common household mold causes asthma and allergy problems, but the genome has not been sequenced. De novo sequencing and error-tolerant methods can facilitate protein identifications in divergent, unsequenced species. But these standard methods can be laborious and only allow single amino acid substitution, respectively. We have developed an alternative approach focusing on database engineering, predicting biologically rational polymorphism using statistically weighted amino acid substitution information held in BLOSUM62. Like other second pass methods, it is based on the initially identified protein. However, this approach allows more control over sequences to be considered, including multiple changes per peptide. The results show considerable improvement for routine protein identification and the potential for rescuing otherwise unconvincing identifications in unusually divergent species.

Proteomic analysis of oxidative stress-resistant cells: a specific role for aldose reductase overexpression in cytoprotection.

We are using a proteomic approach that combines two-dimensional electrophoresis and tandem mass spectrometry to detect and identify proteins that are differentially expressed in a cell line that is resistant to oxidative stress. The resistant cell line (OC14 cells) was developed previously through chronic exposure of a parent cell line (HA1 cells) to increasing hydrogen peroxide concentrations. Biochemical analyses of this system by other investigators have identified elevated content and activity of several classical antioxidant proteins that have established roles in oxidative stress resistance, but do not provide a complete explanation of this resistance. The proteomics studies described here have identified the enzyme aldose reductase (AR) as 4-fold more abundant in the resistant OC14 cells than in the HA1 controls. Based on this observation, the role of AR in the resistant phenotype was investigated by using a combination of AR induction with ethoxyquin and AR inhibition with Alrestatin to test the cytotoxicity of two oxidation-derived aldehydes: acrolein and glycolaldehyde. The results show that AR induction in HA1 cells provides protection against both acrolein- and glycolaldehyde-induced cytotoxicity. Furthermore, glutathione depletion sensitizes the cells to the acrolein-induced toxicity, but not the glycolaldehyde-induced toxicity, while AR inhibition sensitizes the cells to both acrolein- and glycolaldehyde-induced. These observations are consistent with a significant role for AR in the oxidative stress-resistant phenotype. These studies also illustrate the productive use of proteomic methods to investigate the molecular mechanisms of oxidative stress.

Site-specific quantitation of protein nitration using liquid chromatography/tandem mass spectrometry.

The native reference peptide (NRP) method has been adapted to the measure of the degree of protein nitration at a specific tyrosine residue. In these experiments, human serum albumin was modified in a myeloperoxidase-mediated reaction in the presence of nitrite, with nitration detected predominantly at one site, Y162. The time-dependent increase in nitration at this site was measured based on the increasing abundance of the peptide 162YnLYEIAR168 and the corresponding decrease in the 162YLYEIAR168 peptide in in-gel trypsin digests. The peptide 66LVNEVTEFAK75, also formed in the tryptic digest, was used as the native reference peptide. Quantitation was achieved by determining the chromatographic peak area of the two analyte peptides relative to the native reference peptide by LC/tandem mass spectrometric analyses with selected reaction monitoring. The NRP results were validated by correlation to the time-dependent increase in total protein-nitrotyrosine content determined by Western blot analysis. The precision and limit of detection of the assay were also evaluated and were found to be approximately 10% (relative standard deviation) and 5 fmol on-column, respectively. These results demonstrate the utility of the NRP method for quantitative analyses of posttranslation modifications, in terms of broad applicability, ease of experimental design, sensitivity, and precision.