Nuclear magnetic resonance mapping and functional confirmation of the collagen binding sites of matrix metalloproteinase-2.

Interactions of matrix metalloproteinase-2 (MMP-2) with native and denatured forms of several types of collagen are mediated by the collagen binding domain (CBD). CBD positions substrates relative to the catalytic site and is essential for their cleavage. Our previous studies identified a CBD binding site on the alpha1(I) collagen chain. The corresponding synthetic collagen peptide P713 bound CBD with high affinity and was used in this study to identify specific collagen binding residues by NMR analysis of (15)N-labeled CBD complexed with P713. Results obtained showed that P713 caused chemical shift perturbations of several surface-exposed CBD backbone amide resonances in a concentration-dependent manner. The 10 residues that underwent the largest chemical shift perturbations (R(252) in module 1, R(296), F(297), Y(302), E(321), Y(323), and Y(329) in module 2, and R(368), W(374), and Y(381) in module 3) were investigated by site-specific substitution with alanine. The structural integrity of the CBD variants was also analyzed by one-dimensional (1)H NMR. Surface plasmon resonance and microwell protein binding assays of control and CBD variants showed that residues in all three CBD modules contributed to collagen binding. Single-residue substitutions altered the affinity for peptide P713, as well as native and denatured type I collagen, with the greatest effects observed for residues in modules 2 and 3. Additional alanine substitutions involving residues in two or three modules simultaneously further reduced the level of binding of CBD to native and denatured type I collagen and demonstrated that all three modules contribute to substrate binding. These results have localized and confirmed the key collagen binding site residues in the three fibronectin type II-like modules of MMP-2.

Mutations in FN1 cause glomerulopathy with fibronectin deposits.

Glomerulopathy with fibronectin (FN) deposits (GFND) is an autosomal dominant disease with age-related penetrance, characterized by proteinuria, microscopic hematuria, hypertension, and massive glomerular deposits of FN that lead to end-stage renal failure. The genetic abnormality underlying GFND was still unknown. We hypothesized that mutations in FN1, which encodes FN, were the cause of GFND. In a large Italian pedigree with eight affected subjects, we found linkage with GFND at the FN1 locus at 2q32. We sequenced the FN1 in 15 unrelated pedigrees and found three heterozygous missense mutations, the W1925R, L1974R, and Y973C, that cosegregated with the disease in six pedigrees. The mutations affected two domains of FN (Hep-II domain for the W1925R and the L1974R, and Hep-III domain for the Y973C) that play key roles in FN-cell interaction and in FN fibrillogenesis. Mutant recombinant Hep-II fragments were expressed, and functional studies revealed a lower binding to heparin and to endothelial cells and podocytes compared with wild-type Hep-II and an impaired capability to induce endothelial cell spreading and cytoskeletal reorganization. Overall dominant mutations in FN1 accounted for 40% of cases of GFND in our study group. These findings may help understanding the pathogenesis of proteinuria and glomerular FN deposits in GFND and possibly in more common renal diseases such as diabetic nephropathy, IgA nephropathy, and lupus nephritis. To our knowledge no FN1 mutation causing a human disease was previously reported.

Identification of novel fibronectin fragments detected specifically in juvenile urine.

Ugl-Y (young age-related urinary glycoprotein) is an age-specific protein that we have previously identified in urine from healthy subjects under 18 years of age. Isoelectric focusing analysis of Ugl-Y gives a set of three bands, Y1, Y2 and Y3, in the pH region around 3. To determine the complete structure of Ugl-Y, purified Y1 and Y2 from pediatric urine were enzymatically cleaved, and the resulting peptides were analyzed by protein sequencing and/or MALDI-TOF MS. As a result, it was demonstrated that Y1 consists of 189 amino acid residues, and is identical to the region from A723 to R911 of fibronectin, whereas Y2 consists of 181 amino acid residues, and is identical to the region from A723 to R903. Electrophoretic analysis of the lysate prepared from COS-7 cells transfected with Y1- or Y2-expressing vectors gave specific bands corresponding to Y1 or Y2, respectively, showing the validity of the sequences determined. Partial purification of pediatric serum followed by western blotting revealed that Ugl-Y is derived from plasma. Furthermore, Ugl-Y was generated by in vitro digestion of fibronectin by acid protease in extracts of osteoclast cells. These findings suggest that Ugl-Y is probably produced by degradation of fibronectin comprising bone matrix during the process of vigorous bone resorption in children and adolescents. This is the first report on the identification and characterization of juvenile-specific fibronectin fragments excreted into urine.

Interdomain association in fibronectin: insight into cryptic sites and fibrillogenesis.

The process by which fibronectin (FN), a soluble multidomain protein found in tissue fluids, forms insoluble fibrillar networks in the extracellular matrix is poorly understood. Cryptic sites found in FN type III domains have been hypothesized to function as nucleation points, thereby initiating fibrillogenesis. Exposure of these sites could occur upon tension-mediated mechanical rearrangement of type III domains. Here, we present the solution structures of the second type III domain of human FN ((2)FNIII), and that of an interaction complex between the first two type III domains ((1-2)FNIII). The two domains are connected through a long linker, flexible in solution. A weak but specific interdomain interaction maintains (1-2)FNIII in a closed conformation that associates weakly with the FN N-terminal 30 kDa fragment (FN30 kDa). Disruption of the interdomain interaction by amino-acid substitutions dramatically enhances association with FN30 kDa. Truncation analysis of (1-2)FNIII reveals that the interdomain linker is necessary for robust (1-2)FNIII-FN30 kDa interaction. We speculate on the importance of this interaction for FN function and present a possible mechanism by which tension could initiate fibrillogenesis.

A new in vitro wound model based on the co-culture of human dermal microvascular endothelial cells and human dermal fibroblasts.

BACKGROUND INFORMATION: Different in vitro models, based on co-culturing techniques, can be used to investigate the behaviour of cell types, which are relevant for human wound and soft-tissue healing. Currently, no model exists to describe the behaviour of fibroblasts and microvascular endothelial cells under wound-specific conditions. In order to develop a suitable in vitro model, we characterized co-cultures comprising NHDFs (normal human dermal fibroblasts) and HDMECs (human dermal microvascular endothelial cells). The CCSWMA (co-culture scratch wound migration assay) developed was supported by direct visualization techniques in order to investigate a broad spectrum of cellular parameters, such as migration and proliferation activity, the differentiation of NHDFs into MFs (myofibroblasts) and the expression of endothelin-1 and ED-A-fibronectin (extra domain A fibronectin). The cellular response to hypoxia treatment, as one of the crucial conditions in wound healing, was monitored. RESULTS: The comparison of the HDMEC-NHDF co-culture with the respective mono-cultures revealed that HDMECs showed a lower proliferation activity when co-cultured, but their number was stable throughout a period of 48 h. NHDFs in co-culture were slightly slower at proliferating than in the mono-culture. The MF population was stable for 48 h in the co-culture, as well as in NHDF mono-culture. Co-cultures and HDMEC mono-cultures were characterized by a slower migration rate than NHDF mono-cultures. Hypoxia decreased both cell proliferation and migration in the mono-cultures, as well as in the co-cultures, indicating the general suitability of the assay. Exclusively, in co-cultures well-defined cell clusters comprising HDMECs and MFs formed at the edges of the in vitro wounds. CONCLUSIONS: On the basis of these results, the CCSWMA developed using co-cultures, including HDMECs, NHDFs and MFs, proved to be an effective tool to directly visualize cellular interaction. Therefore, it will serve in the future to evaluate the influence of wound-healing-related factors in vitro, as shown for hypoxia in the present study.

High-level expression of a soluble and functional fibronectin type II domain from MMP-2 in the Escherichia coli cytoplasm for solution NMR studies.

We report a method for the expression in Escherichia coli of the isolated second type II fibronectin domain from MMP-2 (FNII-2). FNII-2 was expressed as a His(6)thioredoxin-tagged fusion protein in the thioredoxin reductase deficient E. coli strain BL21trxB(DE3), thus allowing disulfide-bond formation. When cultured at 37 degrees C, the expressed protein is located exclusively in the soluble fraction of the E. coli lysate. The fusion protein from the soluble fraction was purified and the His(6)thioredoxin-tag was cleaved by thrombin, resulting in a yield of approximately 40 mg/L. The recombinant FNII-2 was demonstrated to be functional by its ability to bind to gelatin-Sepharose, correct folding of the purified protein was confirmed by NMR spectroscopy. This approach may generally be applicable to all FNII domains and is a significant simplification relative to existing techniques involving refolding from inclusion bodies or expression in the eukaryotic host, Pichia pastoris.

The importance of sequence diversity in the aggregation and evolution of proteins.

Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of highly debilitating medical conditions including Alzheimer's disease and late-onset diabetes. The issue of how unwanted protein association is normally avoided in a living system is particularly significant in the context of the evolution of multidomain proteins, which account for over 70% of all eukaryotic proteins, where the effective local protein concentration in the vicinity of each domain is very high. Here we describe the aggregation kinetics of multidomain protein constructs of immunoglobulin domains and the ability of different homologous domains to aggregate together. We show that aggregation of these proteins is a specific process and that the efficiency of coaggregation between different domains decreases markedly with decreasing sequence identity. Thus, whereas immunoglobulin domains with more than about 70% identity are highly prone to coaggregation, those with less than 30-40% sequence identity do not detectably interact. A bioinformatics analysis of consecutive homologous domains in large multidomain proteins shows that such domains almost exclusively have sequence identities of less than 40%, in other words below the level at which coaggregation is likely to be efficient. We propose that such low sequence identities could have a crucial and general role in safeguarding proteins against misfolding and aggregation.

Elements in the C terminus of apolipoprotein [a] responsible for the binding to the tenth type III module of human fibronectin.

In previous studies, we showed that the C-terminal domain, F2, but not the N-terminal domain, F1, is responsible for the binding of apolipoprotein [a] (apo[a]) to human fibronectin (Fn). To pursue those observations, we prepared, by both elastase digestion and recombinant technology, subsets of F2 of a different length containing either kringle (K) V or the protease domain (PD). We also studied rhesus monkey apo[a], which is known to contain PD but not KV. In the case of Fn, we used both an intact product and its tenth type III module (10FN-III) expressed in Escherichia coli. The binding studies carried out on microtiter plates showed that the affinity of F2 for immobilized 10FN-III was approximately 6-fold higher than that for Fn (dissociation constants = 1.75 +/- 0.31 nM and 10.25 +/- 1.62 nM, respectively). The binding was also exhibited by rhesus apo[a] and by an F2 subset containing the PD linked to an upstream microdomain comprising KIV-8 to KIV-10 and KV, inactive by itself. Competition experiments on microtiter plates showed that both Fn and 10FN-III, when in solution, are incompetent to bind F2. Together, our results indicate that F2 binds to immobilized 10FN-III more efficiently than whole Fn and that the binding can be sustained by truncated forms of F2 that contain the catalytically inactive PD linked to an upstream four K microdomain.

The role of fibronectin in fibroblast migration during tissue repair.

Fibronectin is known to stimulate cell growth and migration, but research does not provide a complete picture of all the mechanisms involved. Further studies are needed before practitioners can apply in vitro results to in vivo environments.

Clustering of protein domains in the human genome.

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone. For each superfamily, we investigated the distribution, both within and among chromosomes, of genes encoding at least one domain within the superfamily. The results indicate a diversity of clustering behaviours: some superfamilies showed no evidence of any clustering, and others displayed significant clustering either within or among chromosomes, or both. Removal of tandem repeats reduced the levels of clustering observed, but some superfamilies still displayed highly significant clustering. Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies.

In vitro evaluation of the biocompatibility of dental alloys: fibronectin expression patterns and relationships to cellular proliferation rates.

OBJECTIVE: This short-term (72- to 96-hour) in vitro study on fibroblasts evaluated the biocompatibility of 3 single-phase dental alloys by determining cellular proliferation rates and the expression of a glycoprotein, fibronectin, which is involved in cellular adhesion processes. METHOD AND MATERIALS: Flow 2002 fibroblasts were cultured together with 3 single-phase dental alloys of different composition. Proliferation rates were determined by 5-bromodeoxyuridine incorporation. Fibronectin expression was determined by indirect immunofluorescence. RESULTS: At 72 hours, cells cultured with the alloy containing the lowest amount of noble elements (gold, platinum, and palladium) and the highest amount of silver exhibited significantly less proliferation than did controls. At 96 hours, only cultures with the alloy containing the greatest amount of noble elements behaved in a way similar to controls. Fibronectin organization in fibrils and in focal adhesions was correlated to higher cellular proliferation rates. CONCLUSION: Fibronectin organization could be a useful tool to determine the biocompatibility of dental alloys. Among the noble elements, palladium by itself exhibits very good biocompatibility. These indications could be useful for practitioners in the choice of the best alloy for specific clinical applications.

Fibronectin isoform distribution in the mouse. II. Differential distribution of the alternatively spliced EIIIB, EIIIA, and V segments in the adult mouse.

The alternatively spliced EIIIB, EIIIA, and V segments of fibronectin (FN) show widespread codistribution in the mouse embryo, suggesting that EIIIB+, EIIIA+, and V+ isoforms serve to facilitate morphogenesis and organogenesis (Peters, JH, and Hynes, RO, 1996, this issue). To gain further clues to functions of these segments, we have used segment-specific anti-FN antibodies to perform immunofluorescence microscopy on tissue sections obtained from mice aged 9 to 15 weeks. Staining for each of the three spliced segments, relative to that for the total FN pool, was reduced in the adult as compared with the embryo. Anti-V antibodies produced patterns which were most similar to those obtained with anti-total FN antibodies, localizing to basement membranes, connective tissues subjacent to epithelia, walls of blood vessels, and cartilage. Anti-EIIIA antibodies produced the next most widespread pattern, which included prominent staining of the walls of blood vessels of all sizes, the lung interstitium, and smooth muscle associated with the gastrointestinal (GI), genitourinary (GU), and respiratory tracts. Although anti-EIIIB antibodies produced the faintest and most restricted pattern of staining, EIIIB+ FN could be detected in the walls of some smaller blood vessels, smooth muscle of the GI, GU, and respiratory tracts, as well as within cartilaginous structures, and eye. There were quantitative and/or qualitative differences in the staining patterns produced by the three segment-specific antibodies in a variety of tissues, including liver, cartilage, synovium, cornea, muscle, peripheral nerve, and lymph node. These findings suggest that each of the spliced segments of the FN molecule may occupy unique physical or functional positions within the extracellular matrix of the adult mouse.

Fibronectin isoform distribution in the mouse. I. The alternatively spliced EIIIB, EIIIA, and V segments show widespread codistribution in the developing mouse embryo.

Fibronectins (FNs) are extracellular matrix glycoproteins that are essential for embryonic development. In order to gain clues to possible developmental roles played by the particular isoforms of FN, we used indirect immunofluorescence microscopy to examine and compare the distributions of the alternatively spliced EIIIB, EIIIA, and V segments, as well as the total pool of FNs, in serial sections from mouse embryos. Antibodies to each of these segments produced staining patterns that colocalized during gastrulation (E7.5) and during early morphogenesis of somites and notochord (E9.5). During the period of continuing organogenesis in the latter half of gestation (E10.5 to E16.5), the antibodies generally continued to produce similar staining patterns localized to epithelial basement membranes, stromal connective tissues, blood vessel walls, and muscles. However, as development proceeded, there was a gradual decline in the intensity of staining for the spliced segments relative to the total pool of FN, with a particularly noticeable decline in staining for EIIIB and EIIIA segments in certain glandular organs, including the liver. A specific reduction in expression of these latter two segments was also evident in the uterus and placenta at early timepoints in gestation. However, the most dramatic difference in the expression of the spliced segments occurred in developing hyaline cartilage, which showed a selective reduction in staining for the EIIIA segment that was evident in the axial skeletal precursors by E12.5 and complete throughout the embryo by E15.5. Our findings suggest that the alternatively spliced EIIIB, EIIIA, and V segments are included in the FN that is required for the morphogenesis of "FN dependent" structures, including somites, notochord, and the vasculature. Conversely, these segments would appear to play divergent, and sometimes exclusive, biological roles in specific tissues such as liver, cartilage, and placenta.

[Purification of human fibronectin by precipitation and immunoadsorption]. / Purification de la fibronectine humaine par précipitation et immunoadsorption.

Two types of human plasma fibronectin concentrate were obtained by simple, large scale, precipitation methods. Concentrate 1 contains 90% pure fibronectin in a mainly dimeric form. This easy, high yield method provides a functional fibronectin suitable for intravenous therapeutic purposes in deficient patients. Concentrate 2 contains 95-98% pure fibronectin with minimal amounts of fibronectin monomer and degradation products. It seems well adapted to serum free cultures of human cells. A third preparation of an apparently pure fibronectin has also been obtained by immuno-adsorption with a Sepharose 4B column to which has been coupled an anti-fibronectin monoclonal antibody. The capture of dimer, monomers and degradation products by this antibody and their release at pH 2.4 has been demonstrated by gel transfer on nitrocellulose sheet revealed by another monoclonal anti-fibronectin antibody labelled with peroxidase.