Selective Proteolytic Digestion Research Articles

Substrate and Substrate-Mimetic Chaperone Binding Sites in Human α-Galactosidase A Revealed by Affinity-Mass Spectrometry.

Fabry disease (FD) is a rare metabolic disorder of a group of lysosomal storage diseases, caused by deficiency or reduced activity of the enzyme α-galactosidase. Human α-galactosidase A (hαGAL) hydrolyses the terminal α-galactosyl moiety from glycosphingolipids, predominantly globotriaosylceramide (Gb3). Enzyme deficiency leads to incomplete or blocked breakdown and progressive accumulation of Gb3, with detrimental effects on normal organ functions. FD is successfully treated by enzyme replacement therapy (ERT) with purified recombinant hαGAL. An emerging treatment strategy, pharmacologic chaperone therapy (PCT), employs small molecules that can increase and/or reconstitute the activity of lysosomal enzyme trafficking by stabilizing misfolded isoforms. One such chaperone, 1-deoxygalactonojirimycin (DGJ), is a structural galactose analogue currently validated in clinical trials. DGJ is an active-site-chaperone that binds at the same or similar location as galactose; however, the molecular determination of chaperone binding sites in lysosomal enzymes represents a considerable challenge. Here we report the identification of the galactose and DGJ binding sites in recombinant α-galactosidase through a new affinity-mass spectrometry-based approach that employs selective proteolytic digestion of the enzyme-galactose or -inhibitor complex. Binding site peptides identified by mass spectrometry, [39-49], [83-100], and [141-168], contain the essential ligand-contacting amino acids, in agreement with the known X-ray crystal structures. The inhibitory effect of DGJ on galactose recognition was directly characterized through competitive binding experiments and mass spectrometry. The methods successfully employed in this study should have high potential for the characterization of (mutated) enzyme-substrate and -chaperone interactions, and for identifying chaperones without inhibitory effects. Graphical Abstract ᅟ.

Amelogenin as a promoter of nucleation and crystal growth of apatite

Human dental enamel forms over a period of 2–4 years by substituting the enamel matrix, a protein gel mostly composed of a single protein, amelogenin with fibrous apatite nanocrystals. Self-assembly of amelogenin and the products of its selective proteolytic digestion are presumed to direct the growth of apatite fibers and their organization into bundles that eventually comprise the mature enamel, the hardest tissue in the mammalian body. This work aimed to establish the physicochemical and biochemical conditions for the growth of apatite crystals under the control of a recombinant amelogenin matrix (rH174) in combination with a programmable titration system. The growth of apatite substrates was initiated in the presence of self-assembling amelogenin particles. A series of constant titration rate experiments was performed that allowed for a gradual increase of the calcium and/or phosphate concentrations in the protein suspensions. We observed a significant amount of apatite crystals formed on the substrates following the titration of rH174 sols that comprised the initial supersaturation ratio equal to zero. The protein layers adsorbed onto the substrate apatite crystals were shown to act as promoters of nucleation and growth of calcium phosphates subsequently formed on the substrate surface. Nucleation lag time experiments have showed that rH174 tends to accelerate precipitation from metastable calcium phosphate solutions in proportion to its concentration. Despite their mainly hydrophobic nature, amelogenin nanospheres, the size and surface charge properties of which were analyzed using dynamic light scattering, acted as a nucleating agent for the crystallization of apatite. The biomimetic experimental setting applied in this study proves as convenient for gaining insight into the fundamental nature of the process of amelogenesis.

Mass Spectrometric Approaches for Elucidation of Antigen—Antibody Recognition Structures in Molecular Immunology

Mass spectrometric approaches have recently gained increasing access to molecular immunology and several methods have been developed that enable detailed chemical structure identification of antigen-antibody interactions. Selective proteolytic digestion and MS-peptide mapping (epitope excision) has been successfully employed for epitope identification of protein antigens. In addition, "affinity proteomics" using partial epitope excision has been developed as an approach with unprecedented selectivity for direct protein identification from biological material. The potential of these methods is illustrated by the elucidation of a beta-amyloid plaque-specific epitope recognized by therapeutic antibodies from transgenic mouse models of Alzheimer's disease. Using an immobilized antigen and antibody-proteolytic digestion and analysis by high resolution Fourier transform ion cyclotron resonance mass spectrometry has lead to a new approach for the identification of antibody paratope structures (paratope-excision; "parex-prot"). In this method, high resolution MS-peptide data at the low ppm level are required for direct identification of paratopes using protein databases. Mass spectrometric epitope mapping and determination of "molecular antibody-recognition signatures" offer high potential, especially for the development of new molecular diagnostics and the evaluation of new vaccine lead structures.

Caspase-3 cleaves Apaf-1 into an approximately 30 kDa fragment that associates with an inappropriately oligomerized and biologically inactive approximately 1.4 MDa apoptosome complex.

Cytochrome c and dATP/ATP induce oligomerization of Apaf-1 into two distinct apoptosome complexes: an approximately 700 kDa complex, which recruits and activates caspases-9, -3 and -7, and an approximately 1.4 MDa complex, which recruits and processes caspase-9, but does not efficiently activate effector caspases. While searching for potential inhibitors of the approximately 1.4 MDa apoptosome complex, we observed an approximately 30 kDa Apaf-1 immunoreactive fragment that was associated exclusively with the inactive complex. We subsequently determined that caspase-3 cleaved Apaf-1 within its CED-4 domain (SVTD(271) downward arrowS) in both dATP-activated lysates and apoptotic cells to form a prominent approximately 30 kDa (p30) N-terminal fragment. Purified recombinant Apaf-1 p30 fragment weakly inhibited dATP-dependent activation of caspase-3 in vitro. However, more importantly, prevention of endogenous formation of the p30 fragment did not stimulate latent effector caspase processing activity in the large complex. Similarly, the possibility that XIAP, an inhibitor of apoptosis protein (IAP), was responsible for the inactivity of the approximately 1.4 MDa complex was excluded as immunodepletion of this caspase inhibitor failed to relieve the inhibition. However, selective proteolytic digestion of the approximately 1.4 MDa and approximately 700 kDa complexes showed that Apaf-1 was present in conformationally distinct forms in these two complexes. Therefore, the inability of the approximately 1.4 MDa apoptosome complex to process effector caspases most likely results from inappropriately folded or oligomerized Apaf-1.

Tyrosine phosphorylation of the asialoglycoprotein receptor.

The asialoglycoprotein (ASGP) receptor undergoes constitutive endocytosis through the coated pit/coated vesicle pathway in hepatocytes. Studies on HepG2 cells have shown that the receptor is phosphorylated at serine under control conditions and following protein kinase C stimulation. This study examined whether the ASGP receptor could also serve as a substrate for a tyrosine kinase in HepG2 cells. 32P labeling was performed in membrane preparations, in permeabilized cells at 4 degrees C, and in intact cells at 37 degrees C. The phosphorylated ASGP receptor was isolated by immunoprecipitation, hydrolyzed in 6 N HCl at 110 degrees C, and analyzed by two-dimensional high voltage electrophoresis. The receptor isolated from a membrane preparation incubated in vitro with [gamma-32P]ATP incorporated radiolabel predominantly (greater than 90%) into phosphotyrosine. ASGP receptor phosphorylation at both tyrosine and serine was detected in intact cells incubated with phosphatase inhibitors for 60 min at 37 degrees C. The presence of both phenylarsine oxide (20 microM) and sodium orthovanadate (200 microM) was required for tyrosine phosphorylation. Use of these inhibitors together resulted in a 16.4-fold increase in phosphorylation of the immunoprecipitated ASGP receptor, whereas phosphorylation of total HepG2 membrane proteins was not significantly augmented by this procedure. Selective proteolytic digestion of ASGP receptors in isolated vesicles demonstrated that the phosphorylation site identified in these studies is located at tyrosine 5 in the cytoplasmic tail.

Folding of collagen IV.

Collagen IV dimers of two collagen IV molecules connected by their C-terminal globular NC1 domains were isolated by limited digestion with bacterial collagenase from mouse Engelbreth-Holm-Swarm (EHS) sarcoma tissue. The collagenous domains were only 300 nm long as compared to 400 nm of intact collagen IV but the disulfide bonds in the N-terminal region of the major triple helix were retained. Unfolding of the collagenous domains as monitored by circular dichroism occurred in a temperature range of 30 to 44 degrees C with a midpoint at 37 degrees C. The transition is significantly broader than that of the continuous triple helices in collagens I, II and III, a feature which can be explained by the frequent non-collagenous interruptions in the triple-helical domain of collagen IV. Refolding at 25 degrees C following complete unfolding at 50 degrees C was monitored by circular dichroism, selective proteolytic digestion of non-refolded segments and by a newly developed method in which the recovered triple-helical segments were visualized by electron microscopy. Triple-helix formation was found to proceed in a zipper-like fashion from the C-terminal NC1 domains towards the N-terminus, indicating that this domain is essential for nucleations. For collagen IV dimers with intact NC1 domains the rate of triple-helix growth was of comparable magnitude to that of collagen III, demonstrating that the non-collagenous interruptions do not slow down the refolding process where the rate-limiting step is the cis-trans isomerization of proline peptide bonds. Refolding was near to 100% and the refolding products were similar to the starting material as judged by thermal stability and electron microscopic appearance. Removal of the NC1 domains by pepsin or dissociation of their hexametric structures by acetic acid led to a loss of the refolding ability. Instead products with randomly dispersed short triple-helical segments were formed in a slow reaction. In no case, even when the disulfide bonds in the N-terminal region of the triple-helical domain were intact, was refolding from the N- towards the C-terminus observed. Taken together with results in other collagens, this suggests that C to N directionality might be an intrinsic property of triple-helix folding.

Bovine nucleus caudatus acetylcholinesterase: active site determination and investigation of a dimeric form obtained by selective proteolysis.

The number of catalytic subunits of purified bovine nucleus caudatus acetylcholinesterase (E.C. 3.1.1.7) has been determined by active site labelling with [3H]diisopropyl fluorophosphate ([3H]DFP). The 10.5 S, 16 S, and 20 S forms were estimated to contain two, four, and six active sites, respectively, per molecule. A 4.8 S form, which showed a weak amphiphile-dependent activity behavior, was obtained by selective proteolytic digestion with pronase. The inability of the purified 4.8 S form to aggregate after detergent removal, and the molecular mass in the range of 130-165 kD under nondenaturating conditions, indicate that this form is a dimeric form, lacking those hydrophobic regions responsible for aggregation.

Selective proteolytic digestion as a method for the modification of human HDL3 structure

Trypsin digestion of human high density lipoprotein (d 1.125-1.21 g/ml) on which the lysine residues have been masked with the reversible blocking group, 2,3,4,5-tetrahydrophthallic anhydride (THPA), was found to result in the fragmentation of the apoA-I component, but not the apoA-II component of this lipoprotein particle. Approximately 50-80% of the apoA-I polypeptide was found in a lipid-free fraction, while the residual apoA-I material plus the apoA-II moiety constituted a core particle that contained most of the original lipid. Immunological analysis indicated that such fragmentation did not affect the immunoreactivity of apoA-II, but that all immunoreactivity of apoA-I was lost within the first 30 min of trypsinization. By column chromatography and electron microscopy this core particle appeared identical in size with the untrypsinized THPA-modified HDL(3) material. Size analysis of the core particle peptides suggests that not all of the A-I molecules present on the HDL(3) are trypsinized to the same extent, which indicates possible nonequivalence of these peptide chains. Analysis of the amino acid composition revealed a somewhat greater proportion of hydrophobic residues in the lipid-bound fraction than in the lipid-free fraction. Analysis of tryptophan showed that almost all of this highly hydrophobic residue was found in the lipid-bound fraction; this suggests that lipid binding occurs preferentially in the more hydrophobic domains of the A-I molecule. Incubation of the core particle with intact apoA-I, obtained from either human or bovine HDL, showed that these proteins could be incorporated to regenerate an HDL(3) of selectively altered protein composition, compared to the original lipoprotein. It is concluded that some latitude is allowable in the surface/volume relationship in lipoproteins before reorganization of the particle is required; this might, for example, provide a mechanism whereby the HDL could serve in a storage role for the C apolipoproteins in plasma.-Swaney, J. B. Selective proteolytic digestion as a method for the modification of human HDL(3) structure.

The two-sited nature of transferrin: Spectroscopic, thermodynamic and physiologic studies

Abstract The transferrins comprise a class of two-sited metal-binding proteins widely distributed in cells and fluids of vertebrates. Each of the major transferrin varieties—serum transferrin, ovotransferrin (conalbumin) and lactoferrin (lactotransferrin)—consists of a single polypeptide chain with extensive internal homology indicating evolutionary origin from a single-sited precursor protein. In human transferrin and hen ovotransferrin, at least, evolutionary development has altered the two sites so that they are chemically and spectroscopically distinguishable, but whether the differences between the sites are physiologically important is not yet clear. The metal-binding activities of all transferrins are dependent on the concomitant binding of stucturally-suitable anions. In human serum transferrin, anion- and metal-binding activities alike vary between the two sites. For example, the sites may be distinguished by the thightness with which they bind ion, by their accesibility to different chemical forms of iron, by their vulnerability to acid, by the rates at which they exchange anions with the medium, by their capacity to accomodate different anions when Cu(II) is the bound metal ion, and by their spectroscopic features. When single-sited transferrin fragments are prepared by selective proteolytic digestion, the tightness of ion-binding by these fragments is virtually identical to that of corresponding sites in the holoprotein.Evidently, therefore, site-site interactions are not responsible for the observed differences between the sites in native transferrin. Because each of the sites of transferrin resides in its own independent domain, and empty-sited domains are more susceptible to denaturation than occupied domains, each of the four possible molecular species of transferrin (apoprotein, monoferric-A and monoferric-B proteins, and differic protein) can be separated and displayed by electrophoresis in a 6M urea-gel system introduced by Makey and Seal. This procedure has been exploited to study the physiological iron-exchanging properties of the sites, in vitro and in vivo . In studies conducted in our laboratory, the two sites of diferric transferrin differ considerably in their ability to donate iron to isolated hemoglobin-synthesizing reticulocytes in an artificial culture medium. In in vivo studies in the rabbit, however, the two iron atoms are removed from diferric transferrin in pairwise fashion, so that the sites now appear equivalent in their iron-donating properties. Furthermore, iron, from stores and sites where it is absorbed or recovered from senescent red blood cells, is returned to empty sites of circulating transferrin, predominantly one atom at a time. Since studies of iron distribution among the sites of circulating transferrin in normal human subjects indicate that the sites are unequally occupied, with the more weakly binding site of the N-terminal half of the molecule favored, it seemed that the sites might differ not in their iron-donating abilities, but in their iron-accepting properties. Accordingly, the distribution of absorbed radioactive iron between the two sites of circulating transferrin was studied in the rabbit. In four of five animals the B-site was strongly favored by the newly absorbed iron. This may account, then, for the unequal distribution of iron between the sites of circulating transferrin. If the chemical differences between the two sites of transferrin are mapped into differences in function, therefore, it is probably on the ‘supply side’ of the iron economy.