Primary structure of porcine plasminogen. Isolation and characterization of CNBr-fragments and their alignment within the polypeptide chain

Analysis of the aromatic 1H NMR spectrum of chicken plasminogen kringle 4

The intact kringle 4 domain of chicken plasminogen has been characterized by 1H NMR spectroscopy at 300 and 620 MHz in both the presence and absence of epsilon-aminocaproic acid, an antifibrinolytic drug. The study focuses on the aromatic resonances. Comparisons with spectra from human, porcine and bovine kringle 4 homologs indicates a strict conservancy of conformation, reflecting the underlying primary sequence homology, and leads to an unambiguous assignment of all the aromatic resonances, including those of Phe15 and His40 which are unique to the chicken domain. Conclusive evidence is found that the Tyr9 ring fluctuates between two states, one in which it flips fast and other in which it is severely hindered. Similarly, the Tyr64 side chain finds itself in a structurally constrained locus. The Trp62, Tyr64, and Trp72 aromatic resonances are most sensitive to ligand presence, supporting a previously reported model of the kringle 4 lysine-binding site. His40, Phe41, and Tyr74 are also perturbed by ligand indicating proximity to the site. In contrast, the Phe15 aromatic spectrum indicates a rather mobile phenyl ring which is insensitive to ligand presence, thus confirming the lesser importance of the corresponding segment within the first kringle loop in determining kringle structure and/or function.

Analysis of the aliphatic 1H-NMR spectrum of plasminogen kringle 4. A comparative study of human, porcine, bovine and chicken homologs

The aliphatic 1H-NMR spectrum of the kringle 4 domain of human plasminogen has been studied via two-dimensional chemical shift correlated (COSY) and nuclear Overhauser correlated (NOESY) experiments at 300 MHz and 620 MHz. A number of aliphatic proton spin systems have been identified and several definite assignments have been made. This was mainly achieved by comparison of the human kringle 4 spectrum with spectra of the porcine, bovine and chicken homologs and also with that of the kringle 1 from human plasminogen on which we have reported previously. The three valyl and two leucyl residues of human kringle 4 have been assigned. The eleven threonyl spin systems have been identified via a RELAYED-COSY experiment and Thr17 has been assigned. The three alanyl spin systems have been identified and assigned. Six seryl spin systems have been identified and the signals from the seven glycyl residues of human kringle 4 have been located with Gly45 assigned. Furthermore, 24 AMX spin systems have been mapped in the COSY spectrum of human kringle 4 and H alpha-H beta,beta' spin systems of Tyr2, Tyr41, Tyr50, Tyr74, Trp25 and Trp62 have been assigned. From the spectrum of a deglycosylated chicken homolog, the epsilon-methyl singlets of Met28 and Met48 have been assigned. Finally, ligand effects on selected aliphatic resonances were observed which could be analyzed in terms of residues likely to neighbor the kringle lysine-binding site.

The aromatic 1H-NMR spectrum of plasminogen kringle 4. A comparative study of human, porcine and bovine homologs

The isolated kringle 4 domain of human plasminogen has been compared with homologous structures from bovine and porcine sources, both free and in the presence of the ligand 6-aminohexanoic acid, by two-dimensional 1H-NMR spectroscopies at 300 MHz and 600 MHz. The chemical-shift-correlated, spin-echo-correlated, and double-quantum-correlated aromatic spectra of the three proteins reveal that the globular conformation of the fourth kringle is closely maintained throughout the set of homologs. Direct comparison shows that the three conserved Trp residues (at sites 25, 62 and 72) which exhibit highly non-degenerate subspectra, find themselves in similar intramolecular environments. In particular, proton Overhauser experiments reveal that the close steric interaction between the Trp-II (Trp62 or Trp25) indole group and the aromatic ring at site 74 (Tyr74 or Phe74) is strictly preserved. This feature forces the kringle inner loop, closed by the Cys51-Cys75 link, to fold back onto itself so as to place the site 74 residue proximal to the Cys22-Cys63 bridge. Single-residue substitutions enable unambiguous assignments of His-I to His3, Tyr-III to Tyr41 and Tyr-IV to Tyr74. From this direct evidence, comparison with the kringle 1 spectrum, and the previously reported chemical modification of Tyr-II (Tyr50) [Trexler M., Bányai L., Patthy L., Pluck N. D. & Williams R. J. P. (1985) Eur. J. Biochem. 152, 439-446], Tyr-I and Tyr-V (the latter, an immobile ring on the 600-MHz time scale) could be assigned to Tyr2 and Tyr9, respectively. Since Trp-III has previously been assigned to Trp72 at the lysine-binding site, the present study completes the assignment of 10 out of 12 aromatic spin systems in the kringle 4 1H-NMR spectrum; the only ambiguity which remains concerns the Trp-I and Trp-II indole spin systems, which are totally identified but as yet only tentatively assigned to Trp25 and Trp62, respectively.

The kringle 4 domain of chicken plasminogen

The kringle 4 unit of chicken plasminogen is similar to mammalian kringle 4 domains in possessing a lysine-binding site. Chicken kringle 4 shows 73-77% sequence identity with the fourth kringle units of porcine, bovine and human plasminogens. A major difference between mammalian and chicken kringle 4 species is that in the latter a glucosamine-based carbohydrate substituent is linked to asparagine-34. Complexation of this carbohydrate with concanavalin A does not interfere with the binding of kringle 4 to lysine-Sepharose, suggesting that in the kringle-fold the glycosylated region is distant from the entrance of the lysine-binding pocket.

Complete amino acid sequence of bovine plasminogen. Comparison with human plasminogen

The amino acid sequence of the single polypeptide chain of bovine plasminogen (786 residues, Mr 88092) was determined. Cleavage with CNBr yielded 13 fragments of which six originated from cleavage sites different from human plasminogen. Digestion with elastase gave three major fragments: kringles (1 + 2 + 3) and kringle 4, both with intact lysine binding sites, and mini-plasminogen. Subfragmentation was achieved mainly with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole), Staphylococcus aureus V8 protease and trypsin. The sequences of fragments which were determined by automated Edman degradation, were aligned with overlapping sequences, or, in a few instances, by homology with the known sequence of human plasminogen. Sequence comparison with the human protein showed varying degrees of homology in the different functional and structural domains. The overall identity (78%) is practically the same as that found in those regions corresponding to the heavy (79%) and the light chain (80%) of plasmin. The average degree of identity among the kringles is 83%. Outside the kringle structures the extent of identity decreases, to 65% in the N-terminal region and to about 50% in the connecting strands between the kringles except for the strand between kringles 2 and 3, where only one out of 12 residues is exchanged. The results reported show that bovine plasminogen apparently contains the same structural and functional domains as human plasminogen. Bovine plasminogen also contains two carbohydrate moieties. The only partially substituted N-glycosidic site, Asn289, corresponds to partially glycosylated Asn288 in human plasminogen, whereas the O-glycosidic site of the human sequence, Thr345, is shifted to Ser339 in bovine plasminogen.

Determination of the complete amino-acid sequence of porcine miniplasminogen

The complete amino acid sequence of porcine miniplasminogen (Mr 37 600), comprising 341 residues, was determined by automated Edman degradation in a liquid-phase or solid-phase sequenator. Selected fragments were produced by cleavage with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole), cyanogen bromide, hydroxylamine, Staphylococcus aureus protease or trypsin or with combinations thereof and by activation with urokinase. The sequence obtained was compared with the known sequences of human and bovine miniplasminogen, indicating that the porcine molecule apparently contains the same structural and functional domains as the protein of the other two species. Porcine miniplasminogen has a sequence homology of 83% with human and of 79% with bovine miniplasminogen; 74% of the amino acids are identical in all three species. The results show a higher degree of evolutionary conservatism in the structurally and/or functionally vital regions of the molecule (active site residues, kringle 5).

The light-harvesting polypeptides of Rhodopseudomonas viridis. The complete amino-acid sequences of B1015-alpha, B1015-beta and B1015-gamma

Three low molecular mass polypeptides have been isolated by using the technique of organic solvent extraction of thylakoid membranes or whole cells from Rhodopseudomonas viridis. Their primary structures were determined by long liquid phase sequencer runs, combined with the isolation and sequence analysis of the C-terminal o-iodosobenzoic acid fragment and carboxypeptidase degradation. The polypeptide which consists of 58 amino-acids and is 46% homologous to the antenna polypeptide B880-alpha from Rhodospirillum rubrum was designated as B1015-alpha (1 His residue). The sequence homology between the second polypeptide, named B1015-beta (55 amino acids, 2 His residues) and B880-beta from Rs. rubrum is 52%. For the third polypeptide consisting of 36 amino acids and exhibiting a high hydrophobicity, no equivalent polypeptide has so far been found in other purple bacteria. The molar ratio of these three organic solvent soluble polypeptides from Rp. viridis was estimated to be 1:1:1. Accordingly, the 36 amino-acid polypeptide is likely to be an additional constituent of the light-harvesting complex B1015, consequently termed as B1015-gamma. According to hydrophathy profiles, the transmembrane arrangement of B1015-alpha and B1015-beta within the thylakoid membrane is supposed to be similar. B1015-gamma, however, shows a somewhat different hydropathy profile. A particular feature of this polypeptide is its high amount of aromatic amino acids. It is postulated that B1015-gamma is involved in the formation of regular arrays of light-harvesting complexes.

Site-directed fluorogenic modification of bacteriorhodopsin by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole

Site-directed covalent modification of bacteriorhodopsin is achieved by reacting the hydrophobic probe 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl) at neutral pH with purple membranes. The bacteriorhodopsin fluorescence thus produced is specific for a nucleophilic group. The spectral properties of NBD-modified bacteriorhodopsin indicate covalent interaction of the probe with the nucleophilic epsilon-amino group of a lysine residue. Modification of tyrosine can be excluded. As demonstrated by polypeptide fragmentation and subsequent sequence analysis, NBD binding is confined to lysine 41 within the primary structure of bacteriorhodopsin. Collisional fluorescence quenching with iodide demonstrates that, in NBD-treated purple membranes, the covalently bound label is not accessible in the aqueous phase. A hydrophobic location for the introduced fluorophor is thereby implied.