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L Patthy

Publications and source records attributed to L Patthy.

At least 55 records · Page 3Linked to original sources
PubMed1991

Homology of the precursor of pulmonary surfactant-associated protein SP-B with prosaposin and sulfated glycoprotein 1.

The precursor of pulmonary surfactant-associated protein, SP-B, is composed of an NH2-terminal domain of 30 residues (a-type domain) and three tandem repeats of about 90 residues (b-type domain); biophysically active mature SP-B corresponds to the second b-type repeat. Consensus sequences constructed for the b-type repeats were used to search the data base for homologous sequences, and the search has revealed that prosaposin and sulfated glycoprotein 1 show a remarkable homology with these repeats. The domain organizations of the latter proteins, however, differ from that of SP-B precursor inasmuch as they contain four tandem copies of the b-type domain and a-type domains are present both in the NH2-terminal and COOH-terminal parts of the proteins. The implications of the homology of saposins and SP-B for their structure and function are discussed.

Amino Acid Sequence↗
PubMed1991

Sequence-specific 1H NMR assignments and structural characterization of bovine seminal fluid protein PDC-109 domain b.

Sequence-specific resonance assignments for the isolated second or b domain of the bovine seminal fluid protein PDC-109 have been obtained from analysis of two-dimensional 1H NMR experiments recorded at 500 MHz. These assignments include the identification of all aromatic and most aliphatic amino acid resonances. Stereospecific assignment of resonances stemming from the Val2 CH3 gamma,gamma' groups and from seven CH beta,beta' geminal pairs has been accomplished by analysis of 3J alpha beta coupling constants in conjunction with patterns of cross-peak intensities observed in two-dimensional nuclear Overhauser effect (NOESY) spectra. Analysis of NOESY and 3J alpha NH data reveals a small antiparallel beta-sheet involving stretches containing residues 25-28 and 39-42, a cis-proline residue (Pro4), antiparallel strands consisting of residues 1-3, 5-7, and 10-13, and an aromatic cluster composed of Tyr7, Trp26, and Tyr33. The results of distance geometry and restrained molecular dynamics calculations indicate that the global fold of the PDC-109 b domain, a type II module related to those found in fibronectin, is somewhat different from that predicted by modeling the structure on the basis of homology between type II and kringle units. A shallow depression in the molecular surface which presents a solvent-exposed hydrophobic area--a potential ligand-binding site-is identified in the NMR-based models.

Amino Acid Sequence↗
PubMed1991

Exons--original building blocks of proteins?

In a recent paper, Walter Gilbert's group has estimated the number of original exons from which all extant proteins might have been constructed. The approach used is subjected to a critical analysis here. It is shown that there are flawed assumptions about both the mechanism and generality of exon-shuffling and in the sequence comparison procedures employed, the latter failing to distinguish chance similarity from similarity due to common ancestry. These methodological errors lead to the omission of many known cases of exon-shuffling and the inclusion of others which may not be genuine. In consequence, the analysis from the Gilbert group cannot give a reliable estimate of those modules that actually participated in exon-shuffling and provides no information on the number of protein archetypes that did not participate in these processes.

Amino Acid Sequence↗
PubMed1990

The collagen-binding site of type-II units of bovine seminal fluid protein PDC-109 and fibronectin.

A single type-II domain has been isolated by limited proteolysis of the collagen-binding bovine seminal fluid protein, PDC-109. The 45-residue fragment corresponding to the second type-II domain of the parent molecule was found to have retained affinity for immobilized collagen, indicating that this minidomain carries critical regions of the collagen-binding site. Studies on various fragments of fibronectin have also implicated the two type-II units of this molecule in collagen-binding. In the present work we have found that type-II domains of human fibronectin, expressed in Escherichia coli as beta-galactosidase fusion proteins, bind specifically to immobilized collagen.

Amino Acid Sequence↗
PubMed1990

Evolution of blood coagulation and fibrinolysis.

The key steps in the evolution of blood coagulation and fibrinolysis have been reconstructed from an analysis of the molecular evolution of their constituents. The data suggest that the blood coagulation and complement cascades are descendants of an ancestral defence system that served the dual role of immobilization and destruction of invading bacteria and the prevention of loss of body fluids. The enzymes of the fibrinolytic, tissue-remodelling cascades form a distinct group, more closely related to the proteases of the digestive tract than to the components of the blood coagulation and complement cascades. Molecular evolution of these enzymes therefore suggests that they are descendants of an ancestral protease responsible for degradation of extracellular proteins. It is shown that the regulatory extensions of the proteases of the blood coagulation, fibrinolytic and complement cascades were assembled from domains borrowed from other proteins. Most non-protease components of these systems were also constructed by this evolutionary mechanism.

Animals↗
PubMed1989

Homology of cytotoxic protein of eosinophilic leukocytes with IgE receptor Fc epsilon RII: implications for its structure and function.

The major protein constituent of eosinophilic leukocyte granules is a cytotoxic protein that plays a key role in antiparasitic defence mechanisms and immune hypersensitivity reactions. We show here that the protein is homologous with animal lectins; it exhibits greatest similarity to the lectin domain of the low-affinity IgE receptor of lymphocytes. On the basis of homology with lectins the disulphide bond pattern of the protein is predicted. It is proposed that certain cysteines unique to major basic protein are on the surface of the molecule and are involved in forming disulphide-bonded polymers. Homology with IgE receptor raises the possibility that major basic protein may also bind to IgE antibodies. Such an interaction could provide an efficient way of targeting the cytotoxic protein to parasites and allergens recognized by IgE antibodies.

Amino Acid Sequence↗
PubMed1989

Prediction of surface loops of protein-folds from multiple alignments of homologous sequences.

Multiple alignments of distantly related homologous sequences may be used for the construction of consensus sequences that identify conserved motifs, variable segments and regions that tolerate gap events. It is suggested that such consensus sequences may be used for the prediction of key features of protein-folds. The validity of the proposed approach is illustrated in the case of the alpha 2 mu globulin superfamily: the consensus sequence derived from the multiple alignment of sequences succeeded in identifying conserved structural motifs and in predicting the location of surface loops that connect these motifs.

Amino Acid Sequence↗
PubMed1988

Detecting distant homologies of mosaic proteins. Analysis of the sequences of thrombomodulin, thrombospondin complement components C9, C8 alpha and C8 beta, vitronectin and plasma cell membrane glycoprotein PC-1.

Recognition of homologies may give hints about the structure and function of proteins; therefore, we are developing strategies to aid sequence comparisons. Detecting homology of mosaic proteins is especially difficult since the modules constituting these proteins are usually distantly related and their homology is not readily recognized by conventional computer programs. In the present work we show that the rules of the evolution of mosaic proteins can guide the identification of modules of mosaic proteins and can delineate the group of sequences in which the presence of homologous sequences may be expected. By this approach we can concentrate the search for homology to a limited group of sequences; thus ensuring a more intense and more fruitful search. The power of this approach is illustrated by the fact that it could detect homologies not identified by earlier methods of sequence comparison. In this paper we show that thrombomodulin contains a domain homologous with animal lectins, that complement components C9, C8 alpha and C8 beta have modules homologous with one of the repeat units of thrombospondin and that the somatomedin B module of vitronectin is homologous with the internal repeats of plasma cell membrane glycoprotein PC-1.

Amino Acid Sequence↗
PubMed1988

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.

Amino Acid Sequence↗
PubMed1988

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.

Amino Acid Sequence↗
PubMed1987

Detecting homology of distantly related proteins with consensus sequences.

A simple protocol is described that is suitable for the detection of distantly related members of a protein family. In this procedure, similarity to a consensus sequence is used to distinguish chance similarity from similarity due to common ancestry. The consensus sequence is constructed from the sequences of established members of a protein family and it incorporates features characteristic of the protein fold of this family: conserved residues, the pattern of variable and conserved segments, preferred location of gaps etc. The database is searched with the consensus sequence, using the unitary matrix or log odds matrix for scoring the alignments, with variable gap penalty. The advantage of the method is that it weights key residues, ignores sequence similarity in variable segments (thus partially eliminating "background noise" coming from chance similarity), distinguishes gaps disrupting conserved segments from those occurring in positions known to be tolerant of gap events. The utility of the method was demonstrated in the case of the protein family homologous with the internal repeats of complement B as well as the internal repeats identified in fibroblast proteoglycan PG40. The consensus sequence method succeeded in finding some new members of these protein families that could not be detected by earlier methods of sequence comparison.

Algorithms↗
PubMed1987

Intron-dependent evolution: preferred types of exons and introns.

Exon insertions and exon duplications, two major mechanisms of exon shuffling, are shown to involve modules that have introns of the same phase class at both their 5'- and 3'-ends. At the sites of intronic recombinations exon insertions and duplications create new introns which belong to the same phase class as the recipient introns. As a consequence of repeated exon insertions and exon duplications introns of a single phase class predominate in the resulting genes, i.e. gene assembly by exon shuffling is reflected both by this nonrandom intron phase usage and by the correlation between the domain organization of the proteins and exon-intron organization of their genes. Genes that appeared before the eukaryote-prokaryote split do not show these diagnostic signs of exon shuffling. Since ancestral introns (e.g. self-splicing introns) did not favour intronic recombination, exon shuffling may not have been significant in the early part of protein evolution.

Animals↗
PubMed1986

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.

Animals↗
PubMed1985

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.

Amino Acid Sequence↗
PubMed1985

Proximity of the catalytic region and the kringle 2 domain in the closed conformer of plasminogen.

Introduction of a single intramolecular cross-link with 1,5-difluoro-2,4-dinitrobenzene into Glu-plasminogen freezes the molecule in its closed conformational state (Bányai, L. and Patthy, L. (1984) J. Biol. Chem. 259, 6466-6471). Here we show that the cross-link connects Lys-203 of the kringle 2 domain and Tyr-671 of the catalytic domain, indicating that these regions are in close proximity in the closed conformer of Glu-plasminogen. Comparison of the parameters of the urokinase-catalysed activation of native and cross-linked Glu-plasminogen species indicates that cross-linking of kringle 2 and the catalytic region interferes with the productive binding of urokinase to plasminogen.

Amino Acid Sequence↗