scholarly journals Interspecies conservation of structure of interphotoreceptor retinoid-binding protein Similarities and differences as adjudged by peptide mapping and N-terminal sequencing

1986 ◽  
Vol 240 (1) ◽  
pp. 19-26 ◽  
Author(s):  
T M Redmond ◽  
B Wiggert ◽  
F A Robey ◽  
G J Chader
Keyword(s):  
Amino Acid ◽  
Time Course ◽  
Peptide Mapping ◽  
Binding Protein ◽  
Protein Pattern ◽  
Electrophoretic Analysis ◽  
Reversed Phase ◽  
Hydrophobic Peptides ◽  
Interphotoreceptor Retinoid Binding Protein ◽  
Human Proteins

Structural properties of the retinal extracellular-matrix glycolipoprotein interphotoreceptor retinoid-binding protein (IRBP) from human, monkey and bovine retinas have been compared. SDS/polyacrylamide-gel-electrophoretic analysis of limited tryptic and Staphylococcus aureus-V8-proteinase digests show virtually identical patterns for the monkey and human proteins, whereas both sets differ considerably from the bovine protein pattern. Time-course digestion shows monkey IRBP to be more readily cleaved than bovine IRBP and also cleaved to smaller fragments. Also, reversed-phase h.p.l.c. of complete tryptic digests of the IRBPs indicate that, although they have in common a similar preponderance of hydrophobic peptides, all three proteins differ extensively in their fine structure. The N-terminal sequences of monkey and bovine IRBPs have been extended beyond those presented in our previous report [Redmond, Wiggert, Robey, Nguyen, Lewis, Lee & Chader (1985) Biochemistry 24, 787-793] to over 30 residues each. The sequences yet show extensive homology, differing at only two positions, although the major monkey sequence has an additional five amino acid residues at its N-terminus (‘n + 5’ sequence) not observed with bovine IRBP (‘n’ sequence). The newly determined N-terminal sequence of human IRBP demonstrates the presence of equal amounts of the ‘n’ and ‘n+5’ sequences that are qualitatively identical with those of the monkey. The presence of the five-amino-acid-residue extension in primate, but not bovine, IRBP may indicate variation in post-translational processing.

CLEAVAGE PATHWAY,AND SPECIFICITY OF LEUCOCYTE ELASTASE AS COMPARED TO PLASMIN DURING FIBRINOGEN DEGRADATION

1987 ◽  
Author(s):  
L Goretzki ◽  
E Miller ◽  
A Henschen
Keyword(s):  
Amino Acid ◽  
Time Course ◽  
Proteolytic Enzymes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecylsulfate ◽  
Reversed Phase ◽  
Cleavage Sites ◽  
Human Fibrinogen ◽  
Leucocyte Elastase ◽  
N Terminus

Plasmin and leucocyte elastase are regarded as the two medically most important fibrin(ogen)-degrading proteolytic enzymes. There is, however, a considerable difference in information available about the cleavage specificities and fragmentation pathways of these two enzymes. Degradation by plasmin has been studied already for a long time in great detail so that now the time course of the degradation, the cleavage sites and the functional properties of many fragments are well known. In contrast, relatively little is known about the degradation by leucocyte elastase, except that the overall cleavage pattern resembles that obtained with plasminIn this investigation the leucocyte elastase-mediated degradation of fibrinogen has been examined by means of proteinchemi-cal methods. Human fibrinogen was incubated with human enzyme material for various periods of time and at some different enzyme concentrations. The split products formed at the various stages were isolated in pure form by gel filtration followed by reversed-phase high-performance liquid chromatography. The fragments were identified by N-terminal amino acid sequence and amino acid composition. The course of the degradation was also monitored by sodium dodecylsulfate-polyacrylamide gel electrophoresis. All cleavage patterns were compared with the corresponding patterns from plasmic degradation. It could be confirmed that X-, D- and E-like fragments are formed also with elastase. However, several early elastolytic Aα-chain fragments are characteristically different from plasmic fragments. The previously identified N-terminal cleavage site in the Aα-chain, i.e. after position 21, was found to be the most important site in this region of fibrinogen. The very early degradation of the Aα-chain N-terminus by elastase is in strong contrast to the stability against plasmin. Several cleavage sites in N-terminal region of the Bβ-chain were observed, though the low amino acid specificity of elastase partly hampered the identification. The γ-chain N-terminus was found to be as highly stable towards elastase as towards plasmin. The results are expected to contribute to the understanding of the role of leucocyte elastase in pathophysiologic fibrino(geno)lysis

scholarly journals Separation and characterization of the two Asn-linked glycosylation sites of chicken serum riboflavin-binding protein. Glycosylation differences despite similarity of primary structure

1992 ◽  
Vol 285 (1) ◽  
pp. 275-280 ◽  
Author(s):  
J S Rohrer ◽  
H B White
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Primary Structure ◽  
Tertiary Structure ◽  
Binding Protein ◽  
Attachment Site ◽  
Reversed Phase ◽  
Exchange Chromatography ◽  
Protein Glycosylation ◽  
Oligosaccharide Structure

Serum riboflavin-binding protein, a phosphoglycoprotein from the blood of laying hens, contains two Asn-Xaa-(Thr)Ser sequons in very similar but well-separated regions of amino acid sequence. In order to evaluate the effect of local amino acid sequence on the structure of the attached oligosaccharides, serum riboflavin-binding protein was purified to homogeneity, reduced and alkylated, digested with trypsin, and the two glycopeptides were separated by reversed-phase chromatography. After digestion with peptide-N-glycosidase F the released oligosaccharides were separated by high-pH anion-exchange chromatography and the oligosaccharide profiles of the two glycopeptides were compared. Although the two asparagine residues that are glycosylated are contained in pentapeptide segments in which four out of five amino acids are identical, the array of oligosaccharides present at each site show differences in both type and distribution. This suggests that local secondary or tertiary structure, or the order of glycosylation, influences the oligosaccharide structure more than does the primary structure flanking the attachment site.

scholarly journals Glial hyaluronate-binding protein: a product of metalloproteinase digestion of versican?

1995 ◽  
Vol 312 (2) ◽  
pp. 377-384 ◽  
Author(s):  
G Perides ◽  
R A Asher ◽  
M W Lark ◽  
W S Lane ◽  
R A Robinson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Brain ◽  
Peptide Mapping ◽  
Binding Protein ◽  
Protein A ◽  
Immunoblot Analysis ◽  
Bovine Brain ◽  
Naturally Occurring ◽  
Brain Extracts ◽  
The Brain

Glial hyaluronate-binding protein (GHAP) is a 60 kDa glycoprotein with an amino acid sequence identical to that of the hyaluronate-binding region of versican, a large fibroblast aggregating proteoglycan found in the brain. Both GHAP and versican were identified by immunoblot in bovine brain extracts prepared only minutes after death. Human recombinant collagenase, stromelysin, mouse gelatinase and gelatinases isolated from human brain by affinity chromatography digest versican and give rise to a polypeptide with electrophoretic mobility identical to GHAP. Immunoblot analysis, peptide mapping and C-terminal amino acid sequencing indicate that the polypeptide generated by digestion with human brain gelatinases is identical to GHAP. We suggest that GHAP is a naturally occurring versican degradation product.

scholarly journals Avoided motifs: short amino acid strings missing from protein datasets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Large Protein ◽  
New Approach ◽  
Cellular Context ◽  
Human Proteins ◽  
Context Specific ◽  
Protein Datasets

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.

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