Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.4.21.4 (trypsin)
 42,187 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A distance-based database search scheme is proposed for modeling Pro----in non-Pro and insertion/deletion regions of homologous globular proteins up to six residues in length. In the first step, geometric descriptors, the number of residues involved and target distances corresponding to the separation of C alpha atom positions adjacent to the "missing" segment, are chosen. In the second step, a database of high-resolution X-ray structures is scanned for segments with similar descriptors and selected segments are binned according to conformational type. In the third and fourth steps, the selected conformations are docked into the protein, and geometric and energetic criteria are used to determine their viability as segment models. The fifth step consists of an interaction scheme in which the geometric descriptors are redefined. This compensates for the use of a limited database and/or for the use of a poor original protein model adjacent to the missing segment. The procedure has been tested on Pro----non-Pro mutations in the homologous proteins penicillopepsin and endothiapepsin, and on the insertion/deletion regions of the homologs penicillopepsin and endothiapepsin, trypsin and gamma-chymotrypsin and hen and human lysozyme. The test cases represent a wide variety of secondary structural elements (helix, sheet, turn and coil) and insertion/deletion lengths (0 to 4 residues). It is shown that 79% of the test cases are accurately modeled (within 0.54 A root-mean-square (r.m.s.) deviation for main-chain atoms) using the proposed scheme. Failure of the scheme (main-chain atom r.m.s. deviations greater than 1.29 A) in 21% of the cases appears to be related to the presence of infrequently observed conformations or locally unique folds of the target proteins with respect to the database (18% of the test cases); the remaining 3% are unexplained. Geometric and energetic criteria are able to discriminate between trial conformations that correspond to the X-ray structures and those that are different in 97% of the conformations generated by the distance-weighted database search scheme. The scheme is shown to be relatively insensitive to uncertainty in the template co-ordinates, since the geometric descriptors were taken from the homologous protein (r.m.s. deviations in the position of descriptors range from 0.18 to 1.35 A for the accurately modeled test cases). It is demonstrated that the scheme can be used to correct local sequence misalignments.
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PMID:Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. 226 66

The complete amino acid sequence of rhizopuspepsin, an aspartic proteinase from the fungus Rhizopus chinensis was determined by conventional protein sequencing, using peptide fragments obtained mainly by several enzymatic cleavages of the reduced and carboxymethylated (RCm-) protein. The RCm-protein was first cleaved by trypsin, and the resulting peptides were purified and their amino acid sequences determined extensively. These tryptic peptides were aligned by the aid of overlapping peptides isolated from a tryptic and a chymotryptic digest of the citraconylated RCm-protein and the RCm-protein, respectively. The amino acid sequence thus deduced was further confirmed by isolation and sequence determination of peptides obtained by digestion of the RCm-protein with Staphylococcus aureus V8 protease. The location of the disulfide bonds was determined by isolation and analysis of cystine-containing peptides from a chymotryptic digest of intact rhizopuspepsin. These results showed that the protein is composed of a single polypeptide chain of 325 amino acid residues cross-linked by two disulfide bonds, and shows overall homology with other aspartic proteinases, including 36% identity with penicillopepsin and 38% identity with porcine pepsin.
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PMID:The amino acid sequence of rhizopuspepsin, an aspartic proteinase from Rhizopus chinensis. 310 May 34

The aminopeptidase A of the porcine intestinal brush-border membrane has been purified following solubilization by trypsin (p-form) or Emulphogen (d-form). Full purification of d-amino-peptidase A required the use of anti-impurities immunoabsorbant chromatography. The d-amino-peptidase A constitutes about 4% of the total proteins of the membrane, compared to 8-12% for another, already characterized, brush-border aminopeptidase N. Both d-form and p-form of aminopeptidase A have been clearly shown to be dimeric. Experimental evidence is presented favoring the view that they are symmetrical dimers, with the consequence that each of the two subunits of the d-form possesses an hydrophobic anchor holding them at the membrane surface. As already demonstrated for several other brush border hydrolases, the hydrophobic anchor is N-terminal in porcine intestinal aminopeptidase A. The molecular weight of the peptide including the anchor liberated by trypsin during the conversion of the d-form into the p-form has been estimated by an isotopic dilution method to be about 4500 (42 residues). This value which compares well with those recently obtained in the case of rabbit aminopeptidase N (3700-3800; 36-38 residues), indicates that the anchor is much shorter than believed earlier. A preliminary survey of the specificity of both aminopeptidases A and N towards four synthetic amino acid p-nitroanilides confirms that aminopeptidase A mostly cleaves acidic residues. Its activity towards neutral residues is much lower, but probably significant in certain cases.
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PMID:Purification and characterization of an aminopeptidase A from hog intestinal brush-border membrane. 610 77

To determine the structural basis for the highly specific action of renin, structural features of the active site and the complete amino acid sequence of mouse submaxillary gland renin were determined. A rapid method was developed for a large scale purification of renin from mouse submaxillary gland. The active site of renin was shown to consist of 2 aspartyl residues, 2 tyrosyl residues and one arginyl residue, the structures analogous to the active site of pepsin and other acid proteases. Renin was found to consist of one heavy chain (Mr = 31,036) and one light chain (Mr = 5,458) connected by a disulfide bridge. Amino acid sequences of these chains were determined using overlapping peptides generated by cleavage with cyanogen bromide, trypsin, Staphylococcus aureus protease and Lysobacter enzymogenes endoproteinase Lys-C. Sequences involving 2 catalytically essential aspartyl residues 32 and 215, characteristic to acid proteases, were found identical with pepsin, penicillopepsin and chymosin. The sequence of L-chain was homologous with carboxyl terminal region of porcine pepsin in 46% of amino acid residues. H-chain showed 41% homology with 284 residues on the amino-terminal side of the porcine pepsin molecule. Residues identical in renin and acid proteases are distributed throughout the length of the molecules, suggesting a similarity in their overall structure.
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PMID:Structure of mouse submaxillary gland renin. 635 66