X-ray analyses of aspartic proteinases

Cooper, J.B.; Khan, Gulraiz; Taylor, G.L.; Tickle, Ian J.; Blundell, Tom L.

doi:10.1016/0022-2836(90)90156-g

Cited by 216 publications

(81 citation statements)

References 43 publications

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“…A special @-bulge is found in all these proteins, but the subclass is not the same in each case. Pepsin (SPEP; Cooper et al, 1990) and chymosin (4CMS; Newman et al, 1991) have an SP3 bulge, whereas endothiapepsin (2ER7; Veerapandian et al, 1991) and penicillopepsin (3APP; James & Sielecki, 1983) have an SP4 bulge. The change in bulge type seems to accommodate the extra residue (glycine) in 2ER7 and 3APP.…”

Section: Role Of @-Bulgesmentioning

confidence: 99%

Identification, classification, and analysis of beta‐bulges in proteins

et al. 1993

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A @-bulge is a region of irregularity in a &sheet involving two @-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in 0-sheets were iden- A set of 182 protein chains (170 proteins) was used, and a total of 362 bulges were extracted. Five types of @-bulges were found: classic, G1, wide, bent, and special. Their characteristic amino acid preferences were found for most classes of bulges.Basically, bulges occur frequently in proteins; on average there are more than two bulges per protein. In general, @-bulges produce two main changes in the structure of a @-sheet: (1) disrupt the normal alternation of side-chain direction; (2) accentuate the twist of the sheet, altering the direction of the surrounding strands.

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Section: Role Of @-Bulgesmentioning

confidence: 99%

Identification, classification, and analysis of beta‐bulges in proteins

et al. 1993

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“…A rule-based automated approach to comparative protein modelling [I I-141 encoded in the COMPOSER suite of computer programs and based on the crystal structures of six aspartic proteinases (porcine pepsin [15], bovine chymosin [ 161, human renin [ 171, mouse renin [ 181, human cathepsin D [19], yeast proteinase A [20]) which have greater than 40% sequence identity to the sequence of HvAP, was used to model the barley-grain aspartic proteinase. The model was further refined using energy minimization techniques (SYBYL; Tripos Co., USA).…”

Section: Modellingmentioning

confidence: 99%

Comparative modelling of barley‐grain aspartic proteinase: A structural rationale for observed hydrolytic specificity

et al. 1994

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A model of the barley-grain aspartic proteinase (HvAP; Hordeum vulgare aspartic proteinase) has been constructed using the rule-based comparative modelling approach encoded in the COMPOSER suite of computer programs. The model was based on the high resolution crystal structures of six highly homologous aspartic proteinases. Results suggest that the overall three-dimensional structure of HvAP (excluding the plant-specific insert; 104 residues in HvAP) is closer to human cathepsin D than other aspartic proteinases of known three-dimensional structure.

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“…Pepsin is a particularly good model for the study of aspartic proteases because detailed information is available on its structure (Abad-Zapatero et al, 1990;Cooper et al, 1990;Sielecki et al, 1990), enzymic properties (Fruton, 1976), and zymogen activation (Tang & Wong, 1987;Hartsuck et al, 1992). Like other eukaryotic aspartic proteases, pepsin is a single-chain protein, and its tertiary structure consists of two homologous lobes.…”

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confidence: 99%

Conformational instability of the N‐ and C‐terminal lobes of porcine pepsin in neutral and alkaline solutions

et al. 1993

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Pepsin contains, in a single chain, two conformationally homologous lobes that are thought to have been evolutionarily derived by gene duplication and fusion. We have demonstrated that the individual recombinant lobes are capable of independent folding and reconstitution into a two-chain pepsin or a two-chain pepsinogen (Lin, X . , et al., 1992, J. Biol. Chem. 267,[17257][17258][17259][17260][17261][17262][17263]. Pepsin spontaneously inactivates in neutral or alkaline solutions. We have shown in this study that the enzymic activity of the alkaline-inactivated pepsin was regenerated by the addition of the recombinant N-terminal lobe but not by the C-terminal lobe. These results indicate that alkaline inactivation of pepsin is due to a selective denaturation of its N-terminal lobe. A complex between recombinant N-terminal lobe of pepsinogen and alkaline-denatured pepsin has been isolated. This complex is structurally similar to a two-chain pepsinogen, but it contains an extension of a denatured pepsin N-terminal lobe. Acidification of the complex is accompanied by a cleavage in the pro region and proteolysis of the denatured N-terminal lobe. The structural components that are responsible for the alkaline instability of the N-terminal lobe are likely to be carboxyl groups with abnormally high pK, values. The electrostatic potentials of 23 net carboxyl groups in the N-terminal domain (as compared to 19 in the C-terminal domain) of pepsin were calculated based on the energetics of interacting charges in the tertiary structure of the domain. The groups most probably causing the alkaline denaturation are Asp", Asp"', Glu4, Glu13, and Asp"'. Especially, the partially buried Asp", which interacts with Asp159, could cause one of these two groups to have an abnormally high pK, and the other an abnormally low pK, value. Thus, the ionization of Asp'' at a high pH may place two negatively charged residues in close vicinity. This unfavorable situation may be the trigger for the denaturation of the N-terminal lobe of pepsin.Keywords: carboxyl ionization; denaturation; domain structure; electrostatic potentials; porcine pepsinThe fact that some aspartic proteases, such as HIV protease and renin, are involved in human diseases has stimulated much interest recently in the understanding of the structure-function relationships of this group of enzymes. Reprint requests to: Jordan Tang, Protein Studies Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, Oklahoma 73104.Abbreviations: bis-Tris, bis(2-hydroxyethyl)-iminotris(hydroxymethy1)methane; FPLC, fast protein liquid chromatography (chromatograph); HIV, human immunodeficiency virus; PAGE, polyacrylamide gel electrophoresis; pep, the NH,-terminal lobe of pepsin; pep.sin, twochain pepsin; pepsin,, alkaline-inactivated pepsin; pro, propeptide; propep, the NH2-terminal lobe of pepsinogen; propep.pepsin,, complex between propep and alkaline-inactivated pepsin; propep.sin, twochain pepsinogen; SDS, sodium dodecyl sulfate; sin, the C-terminal lob...

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X-ray analyses of aspartic proteinases

Cited by 216 publications

References 43 publications

Identification, classification, and analysis of beta‐bulges in proteins

Identification, classification, and analysis of beta‐bulges in proteins

Comparative modelling of barley‐grain aspartic proteinase: A structural rationale for observed hydrolytic specificity

Conformational instability of the N‐ and C‐terminal lobes of porcine pepsin in neutral and alkaline solutions

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