Dataset Information

Role of the P2 residue of human alpha 1-antitrypsin in determining target protease specificity.

ABSTRACT: Alpha 1-antitrypsin (A1AT) is a serine protease inhibitor that mainly inhibits neutrophil elastase in the lungs. A variant of A1AT at the P1 position with methionine 358 to arginine (A1AT-Pittsburgh) is a rapid inhibitor of thrombin with greatly diminished anti-elastase activity. The P2 residue (position 357) of A1AT-Pittsburgh has been shown to play an important role in interactions with thrombin and kallikrein, but the role of P2 residue in wild-type A1AT has largely been unraveled. Here, we investigated the effects of P2 proline substitutions in wild-type A1AT on interactions with porcine pancreatic elastase (PPE) and human neutrophil elastase (HNE). The mutant A1AT proteins (P357A, P357D, P357K, P357L, P357N, P357S, and P357W) were less efficient than the wild-type A1AT at inhibiting PPE and HNE. Among the mutants, P357D did not form a complex with PPE, whereas P357L, P357N, and P357W showed significantly reduced complex formation with PPE. Surprisingly, mass spectrometry analysis revealed that P357D had two cleavage sites after the P9 alanine and the P3 isoleucine residues. Our results indicate that the size and negative charge of the R group of the P2 residue influence the interaction with elastases. Specifically, the negative charge at the P2 residue is disfavored and the resulting conformational changes in the reactive center loop upon interaction with PPE lead to cleavage at new sites. Overall, the results of this study demonstrate a previously unknown role for P2 residue in determining inhibitory specificity of A1AT.

SUBMITTER: Chung HS

PROVIDER: S-EPMC5602671 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Role of the P2 residue of human alpha 1-antitrypsin in determining target protease specificity.

Chung Hye-Shin HS Kim Ji-Sun JS Lee Sang Mee SM Park Soon Jae SJ

PloS one 20170918 9

Alpha 1-antitrypsin (A1AT) is a serine protease inhibitor that mainly inhibits neutrophil elastase in the lungs. A variant of A1AT at the P1 position with methionine 358 to arginine (A1AT-Pittsburgh) is a rapid inhibitor of thrombin with greatly diminished anti-elastase activity. The P2 residue (position 357) of A1AT-Pittsburgh has been shown to play an important role in interactions with thrombin and kallikrein, but the role of P2 residue in wild-type A1AT has largely been unraveled. Here, we i ...[more]

PMID: 28922398

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Project description:BackgroundA large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent these different methods overlap, and if any of the methods have higher predictive potential compared to others when it comes to, in particular, the identification of catalytic residues (CR) in proteins. Using a large set of enzymatic protein families and measures based on different evolutionary signals, we sought to break up the different components of the information content within a multiple sequence alignment to investigate their predictive potential and degree of overlap.ResultsOur results demonstrate that the different methods included in the benchmark in general can be divided into three groups with a limited mutual overlap. One group containing real-value Evolutionary Trace (rvET) methods and conservation, another containing mutual information (MI) methods, and the last containing methods designed explicitly for the identification of specificity determining positions (SDPs): integer-value Evolutionary Trace (ivET), SDPfox, and XDET. In terms of prediction of CR, we find using a proximity score integrating structural information (as the sum of the scores of residues located within a given distance of the residue in question) that only the methods from the first two groups displayed a reliable performance. Next, we investigated to what degree proximity scores for conservation, rvET and cumulative MI (cMI) provide complementary information capable of improving the performance for CR identification. We found that integrating conservation with proximity scores for rvET and cMI achieved the highest performance. The proximity conservation score contained no complementary information when integrated with proximity rvET. Moreover, the signal from rvET provided only a limited gain in predictive performance when integrated with mutual information and conservation proximity scores. Combined, these observations demonstrate that the rvET and cMI scores add complementary information to the prediction system.ConclusionsThis work contributes to the understanding of the different signals of evolution and also shows that it is possible to improve the detection of catalytic residues by integrating structural and higher order sequence evolutionary information with sequence conservation.

Dataset Information

Role of the P2 residue of human alpha 1-antitrypsin in determining target protease specificity.

Publications

Role of the P2 residue of human alpha 1-antitrypsin in determining target protease specificity.

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