scholarly journals Structural determinants of tobacco vein mottling virus protease substrate specificity

2010 ◽  
Vol 19 (11) ◽  
pp. 2240-2251 ◽  
Author(s):  
Ping Sun ◽  
Brian P. Austin ◽  
József Tözsér ◽  
David S. Waugh
Keyword(s):  
Substrate Specificity ◽  
Structural Determinants ◽  
Protease Substrate ◽  
Tobacco Vein Mottling Virus

scholarly journals An automated protocol for modelling peptide substrates to proteases

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rodrigo Ochoa ◽  
Mikhail Magnitov ◽  
Roman A. Laskowski ◽  
Pilar Cossio ◽  
Janet M. Thornton
Keyword(s):  
Substrate Recognition ◽  
Accessible Surface Area ◽  
Conformational Sampling ◽  
Structural Determinants ◽  
Peptide Substrates ◽  
The Family ◽  
Protease Substrate ◽  
Peptide Complexes ◽  
Accessible Surface ◽  
Automated Protocol

Abstract Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.

Investigation of Structural Determinants for the Substrate Specificity in the Zinc-Dependent Alcohol Dehydrogenase CPCR2 fromCandida parapsilosis

ChemBioChem ◽  
2015 ◽  
Vol 16 (10) ◽  
pp. 1512-1519 ◽  
Author(s):  
Christoph Loderer ◽  
Gaurao V. Dhoke ◽  
Mehdi D. Davari ◽  
Wolfgang Kroutil ◽  
Ulrich Schwaneberg ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Substrate Specificity ◽  
Structural Determinants

Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays

PROTEOMICS ◽  
2005 ◽  
Vol 5 (5) ◽  
pp. 1292-1298 ◽  
Author(s):  
Dhaval N. Gosalia ◽  
Cleo M. Salisbury ◽  
Dustin J. Maly ◽  
Jonathan A. Ellman ◽  
Scott L. Diamond
Keyword(s):  
Substrate Specificity ◽  
Serine Protease ◽  
Solution Phase ◽  
Peptide Microarrays ◽  
Protease Substrate ◽  
Fluorogenic Peptide

scholarly journals ZapA, a possible virulence factor from Proteus mirabilis exhibits broad protease substrate specificity

2001 ◽  
Vol 34 (11) ◽  
pp. 1397-1403 ◽  
Author(s):  
M.A.F. Anéas ◽  
F.C.V. Portaro ◽  
I. Lebrun ◽  
L. Juliano ◽  
M.S. Palma ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Virulence Factor ◽  
Proteus Mirabilis ◽  
Protease Substrate

scholarly journals Human and mouse granzyme M display divergent and species-specific substrate specificities

2011 ◽  
Vol 437 (3) ◽  
pp. 431-442 ◽  
Author(s):  
Stefanie A.H. de Poot ◽  
Marijn Westgeest ◽  
Daniel R. Hostetter ◽  
Petra van Damme ◽  
Kim Plasman ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Specific Substrate ◽  
Structural Determinants ◽  
Cytotoxic Lymphocyte ◽  
Potent Inducer ◽  
Methionine Residue ◽  
Positional Scanning ◽  
Methionine Residues ◽  
Species Specific ◽  
Positional Scanning Libraries

Cytotoxic lymphocyte protease GrM (granzyme M) is a potent inducer of tumour cell death and a key regulator of inflammation. Although hGrM (human GrM) and mGrM (mouse GrM) display extensive sequence homology, the substrate specificity of mGrM remains unknown. In the present study, we show that hGrM and mGrM have diverged during evolution. Positional scanning libraries of tetrapeptide substrates revealed that mGrM is preferred to cleave after a methionine residue, whereas hGrM clearly favours a leucine residue at the P1 position. The kinetic optimal non-prime subsites of both granzymes were also distinct. Gel-based and complementary positional proteomics showed that hGrM and mGrM have a partially overlapping set of natural substrates and a diverged prime and non-prime consensus cleavage motif with leucine and methionine residues being major P1 determinants. Consistent with positional scanning libraries of tetrapeptide substrates, P1 methionine was more frequently used by mGrM as compared with hGrM. Both hGrM and mGrM cleaved α-tubulin with similar kinetics. Strikingly, neither hGrM nor mGrM hydrolysed mouse NPM (nucleophosmin), whereas human NPM was hydrolysed efficiently by GrM from both species. Replacement of the putative P1′–P2′ residues in mouse NPM with the corresponding residues of human NPM restored cleavage of mouse NPM by both granzymes. This further demonstrates the importance of prime sites as structural determinants for GrM substrate specificity. GrM from both species efficiently triggered apoptosis in human but not in mouse tumour cells. These results indicate that hGrM and mGrM not only exhibit divergent specificities but also trigger species-specific functions.

POLYANILINE-BASED PEPTIDE ARRAYS: PRODUCTION, PROPERTIES AND APPLICATION IN STUDIES OF SUBSTRATE SPECIFICITY OF PROTEASES

2020 ◽  
pp. 151-152
Author(s):  
N. Kaz’mina ◽  
R. Vakhrenеv ◽  
M. Melnikova ◽  
E. Kolesanova
Keyword(s):  
Substrate Specificity ◽  
Structure And Properties ◽  
Peptide Arrays ◽  
Protease Substrate ◽  
Polymerization Conditions ◽  
Potential Use

Method for peptidyl-polyaniline (peptidyl-PANI) preparation was developed, and obtained substances were characterized. Influence of polymerization conditions on the peptidyl-PANI structure and properties was studied. A potential use of peptidyl-PANI peptide arrays in protease substrate specificity investigations was demonstrated.

Retroviral Protease: Substrate Specificity and Inhibitors

1990 ◽  
pp. 31-39
Author(s):  
Yoshiyuki Yoshinaka ◽  
Iyoko Katoh ◽  
Kohei Oda
Keyword(s):  
Substrate Specificity ◽  
Protease Substrate ◽  
Retroviral Protease

scholarly journals Characterization of Hybrid Toluate and Benzoate Dioxygenases

2003 ◽  
Vol 185 (18) ◽  
pp. 5333-5341 ◽  
Author(s):  
Yong Ge ◽  
Lindsay D. Eltis
Keyword(s):  
Substrate Specificity ◽  
Pseudomonas Putida ◽  
Acinetobacter Calcoaceticus ◽  
The Other ◽  
Β Subunit ◽  
Structural Determinants ◽  
Α Subunit ◽  
Benzoate Dioxygenase

ABSTRACT Toluate dioxygenase of Pseudomonas putida mt-2 (TADOmt2) and benzoate dioxygenase of Acinetobacter calcoaceticus ADP1 (BADOADP1) catalyze the 1,2-dihydroxylation of different ranges of benzoates. The catalytic component of these enzymes is an oxygenase consisting of two subunits. To investigate the structural determinants of substrate specificity in these ring-hydroxylating dioxygenases, hybrid oxygenases consisting of the α subunit of one enzyme and the β subunit of the other were prepared, and their respective specificities were compared to those of the parent enzymes. Reconstituted BADOADP1 utilized four of the seven tested benzoates in the following order of apparent specificity: benzoate > 3-methylbenzoate > 3-chlorobenzoate > 2-methylbenzoate. This is a significantly narrower apparent specificity than for TADOmt2 (3-methylbenzoate > benzoate ∼ 3-chlorobenzoate > 4-methylbenzoate ∼ 4-chlorobenzoate ≫ 2-methylbenzoate ∼ 2-chlorobenzoate [Y. Ge, F. H. Vaillancourt, N. Y. Agar, and L. D. Eltis, J. Bacteriol. 184:4096-4103, 2002]). The apparent substrate specificity of the αBβT hybrid oxygenase for these benzoates corresponded to that of BADOADP1, the parent from which the α subunit originated. In contrast, the apparent substrate specificity of the αTβB hybrid oxygenase differed slightly from that of TADOmt2 (3-chlorobenzoate > 3-methylbenzoate > benzoate ∼ 4-methylbenzoate > 4-chlorobenzoate > 2-methylbenzoate > 2-chlorobenzoate). Moreover, the αTβB hybrid catalyzed the 1,6-dihydroxylation of 2-methylbenzoate, not the 1,2-dihydroxylation catalyzed by the TADOmt2 parent. Finally, the turnover of this ortho-substituted benzoate was much better coupled to O2 utilization in the hybrid than in the parent. Overall, these results support the notion that the α subunit harbors the principal determinants of specificity in ring-hydroxylating dioxygenases. However, they also demonstrate that the β subunit contributes significantly to the enzyme's function.

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