Substrate specificity screening of oat (Avena sativa) seeds aminopeptidase demonstrate unusually broad tolerance in S1 pocket

Gajda, Anna; Pawełczak, Małgorzata; Drąg, Marcin

doi:10.1016/j.plaphy.2012.02.006

Cited by 6 publications

(3 citation statements)

References 19 publications

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“…This approach has been applied to substrate specifi city profi ling of other human (ERAP1, ERAP2, IRAP, MetAP-1, MetAP-2), bacterial ( Escherichia coli MetAP), malaria (PfM1AAP and PfM17LAP), and plant (oat seeds) aminopeptidases, and even in the detection of total aminopeptidase activity in malaria cell lysates (3D7 strain of Plasmodium falciparum ) (Figure 3 ) (Gajda et al , 2012 ;Poreba et al , 2012a,b ). In the case of ERAP1, ERAP2, and IRAP, fl uorogenic substrate libraries were additionally extended by d -enantiomer derivatives of almost all proteinogenic amino acids (Zervoudi et al , 2011 ).…”

Section: Non-proteinogenic Amino Acids In Protease Substrate Specifi mentioning

confidence: 99%

Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity

Kasperkiewicz¹,

Gajda²,

Drąg

2012

Biological Chemistry

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Proteases recognize their endogenous substrates based largely on a sequence of proteinogenic amino acids that surrounds the cleavage site. Currently, several methods are available to determine protease substrate specifi city based on approaches employing proteinogenic amino acids. The knowledge about the specifi city of proteases can be signifi cantly extended by application of structurally diverse families of non-proteinogenic amino acids. From a chemical point of view, this information may be used to design specifi c substrates, inhibitors, or activity-based probes, while biological functions of proteases, such as posttranslational modifi cations can also be investigated. In this review, we discuss current and prospective technologies for application of non-proteinogenic amino acids in protease substrate specifi city profi ling.

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Section: Non-proteinogenic Amino Acids In Protease Substrate Specifi mentioning

confidence: 99%

Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity

Kasperkiewicz¹,

Gajda²,

Drąg

2012

Biological Chemistry

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“…The best P1 residue was hArg, and the phosphinate inhibitor hPhe-P-(CH 2 )Tyr exhibited a K i of 54 nM. Similarly, oat ( Avena sativa ) aminopeptidase accepted basic and aromatic residues in P1-ACC substrates, whereby hCha, hTyr, hPhe and hArg were preferred over the best cAA Arg [ 326 ]. Bestatin is a natural metalloproteinase inhibitor consisting of an α-hydroxy-β-amino acid with a phenyl ring in P1 and Leu as a P1′ residue, whose potency was increased five-fold by a Tyr(OMe) in P1 with a K i of 43 nM for the PfA-M1 protease (M01.029) of Plasmodium falciparum ( Figure 9 A–C) [ 327 ].…”

Section: Protease Substrates Inhibitors and Activity-based Probes Wit...mentioning

confidence: 99%

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

Goettig,

Koch,

Budisa

2023

IJMS

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All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.

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“…This approach was previously used successfully to probe substrate specificity of several human, animal, plant and bacterial aminopeptidases (Poreba et al 2012a, b; Gajda et al 2012; Veillard et al 2012; Zervoudi et al 2011; Drag et al 2010; Weglarz-Tomczak et al 2013). In this approach, in addition to natural amino acids (proteinogenic amino acids), we also employed more than one hundred unnatural amino acids ( d -amino acids, l -amino acids with different unnatural side chains).…”

Section: Introductionmentioning

confidence: 99%

A remarkable activity of human leukotriene A4 hydrolase (LTA4H) toward unnatural amino acids

et al. 2014

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Leukotriene A4 hydrolase (LTA4H––EC 3.3.2.6) is a bifunctional zinc metalloenzyme, which processes LTA4 through an epoxide hydrolase activity and is also able to trim one amino acid at a time from N-terminal peptidic substrates via its aminopeptidase activity. In this report, we have utilized a library of 130 individual proteinogenic and unnatural amino acid fluorogenic substrates to determine the aminopeptidase specificity of this enzyme. We have found that the best proteinogenic amino acid recognized by LTA4H is arginine. However, we have also observed several unnatural amino acids, which were significantly better in terms of cleavage rate (kcat/Km values). Among them, the benzyl ester of aspartic acid exhibited a kcat/Km value that was more than two orders of magnitude higher (1.75 × 105 M−1 s−1) as compared to l-Arg (1.5 × 103 M−1 s−1). This information can be used for design of potent inhibitors of this enzyme, but may also suggest yet undiscovered functions or specificities of LTA4H.Electronic supplementary materialThe online version of this article (doi:10.1007/s00726-014-1694-2) contains supplementary material, which is available to authorized users.

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Substrate specificity screening of oat (Avena sativa) seeds aminopeptidase demonstrate unusually broad tolerance in S1 pocket

Cited by 6 publications

References 19 publications

Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity

Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

A remarkable activity of human leukotriene A4 hydrolase (LTA4H) toward unnatural amino acids

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