Proteases Universally Recognize β Strands in Their Active Sites

Tyndall, Joel D. A.; Nall, Tessa; Fairlie, David P.

doi:10.1002/chin.200521283

Cited by 20 publications

(33 citation statements)

References 1 publication

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“…A review of a large number of proteases in the PDB database has revealed that proteases generally bind their substrates in an extended binding conformation, which is to a large degree defined by β-strand-type backbone interactions [32,33]. The PS-SCLs profile the primary selectivity in the S1-S4-binding pockets of a protease independently, without accounting for cross-talk between subsites and without the requirements for optimal alignment of the peptide backbone.…”

Section: Discussionmentioning

confidence: 99%

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Larsen

Østergaard

Bjelke

et al. 2007

Biochemical Journal

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The remarkably high specificity of the coagulation proteases towards macromolecular substrates is provided by numerous interactions involving the catalytic groove and remote exosites. For FVIIa [activated FVII (Factor VII)], the principal initiator of coagulation via the extrinsic pathway, several exosites have been identified, whereas only little is known about the specificity dictated by the active-site architecture. In the present study, we have profiled the primary P4-P1 substrate specificity of FVIIa using positional scanning substrate combinatorial libraries and evaluated the role of the selective active site in defining specificity. Being a trypsin-like serine protease, FVIIa had P1 specificity exclusively towards arginine and lysine residues. In the S2 pocket, threonine, leucine, phenylalanine and valine residues were the most preferred amino acids. Both S3 and S4 appeared to be rather promiscuous, however, with some preference for aromatic amino acids at both positions. Interestingly, a significant degree of interdependence between the S3 and S4 was observed and, as a consequence, the optimal substrate for FVIIa could not be derived directly from a subsite-directed specificity screen. To evaluate the role of the active-site residues in defining specificity, a series of mutants of FVIIa were prepared at position 239 (position 99 in chymotrypsin), which is considered to be one of the most important residues for determining P2 specificity of the trypsin family members. This was confirmed for FVIIa by marked changes in primary substrate specificity and decreased rates of antithrombin III inhibition. Interestingly, these changes do not necessarily coincide with an altered ability to activate Factor X, demonstrating that inhibitor and macromolecular substrate selectivity may be engineered separately.

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Section: Discussionmentioning

confidence: 99%

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Larsen

Østergaard

Bjelke

et al. 2007

Biochemical Journal

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“…It has been proposed that when released from the triple-helical conformation, the cleavage site sequence in type I collagen has the propensity to form ␤-bend and ␤-strand structures (61). Protease active sites appear to accommodate ␤-strand structures universally (62). Besides liberating the N-terminal region of chain 1T for hydrolysis, the destabilization of the THP also causes a partial detachment of chain 3T near the THP C terminus (Fig.…”

Section: Molecular Mechanisms Of Collagen Catabolismmentioning

confidence: 99%

Interstitial Collagen Catabolism

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2013

Journal of Biological Chemistry

174

135

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Interstitial collagen mechanical and biological properties are altered by proteases that catalyze the hydrolysis of the collagen triple-helical structure. Collagenolysis is critical in development and homeostasis but also contributes to numerous pathologies. Mammalian collagenolytic enzymes include matrix metalloproteinases, cathepsin K, and neutrophil elastase, and a variety of invertebrates and pathogens possess collagenolytic enzymes. Components of the mechanism of action for the collagenolytic enzyme MMP-1 have been defined experimentally, and insights into other collagenolytic mechanisms have been provided. Ancillary biomolecules may modulate the action of collagenolytic enzymes.

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“…Chemical specificity is crucial in biological studies: the function of many biomolecules involves significant processing [7] and many ailments, whether hereditary, environmental, or pathological, are associated with modifications [6,8]. The attraction of imaging mass spectrometry is the ability to map the concentration profiles of specific biomolecules, recording the distributions of multiple analytes in parallel, without using a label and from native samples (such as tissue sections).…”

mentioning

confidence: 99%

Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging

McDonnell

Heeren

Lange

et al. 2006

J. Am. Soc. Mass Spectrom.

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To expand the role of high spatial resolution secondary ion mass spectrometry (SIMS) in biological studies, numerous developments have been reported in recent years for enhancing the molecular ion yield of high mass molecules. These include both surface modification, including matrix-enhanced SIMS and metal-assisted SIMS, and polyatomic primary ions. Using rat brain tissue sections and a bismuth primary ion gun able to produce atomic and polyatomic primary ions, we report here how the sensitivity enhancements provided by these developments are additive. Combined surface modification and polyatomic primary ions provided Ϸ15.8 times more signal than using atomic primary ions on the raw sample, whereas surface modification and polyatomic primary ions yield Ϸ3.8 and Ϸ8.4 times more signal. This higher sensitivity is used to generate chemically specific images of higher mass biomolecules using a single molecular ion

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Proteases Universally Recognize β Strands in Their Active Sites

Abstract: For Abstract see ChemInform Abstract in Full Text.

Cited by 20 publications

References 1 publication

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Interstitial Collagen Catabolism

Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging

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