Limits...
Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.

Valdés JJ, Schwarz A, Cabeza de Vaca I, Calvo E, Pedra JH, Guallar V, Kotsyfakis M - PLoS ONE (2013)

Bottom Line: Using homology-based modeling (and other protein prediction programs) we were able to model and explain the multifaceted function of tryptogalinin.The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases).By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.

View Article: PubMed Central - PubMed

Affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic. valdjj@gmail.com

ABSTRACT

Background: A salivary proteome-transcriptome project on the hard tick Ixodes scapularis revealed that Kunitz peptides are the most abundant salivary proteins. Ticks use Kunitz peptides (among other salivary proteins) to combat host defense mechanisms and to obtain a blood meal. Most of these Kunitz peptides, however, remain functionally uncharacterized, thus limiting our knowledge about their biochemical interactions.

Results: We discovered an unusual cysteine motif in a Kunitz peptide. This peptide inhibits several serine proteases with high affinity and was named tryptogalinin due to its high affinity for β-tryptase. Compared with other functionally described peptides from the Acari subclass, we showed that tryptogalinin is phylogenetically related to a Kunitz peptide from Rhipicephalus appendiculatus, also reported to have a high affinity for β-tryptase. Using homology-based modeling (and other protein prediction programs) we were able to model and explain the multifaceted function of tryptogalinin. The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases).

Conclusions: By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.

Show MeSH
A–D. Tryptogalinin predicted tertiary structure.The modeled tryptogalinin (A), TdPI (PDB: 2UUX) (B) and BPTI (PDB: 5PTI) (C) depict the conserved disulfide bridges (indicated by roman numerals), loops (L1 and L2), the beta-sheets (β1–β2) that form the b-hairpin, the alpha-helixes (α0 and/or α1) and the Lys (K) that interacts with the active site of serine proteases. The Cα superimposition (D) of tryptogalinin (red), TdPI (green) and BPTI (blue) show the similarities/differences in their overall structures.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3643938&req=5

pone-0062562-g005: A–D. Tryptogalinin predicted tertiary structure.The modeled tryptogalinin (A), TdPI (PDB: 2UUX) (B) and BPTI (PDB: 5PTI) (C) depict the conserved disulfide bridges (indicated by roman numerals), loops (L1 and L2), the beta-sheets (β1–β2) that form the b-hairpin, the alpha-helixes (α0 and/or α1) and the Lys (K) that interacts with the active site of serine proteases. The Cα superimposition (D) of tryptogalinin (red), TdPI (green) and BPTI (blue) show the similarities/differences in their overall structures.

Mentions: The tertiary homology structure of tryptogalinin resembles that of TdPI since it contains a short α-helix (α1; seven residues) and lacks the N-terminus 310 α-helix, α0 (Figure 5A-B). The N-terminus α0 is usually a common motif found among Kunitz peptides (see BPTI in Figure 5C). Tryptogalinin also possess the archetypical anti-parallel β-sheets, but the β-hairpin is longer in tryptogalinin (twelve residues) compared to TdPI (two residues) and when compared with the archetypical Kunitz (four to six residues); however, this may be due to the shorter β-sheets of tryptogalinin. It is worth noting that secondary structures do not drastically change throughout evolution (e.g., insertions/deletions) and a common obstacle for 3D modeling programs is to accurately predict β-sheet conformations [76]. We attempted to perform evolutionary protein model building by using Phyre2 [27]. Although Phyre2 provided a 3D model accurately predicting tryptogalinin’s β-sheets (7 aa as opposed to the 4 aa predicted by Modeller), the models produced had low QMEAN score, a truncation at both termini, and the disulfide bridges were not well organized thereby reducing the number of bridges (2 instead of 3) – data not shown.


Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.

Valdés JJ, Schwarz A, Cabeza de Vaca I, Calvo E, Pedra JH, Guallar V, Kotsyfakis M - PLoS ONE (2013)

A–D. Tryptogalinin predicted tertiary structure.The modeled tryptogalinin (A), TdPI (PDB: 2UUX) (B) and BPTI (PDB: 5PTI) (C) depict the conserved disulfide bridges (indicated by roman numerals), loops (L1 and L2), the beta-sheets (β1–β2) that form the b-hairpin, the alpha-helixes (α0 and/or α1) and the Lys (K) that interacts with the active site of serine proteases. The Cα superimposition (D) of tryptogalinin (red), TdPI (green) and BPTI (blue) show the similarities/differences in their overall structures.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3643938&req=5

pone-0062562-g005: A–D. Tryptogalinin predicted tertiary structure.The modeled tryptogalinin (A), TdPI (PDB: 2UUX) (B) and BPTI (PDB: 5PTI) (C) depict the conserved disulfide bridges (indicated by roman numerals), loops (L1 and L2), the beta-sheets (β1–β2) that form the b-hairpin, the alpha-helixes (α0 and/or α1) and the Lys (K) that interacts with the active site of serine proteases. The Cα superimposition (D) of tryptogalinin (red), TdPI (green) and BPTI (blue) show the similarities/differences in their overall structures.
Mentions: The tertiary homology structure of tryptogalinin resembles that of TdPI since it contains a short α-helix (α1; seven residues) and lacks the N-terminus 310 α-helix, α0 (Figure 5A-B). The N-terminus α0 is usually a common motif found among Kunitz peptides (see BPTI in Figure 5C). Tryptogalinin also possess the archetypical anti-parallel β-sheets, but the β-hairpin is longer in tryptogalinin (twelve residues) compared to TdPI (two residues) and when compared with the archetypical Kunitz (four to six residues); however, this may be due to the shorter β-sheets of tryptogalinin. It is worth noting that secondary structures do not drastically change throughout evolution (e.g., insertions/deletions) and a common obstacle for 3D modeling programs is to accurately predict β-sheet conformations [76]. We attempted to perform evolutionary protein model building by using Phyre2 [27]. Although Phyre2 provided a 3D model accurately predicting tryptogalinin’s β-sheets (7 aa as opposed to the 4 aa predicted by Modeller), the models produced had low QMEAN score, a truncation at both termini, and the disulfide bridges were not well organized thereby reducing the number of bridges (2 instead of 3) – data not shown.

Bottom Line: Using homology-based modeling (and other protein prediction programs) we were able to model and explain the multifaceted function of tryptogalinin.The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases).By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.

View Article: PubMed Central - PubMed

Affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic. valdjj@gmail.com

ABSTRACT

Background: A salivary proteome-transcriptome project on the hard tick Ixodes scapularis revealed that Kunitz peptides are the most abundant salivary proteins. Ticks use Kunitz peptides (among other salivary proteins) to combat host defense mechanisms and to obtain a blood meal. Most of these Kunitz peptides, however, remain functionally uncharacterized, thus limiting our knowledge about their biochemical interactions.

Results: We discovered an unusual cysteine motif in a Kunitz peptide. This peptide inhibits several serine proteases with high affinity and was named tryptogalinin due to its high affinity for β-tryptase. Compared with other functionally described peptides from the Acari subclass, we showed that tryptogalinin is phylogenetically related to a Kunitz peptide from Rhipicephalus appendiculatus, also reported to have a high affinity for β-tryptase. Using homology-based modeling (and other protein prediction programs) we were able to model and explain the multifaceted function of tryptogalinin. The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases).

Conclusions: By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.

Show MeSH