The Three-Dimensional Structures of Tick Carboxypeptidase Inhibitor in Complex with A/B Carboxypeptidases Reveal a Novel Double-headed Binding Mode

Arolas, Joan L.; Popowicz, Grzegorz M.; Lorenzo, Júlia; Sommerhoff, Christian P.; Huber, Robert; Aviles, Francesc X.; Holak, Tad A.

doi:10.1016/j.jmb.2005.05.015

Cited by 58 publications

(92 citation statements)

References 47 publications

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“…PCR was conducted as 40 cycles each at 94°C for 1 min, annealing at 48°C for 1 min, and extension at 72°C for 2 min. PCR mixtures were 20-fold diluted and re-amplified using the S2 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22) and R 1 nested oligonucleotides. PCR products were separated by electrophoresis on 2% agarose gels.…”

Section: Methodsmentioning

confidence: 99%

“…their behavior resembles an ideal substrate (2,5,7,8,13). Thus, the trimmed residue, Gly 39 in PCI and Glu 66 in LCI (the inhibitors from potatoes and leech, respectively), remains bound to the S1Ј subsite of the enzyme.…”

Section: Inhibitorsmentioning

confidence: 99%

“…Thus, the trimmed residue, Gly 39 in PCI and Glu 66 in LCI (the inhibitors from potatoes and leech, respectively), remains bound to the S1Ј subsite of the enzyme. The carboxylate group of the penultimate residue (Val 38/65 in PCI/LCI) coordinates with the Zn 2ϩ of the active site, affecting S1Ј and S1 subsites, although the two previous residues of the inhibitor (Tyr 37/64 in PCI/LCI, respectively) interact with the S2 subsite (2,5,7,8,13). Thus, the inhibitor affects most CPs sites essential for substrate binding and catalysis.…”

Section: Inhibitorsmentioning

confidence: 99%

“…Additionally, TCI anchors to the surface of CPs of the A/B-type in a double-headed manner not observed for the other protein inhibitors (13). However, the C-tail of mammalian tissue protein inhibitors does not seem to be a suitable substrate for CPs; such proteins interact with the enzymes through one loop located at the interface of their two subdomains (14).…”

mentioning

confidence: 95%

“…The mechanisms of the inhibitory actions of PCI, LCI, and TCI on CPs rely upon interaction of their C-terminal tail with the active site cleft of the enzyme in a manner that mimics substrate binding (2,5,8,13). Additionally, TCI anchors to the surface of CPs of the A/B-type in a double-headed manner not observed for the other protein inhibitors (13).…”

mentioning

confidence: 99%

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Tri-domain Bifunctional Inhibitor of Metallocarboxypeptidases A and Serine Proteases Isolated from Marine Annelid Sabellastarte magnifica

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Section: Methodsmentioning

confidence: 99%

Section: Inhibitorsmentioning

confidence: 99%

Section: Inhibitorsmentioning

confidence: 99%

mentioning

confidence: 95%

mentioning

confidence: 99%

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Tri-domain Bifunctional Inhibitor of Metallocarboxypeptidases A and Serine Proteases Isolated from Marine Annelid Sabellastarte magnifica

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et al. 2012

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Protein‐protein docking by shape‐complementarity and property matching

2010

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We present a computational approach to protein-protein docking based on surface shape complementarity ("ProBinder"). Within this docking approach, we implemented a new surface decomposition method that considers local shape features on the protein surface. This new surface shape decomposition results in a deterministic representation of curvature features on the protein surface, such as "knobs," "holes," and "flats" together with their point normals. For the actual docking procedure, we used geometric hashing, which allows for the rapid, translation-, and rotation-free comparison of point coordinates. Candidate solutions were scored based on knowledge-based potentials and steric criteria. The potentials included electrostatic complementarity, desolvation energy, amino acid contact preferences, and a van-der-Waals potential. We applied ProBinder to a diverse test set of 68 bound and 30 unbound test cases compiled from the Dockground database. Sixty-four percent of the protein-protein test complexes were ranked with an root mean square deviation (RMSD) < 5 A to the target solution among the top 10 predictions for the bound data set. In 82% of the unbound samples, docking poses were ranked within the top ten solutions with an RMSD < 10 A to the target solution.

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Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes

et al. 2015

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Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

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The Three-Dimensional Structures of Tick Carboxypeptidase Inhibitor in Complex with A/B Carboxypeptidases Reveal a Novel Double-headed Binding Mode

Cited by 58 publications

References 47 publications

Tri-domain Bifunctional Inhibitor of Metallocarboxypeptidases A and Serine Proteases Isolated from Marine Annelid Sabellastarte magnifica

Tri-domain Bifunctional Inhibitor of Metallocarboxypeptidases A and Serine Proteases Isolated from Marine Annelid Sabellastarte magnifica

Protein‐protein docking by shape‐complementarity and property matching

Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes

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