Combinatorial approaches: A new tool to search for highly structured β-hairpin peptides

Pastor, María Teresa; Paz, Manuela López de la; Lacroix, Emmanuel; Serrano, Luís; Pérez‐Payá, Enrique

doi:10.1073/pnas.012583999

Cited by 71 publications

(67 citation statements)

References 35 publications

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“…Then we decided to generate more soluble analogues of peptoid 1. Previous experience in the design of bioactive peptides 24,25 suggested that the presence of positively charged side chains at both N-and C-terminus ends of peptides increased the overall peptide solubility without modifying their conformational or biological properties. Furthermore, in our laboratory, we have used an N-substituted alkylglycine hexamer composed by residues containing a simple benzene ring or a tertiary amino moiety attached to a bioactive hexapeptide sequence to increase both aqueous solubility and cellmembrane permeability (unpublished results).…”

Section: Resultsmentioning

confidence: 99%

Small molecule inhibitors of Apaf-1-related caspase- 3/-9 activation that control mitochondrial-dependent apoptosis

et al. 2005

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Apoptosis is a biological process relevant to human disease states that is strongly regulated through protein-protein complex formation. These complexes represent interesting points of chemical intervention for the development of molecules that could modulate cellular apoptosis. The apoptosome is a holoenzyme multiprotein complex formed by cytochrome c-activated Apaf-1 (apoptotic proteaseactivating factor), dATP and procaspase-9 that link mitochondria disfunction with activation of the effector caspases and in turn is of interest for the development of apoptotic modulators. In the present study we describe the identification of compounds that inhibit the apoptosome-mediated activation of procaspase-9 from the screening of a diversityoriented chemical library. The active compounds rescued from the library were chemically optimised to obtain molecules that bind to both recombinant and human endogenous Apaf-1 in a cytochrome c-noncompetitive mechanism that inhibits the recruitment of procaspase-9 by the apoptosome. These newly identified Apaf-1 ligands decrease the apoptotic phenotype in mitochondrial-mediated models of cellular apoptosis. Keywords: apoptosis; apoptosome; Apaf-1; caspasa-3; caspasa-9; combinatorial libraries; inhibitor; molecular recognition; peptoid; protein-protein interactions; small molecule Abbreviations: Apaf-1, apoptotic protease-activating factor; DEVDase, hydrolysis of Ac-DEVD-afc; DTT, dithiothreitol; FCS, fetal-calf serum; MEFs, mouse embryo fibroblasts; MMP, mitochondrial membrane potential; MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; Ni-NTA, (Ni 2 þ -nitrilotriacetate)-agarose; peptoid f1a, 5 0 -6 0 carboxyfluorescein-labelled peptoid 1a; PBS, phosphate-buffered saline; PGA, poly-(L-glutamic acid); rApaf-1, recombinant Apaf-1

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Section: Resultsmentioning

confidence: 99%

Small molecule inhibitors of Apaf-1-related caspase- 3/-9 activation that control mitochondrial-dependent apoptosis

et al. 2005

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“…These five hairpins (2:2 type I, 2:2 type IЈ, 2:2 type IIЈ, 3:5 F, and 4:4 F) are highly populated in the Protein Data Bank (19) and in NMR structures of well ordered ␤-hairpin peptides (20)(21)(22)(23)(24)(25)(26). For each turn, a polyQ model was built from multiple peptide backbones and the lowest-energy structure after 1,000 steps of minimization was used for MD simulation.…”

Section: Methodsmentioning

confidence: 99%

Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases

Armen

Bernard

Day

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Several neurodegenerative diseases are linked to expanded repeats of glutamine residues, which lead to the formation of amyloid fibrils and neuronal death. The length of the repeats correlates with the onset of Huntington's disease, such that healthy individuals have <38 residues and individuals with >38 repeats exhibit symptoms. Because it is difficult to obtain atomicresolution structural information for poly(L-glutamine) (polyQ) in aqueous solution experimentally, we performed molecular dynamics simulations to investigate the conformational behavior of this homopolymer. In simulations of 20-, 40-, and 80-mer polyQ, we observed the formation of the ''␣-extended chain'' conformation, which is characterized by alternating residues in the ␣L and ␣R conformations to yield a sheet. The structural transition from disordered random-coil conformations to the ␣-extended chain conformation exhibits modest length and temperature dependence, in agreement with the experimental observation that aggregation depends on length and temperature. We propose that fibril formation in polyQ may occur through an ␣-sheet structure ␣-sheet ͉ amyloidosis ͉ misfolding disease ͉ molecular dynamics ͉ poly(L-glutamine)

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“…The key discoveries that improved β-hairpin stabilities outside of protein contexts have been sequences with good turn propensities, for example D-Pro-Gly (pG) (6), heterochiral pP (7), and Aib-Gly (8) [or less favorably, Asn-Gly (NG) (5,9)] and the incorporation of optimized cross-strand pairings [most notably Trp/Trp pairs flanking the turn (10)(11)(12)(13)(14)]. However, longer hairpin models are typically still frayed at the termini; to date, fully folded spectroscopic reference values have only been attained via cyclization (15)(16)(17).…”

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confidence: 99%

Stabilizing capping motif for β-hairpins and sheets

Kier

Shu²,

Eidenschink³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

158

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Although much has been learned about the design of models of β-sheets during the last decade, modest fold stabilities in water and terminal fraying remain a feature of most β-hairpin peptides. In the case of hairpin capping, nature did not provide guidance for solving the problem. Some observations from prior turn capping designs, with further optimization, have provided a generally applicable, "unnatural" beta cap motif (alkanoyl-Trp at the N terminus and Trp-Thr-Gly at the C terminus) that provides a net contribution of 6 þ kJ∕mol to β-hairpin stability, surpassing all other interactions that stabilize β-hairpins including the covalent disulfide bond. The motif, made up entirely of natural residues, is specific to the termini of antiparallel β-strands and reduces fraying at the ends of hairpins and other β-sheet models. Utilizing this motif, 10-to 22-residue peptide scaffolds of defined stereochemistry that are greater than 98% folded in water have been prepared. The β-cap can also be used to staple together short antiparallel β-strands connected by a long flexible loop.beta sheets | capping stabilization | peptide hairpins | Trp/Trp interactions C apping motifs are well-known features of protein and peptide secondary structure; specifically, terminal alpha helix caps (especially N caps) are common both in proteins and designed peptides (1-4). The basis for helix capping is straightforward: countering the helix macrodipole and providing additional H-bonding interactions (1). Caps increase the fold population of isolated α-helical peptides and have been a boon to the design of α-helix models. β-Structures have capping requirements wholly different from those of helices; the ends of canonical β-sheets and hairpins do not have dipole moments or unsatisfied H bonds.The a priori design of model β-sheet systems (5), focused on hairpins, has lagged behind that of α-helix counterparts. The key discoveries that improved β-hairpin stabilities outside of protein contexts have been sequences with good turn propensities, for example D-Pro-Gly (pG) (6), heterochiral pP (7), and Aib-Gly (8) [or less favorably, Asn-Gly (NG) (5, 9)] and the incorporation of optimized cross-strand pairings [most notably Trp/Trp pairs flanking the turn (10-14)]. However, longer hairpin models are typically still frayed at the termini; to date, fully folded spectroscopic reference values have only been attained via cyclization (15-17). With the exception of cyclization, mutations at terminal sites have yielded only modest changes in hairpin stability; terminal coulombic effects (ΔΔG U ¼ 1.5-2.5 kJ∕mol) standing as the only generally observed capping effect (11,18,19). Pi-cation interactions have also been shown to provide significant hairpin stabilization (20), but instances in which the interaction appears near the ends of hairpins have provided only marginal stability increases (18,(21)(22)(23)). An unnatural π-cation interaction has also been shown to stabilize the turn in a tripeptide (24). There has been limited evidence for hairpin fold sta...

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Combinatorial approaches: A new tool to search for highly structured β-hairpin peptides

Cited by 71 publications

References 35 publications

Small molecule inhibitors of Apaf-1-related caspase- 3/-9 activation that control mitochondrial-dependent apoptosis

Small molecule inhibitors of Apaf-1-related caspase- 3/-9 activation that control mitochondrial-dependent apoptosis

Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases

Stabilizing capping motif for β-hairpins and sheets

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