Inactivation of Apaf1 reduces the formation of mutant huntingtin-dependent aggregates and cell death

Polyglutamine expansions in some proteins associated with neurodegenerative diseases, such as Huntington's disease or several ataxias, lead to insoluble aggregates in the cell. These aggregates accumulate through a mechanism that is not yet fully understood, but it activates cell death pathways and contributes to kill the cell. Here, we show that apoptotic protease activating factor 1 (Apaf1) down-regulation, or treatment with pharmacological Apaf1 inhibitor SVT016426, decreases both polyglutamine-induced aggregation and polyglutamine-induced apoptotic cell death in different cellular models. We demonstrate that Apaf1 binds to both Htt and to heat shock protein chaperone Hsp70, and that this interaction is altered in the presence of the pharmacological inhibitor of Apaf1. Based on our findings, we hypothesize that Apaf1 enhances polyglutamine aggregation by reducing the cellular protein levels of available functional Hsp70.

Intrinsic caspase-8 activation mediates sensitization of erlotinib-resistant tumor cells to erlotinib/cell-cycle inhibitors combination treatment

Inhibitors of the tyrosine kinase activity of epidermal growth factor receptor, as erlotinib, have an established role in treating several cancer types. However, resistance to erlotinib, particularly in breast cancer cell lines, and erlotinib treatment-associated disorders have also been described. Also, methods and combination therapies that could reverse resistance and ameliorate non-desirable effects represent a clinical challenge. Here, we show that the ATP non-competitive CDK2/cyclin A inhibitor NBI1 sensitizes erlotinib-resistant tumor cells to the combination treatment (co-treatment) for apoptosis-mediated cell death. Furthermore, in erlotinib-sensitive cells, the effective dose of erlotinib was lower in the presence of NBI1. The analysis in the breast cancer MDA-MB-468 erlotinib-resistant and in lung cancer A549 cell lines of the molecular mechanism underlying the apoptosis induced by co-treatment highlighted that the accumulation of DNA defects and depletion of cIAP and XIAP activates the ripoptosome that ultimately activates caspases-8 and -10 and apoptosis. This finding could have significant implications for future treatment strategies in clinical settings.

Modulation of cellular apoptosis with apoptotic protease-activating factor 1 (Apaf-1) inhibitors

The programmed cell death or apoptosis plays both physiological and pathological roles in biology. Anomalous activation of apoptosis has been associated with malignancies. The intrinsic mitochondrial pathway of apoptosis activation occurs through a multiprotein complex named the apoptosome. We have discovered molecules that bind to a central protein component of the apoptosome, Apaf-1, and inhibits its activity. These new first-in-class apoptosome inhibitors have been further improved by modifications directed to enhance their cellular penetration to yield compounds that decrease cell death, both in cellular models of apoptosis and in neonatal rat cardiomyocytes under hypoxic conditions.

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

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 protease-activating 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 diversity-oriented 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.

Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides

In a previous study we designed a 20-residue peptide able to adopt a significant population of a three-stranded antiparallel beta-sheet in aqueous solution (de Alba et al. [1999]Protein Sci.8, 854-865). In order to better understand the factors contributing to beta-sheet folding and stability we designed and prepared nine variants of the parent peptide by substituting residues at selected positions in its strands. The ability of these peptides to form the target motif was assessed on the basis of NMR parameters, in particular NOE data and 13Calpha conformational shifts. The populations of the target beta-sheet motif were lower in the variants than in the parent peptide. Comparative analysis of the conformational behavior of the peptides showed that, as expected, strand residues with low intrinsic beta-sheet propensities greatly disfavor beta-sheet folding and that, as already found in other beta-sheet models, specific cross-strand side chain-side chain interactions contribute to beta-sheet stability. More interestingly, the performed analysis indicated that the destabilization effect of the unfavorable strand residues depends on their location at inner or edge strands, being larger at the latter. Moreover, in all the cases examined, favorable cross-strand side chain-side chain interactions were not strong enough to counterbalance the disfavoring effect of a poor beta-sheet-forming residue, such as Gly.

Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones

The potentiation of central cholinergic activity has been proposed as a therapeutic approach for improving cognitive function in patients with Alzheimer's disease. Increasing the acetylcholine concentration in brain by modulating acetylcholinesterase (AChE) activity is among the most promising strategies. We have used a combinatorial approach to identify different 2,5-piperazinediones (DKP) with AChE inhibitory activity. Our goal was to find inhibitors exhibiting high AChE/BuChE (butyrylcholinesterase) selectivity, in order to reduce the undesirable side effects elicited by most of the inhibitors that have been developed to date. Screening of a DKP library constructed on solid-phase using the multiple parallel synthesis format, resulted in the identification of several compounds with moderate efficacy on AChE. In particular, DKP-80 had an IC50 = 2.2 microM with no significant inhibitory activity on BuChE. Moreover, estimated values of Clog P and log BB for the most active compounds fulfilled the bioavailability requirements for enzyme inhibitors acting on the central nervous system. In order to understand the inhibitory properties of the ligand at the molecular level, molecular dynamics simulations were computed on DKP-80 complexed to AChE, and the most relevant binding interactions of this inhibitor to the active center of the enzyme were characterized. Overall the present results indicate that the DKP-based compounds identified are novel AChE inhibitors which may be considered likely lead compounds for further development of drug candidates against Alzheimer's disease.

Identification of peptides that neutralize bacterial endotoxins using beta-hairpin conformationally restricted libraries

Bacterial endotoxins are the major mediator of septic shock; therefore, endotoxin-neutralizing molecules could have biomedical applications. The septic shock cascade relies in a series of molecular recognition processes. The large contact-surface described for the interacting macromolecules, in most cases, prevents the identification of small molecules that could modulate such recognition events. Here we report on a beta-hairpin conformationally restricted combinatorial library that has been generated and screened towards the identification of new peptides that neutralize bacterial endotoxins. Starting with a de novo designed linear peptide that shows a beta-hairpin structure population of around 30%, (Ramirez-Alvarado, M., Blanco, F. J. and Serrano, L. Nat. Struc. Biol., 7, 604-612 (1996)), we selected four positions to build up a combinatorial library of 20(4) sequences. Deconvolution of the library reduced such a sequence complexity to 8 defined sequences. The newly identified peptides have a biological activity equivalent to that reported for peptides derived from natural endotoxin-binding proteins.

Stabilization of an alpha-helical conformation in an isolated hexapeptide inhibitor of calmodulin

The conformational properties of two hexapeptides, Ac-LWRILW-NH(2) and its D-amino acid counterpart Ac-lwrilw-NH(2), identified as calmodulin inhibitors using mixture-based synthetic combinatorial library approaches, have been characterised by NMR and CD spectroscopy. The peptides fold into an alpha-helical conformation in aqueous solution. The observed short- and medium-range nuclear Overhauser effects were consistent with the formation of an alpha-helical structure and a reasonably well-defined set of structures was obtained by using restraints from the NMR data in simulated annealing calculations. Analysis of glycine-substitution analogues demonstrated that all the amino acids that make up the peptide sequence are important for the stabilization of the alpha-helical conformation. The results suggest that a well-defined set of interactions is indispensable to allow alpha-helix formation in this short hexapeptide.

Functional and conformational properties of the exclusive C-domain from the Arabidopsis copper chaperone (CCH)

The Arabidopsis thaliana copper chaperone (CCH) is a small copper binding protein involved in copper trafficking. When compared to homologues from other eukaryotes, CCH has two different domains; the conserved N-domain and the plant-exclusive C-domain, a C-terminal extension with an unusual amino-acid composition. In order to characterize this extra C-domain, the CCH protein, the N-domain and the C-domain were all expressed separately in heterologous systems. While the N-domain retained the copper chaperone and antioxidant properties described for the yeast Atx1 and human HAH1 counterparts, the C-domain displayed particular structural properties that would be necessary to optimize copper homoeostasis in plant cells where it could be responsible for the metallochaperone plant-exclusive intercellular transport. The whole CCH protein and the C-domain, but not the N-domain, displayed altered SDS/PAGE mobilities. CD spectroscopy showed that the N-domain fold is representative of an alpha/beta protein, while the C-domain adopts an extended conformation.

Thermal stabilization of the catalytic domain of botulinum neurotoxin E by phosphorylation of a single tyrosine residue

The catalytic domain of clostridial neurotoxins is a substrate of tyrosine-specific protein kinases. The functional role of tyrosine phosphorylation and also the number and location of its (their) phosphorylation site(s) are yet elusive. We have used the recombinant catalytic domain of botulinum neurotoxin E (BoNT E) to examine these issues. Bacterially expressed and purified BoNT E catalytic domain was fully active, and was phosphorylated in vitro by the tyrosine-specific kinase Src. Tyrosine phosphorylation of the catalytic domain increased the protein thermal stability without affecting its proteolytic activity. Covalent modification of the endopeptidase promoted a disorder-to-order transition, as evidenced by the 35% increment of the alpha-helical content, which resulted in a 4 degrees C increase of its denaturation temperature. Site-directed replacement of tyrosine at position 67 completely abolished phosphate incorporation by Src. Constitutively unphosphorylated endopeptidase mutants exhibited functional properties virtually identical to those displayed by the nonphosphorylated wild-type catalytic domain. These findings indicate the presence of a single phosphorylation site in the catalytic domain of clostridial neurotoxins, and that its covalent modification primarily modulates the protein thermostability.

Arginine-rich peptides are blockers of VR-1 channels with analgesic activity

Vanilloid receptors (VRs) play a fundamental role in the transduction of peripheral tissue injury and/or inflammation responses. Molecules that antagonize VR channel activity may act as selective and potent analgesics. We report that synthetic arginine-rich hexapeptides block heterologously expressed VR-1 channels with submicromolar efficacy in a weak voltage-dependent manner, consistent with a binding site located near/at the entryway of the aqueous pore. Dynorphins, natural arginine-rich peptides, also blocked VR-1 activity with micromolar affinity. Notably, synthetic and natural arginine-rich peptides attenuated the ocular irritation produced by topical capsaicin application onto the eyes of experimental animals. Taken together, our results imply that arginine-rich peptides are VR-1 channel blockers with analgesic activity. These findings may expand the development of novel analgesics by targeting receptor sites distinct from the capsaicin binding site.

Influence of the hydrophilic face on the folding ability and stability of alpha-helix bundles: relevance to the peptide catalytic activity

Although not the sole feature responsible, the packing of amino acid side chains in the interior of proteins is known to contribute to protein conformational specificity. While a number of amphipathic peptide sequences with optimized hydrophobic domains has been designed to fold into a desired aggregation state, the contribution of the amino acids located on the hydrophilic side of such peptides to the final packing has not been investigated thoroughly. A set of self-aggregating 18-mer peptides designed previously to adopt a high level of alpha-helical conformation in benign buffer is used here to evaluate the effect of the nature of the amino acids located on the hydrophilic face on the packing of a four alpha-helical bundle. These peptides differ from one another by only one to four amino acid mutations on the hydrophilic face of the helix and share the same hydrophobic core. The secondary and tertiary structures in the presence or absence of denaturants were determined by circular dichroism in the far- and near-UV regions, fluorescence and nuclear magnetic resonance spectroscopy. Significant differences in folding ability, as well as chemical and thermal stabilities, were found between the peptides studied. In particular, surface salt bridges may form which would increase both the stability and extent of the tertiary structure of the peptides. The structural behavior of the peptides may be related to their ability to catalyze the decarboxylation of oxaloacetate, with peptides that have a well-defined tertiary structure acting as true catalysts.

Identification and characterization of a hexapeptide with activity against phytopathogenic fungi that cause postharvest decay in fruits

A hexapeptide of amino acid sequence Ac-Arg-Lys-Thr-Trp-Phe-Trp-NH2 was demonstrated to have antimicrobial activity against selected phytopathogenic fungi that cause postharvest decay in fruits. The peptide synthesized with either all D- or all L-amino acids inhibited the in vitro growth of strains of Penicilium italicum, P. digitatum, and Botrytis cinerea, with MICs of 60 to 80 microM and 50% inhibitory concentration (IC50) of 30 to 40 microM. The inhibitory activity of the peptide was both sequence- and fungus-specific since (i) sequence-related peptides lacked activity (including one with five residues identical to the active sequence), (ii) other filamentous fungi (including some that belong to the genus Penicllium) were insensitive to the peptide's antifungal action, and (iii) the peptide did not inhibit the growth of several yeast and bacterial strains assayed. Experiments on P. digitatum identified conidial germination as particularly sensitive to inhibition although mycelial growth was also affected. Our findings suggest that the inhibitory effect is initially driven by the electrostatic interaction of the peptide with fungal components. The antifungal peptide retarded the blue and green mold diseases of citrus fruits and the gray mold of tomato fruits under controlled inoculation conditions, thus providing evidence for the feasibility of using very short peptides in plant protection. This and previous studies with related peptides indicate some degree of peptide amino acid sequence and structure conservation associated with the antimicrobial activity, and suggest a general sequence layout for short antifungal peptides, consisting of one or two positively charged residues combined with aromatic amino acid residues.

Influence of the C-terminus of the glycophorin A transmembrane fragment on the dimerization process

The monomer-dimer equilibrium of the glycophorin A (GpA) transmembrane (TM) fragment has been used as a model system to investigate the amino acid sequence requirements that permit an appropriate helix-helix packing in a membrane-mimetic environment. In particular, we have focused on a region of the helix where no crucial residues for packing have been yet reported. Various deletion and replacement mutants in the C-terminal region of the TM fragment showed that the distance between the dimerization motif and the flanking charged residues from the cytoplasmic side of the protein is important for helix packing. Furthermore, selected GpA mutants have been used to illustrate the rearrangement of TM fragments that takes place when leucine repeats are introduced in such protein segments. We also show that secondary structure of GpA derivatives was independent from dimerization, in agreement with the two-stage model for membrane protein folding and oligomerization.

Novel, potent calmodulin antagonists derived from an all-D hexapeptide combinatorial library that inhibit in vivo cell proliferation: activity and structural characterization

Calmodulin is known to bind to various amphipathic helical peptide sequences, and the calmodulin-peptide binding surface has been shown to be remarkably tolerant sterically. D-Amino acid peptides, therefore, represent potential nonhydrolysable intracellular antagonists of calmodulin. In the present study, synthetic combinatorial libraries have been used to develop novel D-amino acid hexapeptide antagonists to calmodulin-regulated phosphodiesterase activity. Five hexapeptides were identified from a library containing over 52 million sequences. These peptides inhibited cell proliferation both in cell culture using normal rat kidney cells and by injection via the femoral vein following partial hepatectomy of rat liver cells. These hexapeptides showed no toxic effect on the cells. Despite their short length, the identified hexapeptides appear to adopt a partial helical conformation similar to other known calmodulin-binding peptides, as shown by CD spectroscopy in the presence of calmodulin and NMR spectroscopy in DMSO. The present peptides are the shortest peptide calmodulin antagonists reported to date showing potential in vivo activity.

Calmodulin binds to p21(Cip1) and is involved in the regulation of its nuclear localization

p21(Cip1), first described as an inhibitor of cyclin-dependent kinases, has recently been shown to have a function in the formation of cyclin D-Cdk4 complexes and in their nuclear translocation. The dual behavior of p21(Cip1) may be due to its association with other proteins. Different evidence presented here indicate an in vitro and in vivo interaction of p21(Cip1) with calmodulin: 1) purified p21(Cip1) is able to bind to calmodulin-Sepharose in a Ca(2+)-dependent manner, and this binding is inhibited by the calmodulin-binding domain of calmodulin-dependent kinase II; 2) both molecules coimmunoprecipitate when extracted from cellular lysates; and 3) colocalization of calmodulin and p21(Cip1) can be detected in vivo by electron microscopy immunogold analysis. The carboxyl-terminal domain of p21(Cip1) is responsible for the calmodulin interaction, since p21(145-164) peptide is also able to bind calmodulin and to compete with full-length p21(Cip1) for the calmodulin binding. Because treatment of cells with anti-calmodulin drugs decreases the nuclear accumulation of p21(Cip1), we hypothesize that calmodulin interaction with p21(Cip1) is important for p21(Cip1), and in consequence for cyclin D-Cdk4, translocation into the cell nucleus.

Addressing substrate glutamine requirements for tissue transglutaminase using substance P analogues

We have investigated the effect on the substrate requirements for guinea pig liver (tissue) transglutaminase of a set of 11 synthetic glutamine substitution analogues making up the full sequence of the naturally occurring tissue transglutaminase substrate substance P. While a number of peptide sequences derived from proteins that are well-recognized as tissue transglutaminase substrates have been studied, the enzyme activity using substitution analogues of full-length natural substrates has not been investigated as thoroughly. Thus, our set of substance P analogues only differs from one to other by one amino acid mutation while the length (of the peptide) is maintained as in the natural parent peptide. Our results indicate that a glutamine residue is not recognized as substrate by the enzyme whether it is placed at the N- or C-terminal or between two positively charged residues or between two proline residues. To further address the effect on enzyme activity of charged amino acids in the vicinity of the reactive glutamine residue, a new set of synthetic charge replacement analogues of substance P has been also studied. Together, the results have identified new minimal requirements for modification of a particular glutamine residue in a polypeptide chain. It would be of interest to set up a full set of such requirements in order to highlight potential glutamine residues as enzyme targets in the growing list of proteins that are being described as transglutaminase substrates.

In vivo detection, RNA-binding properties and characterization of the RNA-binding domain of the p7 putative movement protein from carnation mottle carmovirus (CarMV)

Biochemical and structural characterization studies on the p7 putative movement protein from a Spanish isolate of carnation mottle carmovirus (CarMV) have been conducted. The CarMV p7 gene was fused to a sequence coding for a six-histidine tag and expressed in bacteria, allowing the purification of CarMV p7 and the production of a specific antiserum. This antiserum led to the immunological identification of CarMV p7 in infected leaf tissue from the experimental host Chenopodium quinoa. Putative nucleic acid-binding properties of the CarMV p7 have been explored and demonstrated with both electrophoretic mobility shift and RNA-protein blot in vitro assays using digoxigenin-labeled riboprobes. CarMV p7 did not show preferential binding to any of the different regions of the CarMV genomic RNA tested, suggesting that RNA binding was sequence nonspecific. Quantitative analyses of the data allowed calculation of the apparent dissociation constant of the p7-RNA complex (Kd approximately 0.7 microM) and supported a cooperative type of binding. A small 19-amino-acid synthetic peptide whose sequence corresponds to the putative RNA-binding domain of CarMV p7, at the basic central part of the protein, was synthesized, and it was demonstrated that it binds viral RNA probes. Peptide RNA binding was as stable as p7 binding, although data indicated it was not cooperative, thus suggesting that this cooperative binding requires another motif or motifs within the p7 amino acid sequence. The peptide could be induced to fold into an alpha-helix structure in which amino acids that are conserved among carmovirus p7-like proteins are distributed on one side. This alpha-helix motif could define a new and previously uncharacterized RNA-binding domain for plant virus movement proteins.

Environment- and sequence-dependent modulation of the double-stranded to single-stranded conformational transition of gramicidin A in membranes

The role of the membrane lipid composition and the individual Trp residues in the conformational rearrangement of gramicidin A along the folding pathway to its channel conformation has been examined in phospholipid bilayers by means of previously described size-exclusion high-performance liquid chromatography HPLC-based strategy (Bañó et al. (1991) Biochemistry 30, 886). It has been demonstrated that the chemical composition of the membrane influences the transition rate of the peptide rearrangement from double-stranded dimers to beta-helical monomers. The chemical modification of Trp residues, or its substitution by the more hydrophobic residues phenylalanine or naphthylalanine, stabilized the double-stranded dimer conformation in model membranes. This effect was more notable as the number of Trp-substituted residues increased (tetra > tri > di > mono), and it was also influenced by the specific position of the substituted amino acid residue in the sequence, in the order Trp-9 approximately Trp-13 > Trp-11 > Trp-15. Moreover, it was verified that nearly a full contingent of indoles (Trp-13, -11, and -9) is necessary to induce a quantitative conversion from double-stranded dimers to single-stranded monomers, although Trp-9 and Trp-13 seemed to be key residues for the stabilization of the beta-helical monomeric conformation of gramicidin A. The conformation adopted for monomeric Trp --> Phe substitution analogues in lipid vesicles resulted in CD spectra similar to the typical single-stranded beta6.3-helical conformation of gramicidin A. However, the Trp --> Phe substitution analogues showed decreased antibiotic activity as the number of Trp decreased.

Structural characterisation of the natural membrane-bound state of melittin: a fluorescence study of a dansylated analogue

The binding of a dansylated analogue of melittin (DNC-melittin) to natural membranes is described. The cytolytic peptide from honey bee venom melittin was enzymatically labelled in its glutamine-25 with the fluorescent probe monodansylcadaverine using guinea pig liver transglutaminase. The labelled peptide was characterised functionally in cytolytic assays, and spectroscopically by circular dichroism and fluorescence. The behaviour of DNC-melittin was, in all respects, indistinguishable from that of the naturally occurring peptide. We used resonance energy transfer to measure the state of aggregation of melittin on the membrane plane in synthetic and natural lipid bilayers. When bound to erythrocyte ghost membranes, the extent of energy transfer was found to be equivalent to when bound to small unilamellar vesicles of phosphatidylcholine. Our results correlate best with a proposed model in which the initial interaction between melittin and the red blood cells could be merely electrostatic and the peptide remains in a low alpha-helical conformation. The next step would be a peptide stabilisation in the membrane in a monomeric alpha-helical conformation that would imply the collapse of the membrane structure and liberation of the cell contents.

Secondary structure induction in aqueous vs membrane-like environments

The conformational propensity of the 20 naturally occurring amino acids was determined in aqueous 3-[N-morpholino]propane-sulfonic acid (MOPS) buffer, protein interior-like [nonmicellar sodium dodecylsulfate (SDS)] and membrane-like environments (micellar SDS and lysophosphatidylglycerol/lysophosphatidylcholine micelles) using a single "guest" position in a polyalanine-based model host peptide (Ac-KYA13K-NH2). This model system allows the intrinsic alpha-helical or beta-sheet propensity of the amino acids to be determined without intra- and interchain side chain interactions. The overall environment dependence observed for the conformational propensity for the amino acids studied confirms the importance of determining propensity in lipidic environments to better elucidate the biological functions of proteins. The hydrophobic interactions between peptide side chains and lipids appeared to be the primary forces driving the conformational induction in lipidic environments of the model peptides studied. Finally, when comparing the results of these studies with those reported in the literature, the local environment was found to highly influence 65% of the 20 naturally occurring amino acids.

Binding of basic amphipathic peptides to neutral phospholipid membranes: a thermodynamic study applied to dansyl-labeled melittin and substance P analogues

A thermodynamic approach is proposed to quantitatively analyze the binding isotherms of peptides to model membranes as a function of one adjustable parameter, the actual peptide charge in solution z(p)+. The main features of this approach are a theoretical expression for the partition coefficient calculated from the molar free energies of the peptide in the aqueous and lipid phases, an equation proposed by S. Stankowski [(1991) Biophysical Journal, Vol. 60, p. 341] to evaluate the activity coefficient of the peptide in the lipid phase, and the Debye-Hückel equation that quantifies the activity coefficient of the peptide in the aqueous phase. To assess the validity of this approach we have studied, by means of steady-state fluorescence spectroscopy, the interaction of basic amphipathic peptides such as melittin and its dansylcadaverine analogue (DNC-melittin), as well as a new fluorescent analogue of substance P, SP (DNC-SP) with neutral phospholipid membranes. A consistent quantitative analysis of each binding curve was achieved. The z(p)+ values obtained were always found to be lower than the physical charge of the peptide. These z(p)+ values can be rationalized by considering that the peptide charged groups are strongly associated with counterions in buffer solution at a given ionic strength. The partition coefficients theoretically derived using the z(p)+ values were in agreement with those deduced from the Gouy-Chapman formalism. Ultimately, from the z(p)+ values the molar free energies for the free and lipid-bound states of the peptides have been calculated.

Polyalanine-based peptides as models for self-associated beta-pleated-sheet complexes

The occurrence of beta-sheet motifs in a number of neurodegenerative disorders has brought about the need for the de novo design of soluble model beta-sheet complexes. Such model complexes are expected to further the understanding of the interconversion processes that occur from cellular allowed random coil or alpha-helical conformation into insoluble cell-deleterious beta-pleated-sheet motifs. In the present study, polyalanine-based peptides (i.e., derived from Ac-KA14K-NH2) were designed that underwent conformational changes from monomeric random coil conformations into soluble, macromolecular beta-pleated-sheet complexes without any covalent modification. The interconversion was found to be length-, environment-, and concentration-dependent and to be driven by hydrophobic interactions between the methyl groups of the alanine side chains. A series of substitution analogs of Ac-KA14K-NH2 was used to study the amino acid acceptability within the hydrophobic core of the complex, as well as at both termini. The formation of amyloid plaques in a number of amyloidogenic peptides could be related to the presence of amino acids within their sequences that were found to have a high propensity to occur in these model beta-sheet complexes.

Structural characterization and 5'-mononucleotide binding of polyalanine beta-sheet complexes

A study was initiated into the formation and stability of highly soluble beta-sheet macrostructures. Such beta-sheet macrostructures are useful model systems for the study of the biological function of the hydrophobic core of proteins and for the de novo design of novel catalytic mimics. In the current study, a 16-mer-alanine-based peptide (Ac-KA14K-NH2) that is highly water soluble and adopts an extremely stable macromolecular beta-sheet structure was synthesized. A tyrosine-containing analog (Ac-KYA13K-NH1) was used to study the tertiary structure of the complex by circular dichroism spectroscopy, while the influence of the charges on the complex formation and binding affinity was evaluated using a zwitterionic analog (Ac-KEA13KE-NH1). Both the secondary and tertiary structures of the beta-sheet complex were stable to denaturants, as demonstrated by far- and near-ultraviolet circular dichroism spectroscopy. Binding studies with mononucleotides have shown that the beta-sheet complex binds to molecules through both hydrophobic and electrostatic interactions. These intrinsic properties were found to be a prerequisite for the observed enhanced cleavage of phosphodiester bonds.

All D-amino acid hexapeptide inhibitors of melittin's cytolytic activity derived from synthetic combinatorial libraries

The identification of peptides that inhibit the biological functions of proteins was used as a means to explore protein/ligand interactions involved in molecular recognition processes. This approach is based on the use of synthetic combinatorial libraries (SCLs) for the rapid identification of individual peptides that block the interaction of proteins with their biological targets. Thus, each peptide mixture of an all-D-amino acid hexapeptide SCL in a positional scanning format was screened for its ability to inhibit the hemolytic activity of melittin, a model self-assembling protein. The potent inhibitory activity of the identified individual peptides suggests that protein-like complexes are able to specifically bind to peptides having an all-D configuration. These results also show that SCLs are useful for the identification of short, non-hydrolysable sequences having potential intracellular inhibitory activities.

Functionalized protein-like structures from conformationally defined synthetic combinatorial libraries

An approach is described for the de novo design of protein-like structures in which synthetic combinatorial libraries (SCLs) were incorporated into an amphipathic alpha-helical scaffold (an 18-mer sequence made up of leucine and lysine residues) to generate conformationally defined SCLs. In particular, the SCLs in which the "combinatorialized" positions were on the hydrophilic face showed an alpha-helical conformation in mild buffer. These SCLs were used to generate context-independent but position-dependent scales of alpha-helical propensity for the L-amino acids. These scales were then used to design highly alpha-helical peptides that self-associated in mild buffer. The same approach was also found to permit the identification of conformation-dependent decarboxylation catalysts.

Identification of inhibitors of melittin using nonsupport-bound combinatorial libraries

A strategy has been developed for the identification of inhibitors of toxins or regulatory proteins. This approach is based on blocking the access of such proteins to their biological targets during their solution transport. This approach uses the strength of nonsupport-bound synthetic combinatorial libraries (SCLs) for the study of acceptor-ligand interactions. A non-receptor assisted toxin, melittin, was selected for the present study to illustrate this application of the SCL approach. Hexapeptide SCLs were assayed for their ability to inhibit the cytolytic activity of melittin toward bacterial and erythrocyte cells. Over 20 inhibitory hexapeptides were identified following the screening and deconvolution processes from millions of sequences. The identified inhibitory peptides appeared to interact directly with melittin. These interactions appear to decrease melittin's ability to undergo lipid- and/or polysaccharide-induced conformational changes, and are demonstrated by fluorescence and circular dichroism spectroscopy.

Rapid identification of compounds with enhanced antimicrobial activity by using conformationally defined combinatorial libraries

We have combined the strength of our synthetic combinatorial library approach for the rapid identification of highly active compounds with prior knowledge of the relationship between the antimicrobial activities of individual peptides with specific induced conformations in order to identify new peptides with enhanced activity relative to a starting known antimicrobial sequence. In the current study, conformationally defined combinatorial libraries were generated based on an 18-mer antimicrobial peptide known to be induced into an alpha-helical conformation in a lipidic environment. Not only were novel sequences readily identified with 10-fold increases in activity, but detailed information about the structure-activity relationships of the peptides studied was also obtained during the deconvolution process. By using circular dichroism spectroscopy it was found that the individual 18-mer peptides could be induced into alpha-helical conformations on interaction with the cell lipid layer and/or sialic acids, which could result in bacterial cell lysis due to perturbation of the lipid packing of the cell wall.

Inhibition of a plant virus infection by analogs of melittin

An approach that enables identification of specific synthetic peptide inhibitors of plant viral infection is reported. Synthetic analogs of melittin that have sequence and structural similarities to an essential domain of tobacco mosaic virus coat protein were found to possess highly specific antiviral activity. This approach involves modification of residues located at positions analogous to those that are critical for virus assembly. The degree of inhibition found correlates well with sequence similarities between the viral capsid protein and the melittin analogs studied as well as with the induced conformational changes that result upon interaction of the peptides and ribonucleic acid.

Activation of bee venom phospholipase A2 through a peptide-enzyme complex

Phospholipase A2 activation by membrane-bound peptides was investigated in order to understand the role of the membrane-induced conformation on activation, and to examine the occurrence of a peptide-enzyme complex at the lipid/water interface. For the peptides studies, bee venom phospholipase A2 was stimulated regardless of the membrane-bound conformation (alpha-helix, beta-sheet or random coil). Using antisera raised against melittin, we were able to demonstrate the occurrence of a calcium-dependent complex involving the enzyme, phospholipid substrate, and peptide.

Peptide binding domains determined through chemical modification of the side-chain functional groups

A clear understanding of the specific secondary structure and binding domain resulting from the interactions of proteins and peptides with lipid surfaces will provide insight into the specific functions of biologically active molecules. We have shown in earlier studies that the stationary phases used in reverse-phase high-performance liquid chromatography represent a model artificial lipid surface for the study of induced conformational states of peptides on lipid interaction. We have now used reverse-phase high-performance liquid chromatography to determine the binding domains of peptides and, by extension, of proteins to a lipid surface. This approach consists of performing chemical modifications of specific amino acid side-chain functionalities after the interaction of the peptides with the reverse-phase high-performance liquid chromatography C18 groups. The susceptibility to oxidation was also studied after binding of the same peptides to liposomes. Oxidation of a single methionine residue "walked" through an amphipathic alpha-helical 18-mer peptide was selected to illustrate this approach. The extent of oxidation was found to be clearly dictated by the accessibility of the methionine residue to the aqueous mobile phase. The binding domain found for the peptide in its lipid-induced conformational state was unequivocally the entire hydrophobic face of the amphipathic alpha-helix.

Formation of an extremely stable polyalanine beta-sheet macromolecule

We have designed a 16-mer peptide composed of a stretch of alanine residues (Ac-KA14K-NH2) which is an effective, simple model for the study of beta-sheet formation in the hydrophobic cores of proteins. This peptide adopts an aqueous soluble "bundling" macromolecular beta-sheet structure, which is extremely stable to a wide range of pHs, temperatures and/or denaturants. Its unusual stability appears to be due to tight hydrophobic packing of the alanine residues in multilayer sheets or micellar forms with the multimeric lysine array being directed outward at the aqueous environment, allowing aqueous solubility.

The role of amphipathicity in the folding, self-association and biological activity of multiple subunit small proteins

The effect that altering amphipathicity has on the folding process and self association of melittin, a small model protein, has been investigated using single amino acid substitutions of lysine 7, a residue distant from the contact residues involved in the hydrophobic core of tetrameric melittin. While substitutions of such a residue were not expected to interfere with the packing process, the largest alterations in the potential overall amphipathicity of melittin were found to prevent the folding into an alpha-helical conformation to occur and, in turn, to prevent the self association. Amphipathic alpha-helices were found to be a key determining feature in the early folding process of the self association of peptides and protein segments. Those substitutions, which prevented the inducible amphipathic folding ability, were also found to result in a loss in hemolytic and antimicrobial activity. These results, combined with studies of the binding to artificial liposomes and to polysialic acids, indicate that the losses in activity were due to an initial inability to be induced into an amphipathic alpha-helix and to self associate. Ultimately, melittin's self association is proposed to be required to penetrate the carbohydrate barrier present in biological membranes.

Induced conformational states of amphipathic peptides in aqueous/lipid environments

Specific conformational effects have been reported for amphipathic model peptides upon binding of defined hydrophobic domains to nonpolar stationary phases during reversed-phase high performance liquid chromatography (RP-HPLC). Such induced conformations are found to be especially pronounced for peptides that are amphipathic in an alpha-helical conformation. Such induced amphipathic conformations resulted in substantially later elution than predicted using amino acid-based retention coefficients. In the present study, the induced conformational behavior of model peptides observed during RP-HPLC was correlated with their secondary structure as determined by circular dichroism (CD) spectroscopy in both aqueous solution and C18-mimetic environments. The experimental retention times of the peptides studied were found to correlate with their CD spectra in the presence of lipids, whereas a poor correlation was observed with their CD spectra in the presence of trifluoroethanol. A new approach was developed to evaluate the induction of secondary structure in peptides due to interactions at aqueous/lipid interfaces, which involves the measurement of the CD ellipticities of peptides bound to a set of C18-coated quartz plates. An excellent correlation was found in this environment between the RP-HPLC retention times and CD ellipticities of the bound peptides.

Synthetic peptides as binding-step based catalytic mimics

Peptides able to adopt an environment-dependent secondary structure represent attractive models for enzyme mimics. An approach to design new synthetic enzyme-like peptides involves the use of binding-step based mimics. The polypeptide melittin, based on its intrinsic ability to bind to phospholipids, was selected as a potential binding-step based catalytic mimic. Synthetic melittin was found to exhibit weak but reproducible phospholipase-like activity. The rate enhancement of the hydrolysis of phospholipids, although far from that of the natural enzyme, was encouraging as a first step in the development of new catalytic peptides.

Gln5 selectively monodansylated substance P as a sensitive tool for interaction studies with membranes

Substance P (SP) is a neuropeptide endowed with several important biological activities both in the central and peripheral nervous system. Taking advantage of the presence of glutamine residues in SP, the peptide was labelled with the fluorescent probe monodansylcadaverine using the transglutaminase (TGase)-reaction in order to study interactions between SP and model or natural membranes. Although it was verified that both adjacent glutamines of the peptide can act as substrate for TGase in a consecutive reaction, conditions were optimized to selectively label Gln5. This fluorescent SP analogue was found to adopt environment-dependent conformations similar to those of the natural peptide and proved to be functionally active on guinea pig trachea. Fluorescence spectroscopy was used to demonstrate the potential use of dansylated SP in studies involving interactions with membranes.

Determination of the secondary structure of selected melittin analogues with different haemolytic activities

In earlier studies, we have reported that minor modifications in the amino acid sequence of melittin result in dramatic changes in its biological activity. In the current study, we have investigated the secondary structure of melittin analogues with either increased or decreased haemolytic activity in order to further our understanding of the structural features involved in the binding and/or insertion of peptides into a phospholipid membrane from solution. This was accomplished by analysing the c.d. spectra of the analogues in solutions of various ionic strength and, separately, in the presence of micelles. These studies permit the assessment of the effect of small sequence modifications (i.e. single amino acid omission or substitution) on the self-association-induced secondary structure of melittin in aqueous solution, as well as its binding affinity to micelles. It was found that amphipathicity, as well as interchain distances and the orientation of hydrophobic residues, were involved in the induction of stabilized structures.

Influence of tryptophan residues on melittin's hemolytic activity

Earlier studies of melittin have shown that the Trp residue at position 19 is significantly involved in its hemolytic activity. Tryptophan residues have also been reported to play a specific and important role in a number of other biological interactions. In the present study, we investigated what effect the introduction of a second Trp residue would have on melittin's hemolytic activity. This was accomplished through the synthesis and analysis of a complete set of 25 single-position, synthetic Trp substitution analogs. Significant increases in activity were observed upon substituting Trp at a single residue at either extreme of melittin's two alpha-helices, or in its 'hinge' region. Decreases in activity were found upon replacing any of melittin's Leu residues with Trp. The changes in activity of all of the analogs relative to melittin were found to be correlated to their behavior during RP-HPLC, as was their variation in percent helicity in the presence of liposomes.

Selective labelling of melittin with a fluorescent dansylcadaverine probe using guinea-pig liver transglutaminase

Melittin, a C-terminal glutamine peptide, incorporated the fluorescent probe monodansylcadaverine (DNC) when catalysed by guinea-pig liver transglutaminase and Ca2+, as determined by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). A 1:1 adduct DNC-melittin was identified in which a single glutamine residue out of two, i.e. Gln25, acts as acyl donor. Incubation of melittin with transglutaminase in the absence of DNC originated high molecular mass complexes indicative that the peptide lysine residue can act as an acyl acceptor. The DNC-melittin was about 3 times more active in the lysis of red cell membranes than native melittin. Fluorescence study of the labelled melittin in the submicromolar range where it is active on cells showed that while totally exposed to solvent in methanol solution, both Trp and dansyl groups are buried in buffer solution. This strongly suggests that DNC-melittin is self-associated and indeed more active than the native melittin in the same conditions.