Effect Of Peptide Length Research Articles

Localization of 99mTc-GRP Analogs in GRPR-Expressing Tumors: Effects of Peptide Length and Neprilysin Inhibition on Biological Responses.

The overexpression of gastrin-releasing peptide receptors (GRPRs) in frequently occurring human tumors has provided the opportunity to use bombesin (BBN) analogs as radionuclide carriers to cancer sites for diagnostic and therapeutic purposes. We have been alternatively exploring human GRP motifs of higher GRPR selectivity compared to frog BBN sequences aiming to improve pharmacokinetic profiles. In the present study, we compared two differently truncated human endogenous GRP motifs: GRP(14–27) and GRP(18–27). An acyclic tetraamine was coupled at the N-terminus to allow for stable binding of the SPECT radionuclide 99mTc. Their biological profiles were compared in PC-3 cells and in mice without or with coinjection of phosphoramidon (PA) to induce transient neprilysin (NEP) inhibition in vivo. The two 99mTc-N4-GRP(14/18–27) radioligands displayed similar biological behavior in mice. Coinjection of PA exerted a profound effect on in vivo stability and translated into notably improved radiolabel localization in PC-3 experimental tumors. Hence, this study has shown that promising 99mTc-radiotracers for SPECT imaging may indeed derive from human GRP sequences. Radiotracer bioavailability was found to be of major significance. It could be improved during in situ NEP inhibition resulting in drastically enhanced uptake in GRPR-expressing lesions.

Sequence and length optimization of membrane active coiled coils for triggered liposome release

Defined and tunable peptide-lipid membrane interactions that trigger the release of liposome encapsulated drugs may offer a route to improving the efficiency and specificity of liposome-based drug delivery systems, but this require means to tailor the performance of the membrane active peptides. In this paper, the membrane activity of a de novo designed coiled coil peptide has been optimized with respect to sequence and size to improve release efficiency of liposome encapsulated cargo. The peptides were only membrane active when covalently conjugated to the liposomes. Two amino acid substitutions were made to enhance the amphipathic characteristics of the peptide, which increased the release by a factor of five at 1 μM. Moreover, the effect of peptide length was investigated by varying the number of heptad repeats from 2 to 5, yielding the peptides KVC2-KVC5. The shortest peptide (KVC2) showed the least interaction with the membrane and proved less efficient than the longer peptides in releasing the liposomal cargo. The peptide with three heptads (KVC3) caused liposome aggregation whereas KVC4 proved to effectively release the liposomal cargo without causing aggregation. The longest peptide (KVC5) demonstrated the most defined α-helical secondary structure and the highest liposome surface concentration but showed slower release kinetics than KVC4. The four heptad peptide KVC4 consequently displayed optimal properties for triggering the release and is an interesting candidate for further development of bioresponsive and tunable liposomal drug delivery systems.

Binding of anti-apoptotic Bcl-2 with different BH3 peptides: A molecular dynamics study

In this work, molecular dynamics simulation and free energy calculations are utilized to study how different BH3 peptides originating from Bax, Bim, Bik and Noxa interact with Bcl-2, one of the main members of anti-apoptotic proteins. The effects of peptide length, sequence and helical content on the binding affinity are discussed, on which a novel BH3-like peptide is designed in silico with an improved binding property.

Structure-function relationship of the influenza fusion peptide

Influenza is an enveloped virus which enters the host cell through en-docytosis-mediated mechanism. To enable the release genetic material, a process of fusion between viral and host cell membranes occurs, which is mediated by influenza hemagglutinin (HA) protein. The N-terminal fragment of hemagglutinin HA2 subunit, directly interacting with the membrane, is named a fusion peptide (HAfp), since it is able to promote fusion also as a synthetic fragment. Its C-terminal part contains three residues (W21-Y22-G23), which are highly conserved among various serotypes of Influenza A. It has been shown that the peptide length has an influence on its structure: HAfp1-20 forms a boomerangin contrast to a tight helical hairpin formed by HAfp1-23. To gain more insight into the role of the conserved residues, we studied the effect of peptide length on fusion properties, its structural dynamics, and par-titioning to the phospholipid bilayer. By means of molecular dynamics simulations and spectroscopic measurements, we showed that the presence of three C-terminal residues in HAfp1-23 promotes the for-mation of hairpin structure. In contrast to less structured HAfp1-20,it orients perpendicularly to the membrane plane and induces more disorder in the surrounding lipids. Using a novel fusion visualization assay based on FLIM microscopy on giant unilamellar vesicles (GUV), we observed that HAfp1-23 promotes fusion to a higher extent than HAfp1-20. Moreover, we report cholesterolenriched domain formation exclusively by the longer fusion peptide. This redistribution of membrane components in fluid phases is likely to play a role during membrane fusion.

Hydrocarbon‐stapled lipopeptides exhibit selective antimicrobial activity

Antimicrobial peptides (AMPs) occur widely in nature and have been studied for their therapeutic potential. AMPs are of interest due to the large number of possible chemical structural combinations using natural and unnatural amino acids, with varying effects on their biological activities. Using physicochemical properties from known naturally occurring amphipathic cationic AMPs, several hydrocarbon-stapled lipopeptides (HSLPs) were designed, synthesized, and tested for antimicrobial properties. Peptides were chemically modified by N-terminal acylation, C-terminal amidation, and some were hydrocarbon stapled by intramolecular olefin metathesis. The effects of peptide length, amphipathic character, and stapling on antimicrobial activity were tested against Escherichia coli, three species of Gram-positive bacteria (Staphylococcus aureus, Bacillus megaterium, and Enterococcus faecalis), and two strains of Candida albicans. Peptides were shown to disrupt liposomes of different phospholipid composition, as measured by leakage of a fluorescent compound from vesicles. Peptides with (S)-2-(4'-pentenyl)-alanine substituted for l-alanine in a reference peptide showed a marked increase in antimicrobial activity, hemolysis, and membrane disruption. Stapled peptides exhibited slightly higher antimicrobial potency; those with greatest hydrophobic character showed the greatest hemolysis and liposome leakage, but lower antimicrobial activity. The results support a model of HSLPs as membrane-disruptive AMPs with potent antimicrobial activity and relatively low hemolytic potential at biologically active peptide concentrations.

The Role of Lipid Environment on Peptide Structure and Folding

Membrane proteins are an important class of proteins that are difficult to characterize structurally and functionally. In order to gain a better understanding of the forces that govern membrane protein folding and structure, a series of simple leucine-alanine peptides ranging from 12 to 18 residues were designed. The peptides were anchored by two lysine residues at each end and spontaneously inserted into negatively charged lipid bilayers. The effects of peptide length, lipid length, bilayer/micelle composition and the presence of structure breaking residues glycine and proline on the uniformity of helical structure were evaluated. An increase in the intensities of the amide III and S bands in deep-UV resonance Raman spectra indicated loss of helical structure. Differences in peptide hydration were monitored using tryptophan fluorescence. Loss of helical structure was observed in cases of negative hydrophobic mismatch, increased peptide hydration and upon introduction helix breaking residues. No loss of helical structure was observed in cases of positive hydrophobic mismatch while the shortest peptide adopted beta-sheet structure in instances of negative hydrophobic mismatch. Greater hydration of the peptide, which occurred in surfactant/lipid micelles, magnified the helix breaking- effects of glycine and proline. These studies highlight the potential importance of the lipid environment itself on membrane protein structure.

Antimicrobial and cell-penetrating properties of penetratin analogs: Effect of sequence and secondary structure

Cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs) show great potential as drug delivery vectors and new antibiotic drug entities, respectively. The current study deals with the properties of a variety of peptide analogs derived from the well-known CPP penetratin as well as octaarginine and different Tat sequences. The effects of peptide length, guanidinium content, and sequence of non-cationic residues were assessed in mammalian and bacterial cells. The arginine (Arg) content in the penetratin analogs was found to influence eukaryotic cell uptake efficiency, antimicrobial activity towards both Gram-positive and Gram-negative bacteria as well as eukaryotic cell viability. All examined analogs retained the ability to cross eukaryotic membranes giving rise to a distribution within the vacuolar apparatus. Interestingly, a series of shuffled analogs of penetratin with the cationic residues in conserved positions, attain the same α-helical conformation as native penetratin in the presence of cholesterol-containing liposomes, while conformational differences were observed in the presence of highly anionic liposomes. While the antibacterial effect of the two groups of peptides was similar, the eukaryotic cellular uptake of the shuffled analogs was noticeably lower than for native penetratin. Moreover, a point substitution of Met to Leu in native penetratin had no influence on eukaryotic cellular uptake and antimicrobial effect, and only a minor effect on cytotoxicity, in contrast to the fact that the same substitution in the shuffled analog gave rise to reduced eukaryotic cellular uptake while increasing the antibacterial effect and cytotoxicity.

Peptide–Microgel Interactions in the Strong Coupling Regime

The interaction between lightly cross-linked poly(acrylic acid) microgels and oppositely charged peptides was investigated as a function of peptide length, charge density, pH, and salt concentration, with emphasis on the strong coupling regime at high charge contrast. By micromanipulator-assisted light microscopy, the equilibrium volume response of single microgel particles upon oligolysine and oligo(lysine/alanine) absorption could be monitored in a controlled fashion. Results show that microgel deswelling, caused by peptide binding and network neutralization, increases with peptide length (3 < 5 < 10) and charge density (30% < 50% < 100%). Furthermore, oligomer-induced microgel deswelling was more pronounced at pH 5 than at pH 8, reflecting the lower network charge density in the former case (pK(a) for the isolated acrylic acid ≈4.7). In order to describe these highly coupled systems, a model was developed, in which counterion/peptide-mediated electrostatic attraction between the network chains is described using an exponential force law, and the network elasticity by the inverse Langevin theory. The model was used to calculate the composition of microgels in contact with reservoir solutions of peptides and simple electrolytes. At high electrostatic coupling, the calculated swelling curves were found to display first-order phase transition behavior. The model was demonstrated to capture pH- and electrolyte-dependent microgel swelling, as well as effects of peptide length and charge density on microgel deswelling. The analysis demonstrated that the peptide charge (length), rather than the peptide charge density, determines microgel deswelling. Furthermore, a transition between continuous and discrete network collapse was identified, consistent with experimental results in the present investigations, as well as with results from the literature on microgel deswelling caused by multivalent cations.

Investigation of Novel Peptide Chiral Selectors Prepared by Solid-Phase Synthesis with a tert-Butoxycarbonyl Amino Acid

A new class of chiral stationary phases (CSP) with peptide chiral selectors was prepared by solid-phase synthesis with a tert-butoxycarbonyl-L-amino acid on silica. The type of amino acid that is favorable for this class of CSP is discussed. Using the CSP with the phenylalanine peptide selector, the effect of peptide length on the enantioselectivity was investigated in normal-phase mode. The applicability of the CSP with a phenylalanine peptide to chiral ligand-exchange chromatography was also examined.

Effect of Peptide Length on the Interaction between Consensus Peptides and DOPC/DOPA Bilayers

The effect of peptide length and electrostatics on the interaction between Cardin motif peptides and lipid membranes was investigated for (AKKARA)(n) (n = 1-4) and (ARKAAKKA)(n) (n = 1-3) peptides (A, K, and R refer to alanine, lysine, and arginine, respectively) by fluorescence spectroscopy, circular dichroism, ellipsometry, z potential, and photon correlation spectroscopy measurements. The effect of the peptides regarding leakage induction of both zwitterionic and anionic liposomes increased with increasing peptide length, as did the peptide-induced killing of Enterococcus faecalis and Bacillus subtilis bacteria. The peptides, characterized by a random coil conformation both in buffer and when attached to the liposomes (helix content less than 20%), displayed an increased adsorption with increasing peptide length, and plateau adsorption for the longest peptides corresponded to 1 peptide per 65 and 17 lipid molecules for zwitterionic and anionic membranes, respectively. Control experiments with uncharged peptide analogues as well as experiments at high excess electrolyte concentration showed that peptide charges are important both for peptide adsorption and leakage induction. These observations, together with observations of the liposome z potential at different peptide additions as well as a comparison between the results for zwitterionic and anionic liposomes, suggest that electrostatically affected local packing effects are crucial for the action of these peptides, although pore formation such as that observed for many AMPs cannot be excluded at present.

The effect of peptide length on the cleavage kinetics of 2‐chlorotrityl resin‐bound ethers

Different characteristics of cleavage kinetics of resin-bound amino alcohols and their peptide derivatives were observed in acid containing protic and aprotic solvent mixtures. The hydrolysis reactions are hindered by steric crowding around the cleaving C--O bond and accelerated by the special solvation effect of CF(3)CH(2)OH on the peptide chain as well as the increase of the strength and concentration of the acid. In trifluoroacetic acid containing mixtures, trifluoroacetylation of the peptide alcohols was detected. The appearance of O-trifluoroacetyl serine and threonine derivatives is detected in cleavage mixtures containing trifluoroacetic acid in anhydrous solvent.

Structural Characterization of α-Helices of Implicitly Solvated Poly-Alanine

The structural characteristics of alpha-helices in poly-alanine-based peptides have been investigated via molecular dynamics simulation with the goal of understanding the basic features of peptide simulations within the context of a model system, classical molecular dynamics with generalized Born (GB) solvation, and to shed insight into the formation and stabilization of alpha-helices in short peptides. The effects of peptide length, terminal charges, proline substitution, and temperature on the alpha-helical secondary structure have been studied. The simulations have shown that distinct secondary structure begins to develop in peptides with lengths approaching 10 residues while ambiguous structures occur in shorter peptides. The helical content of peptides with lengths > or =10 amino acids is observed to be nearly constant up to (Ala)(40). Interestingly, terminal charges and proline in the second position from the N-terminus alter the secondary structure locally with little effect on the overall alpha-helical content of the peptide. The free energy profile of helix formation was also investigated. A large increase in free energy accompanying the formation of helices with more than two consecutive hydrogen bonds in the (i, i + 4) pattern was observed while the free energy increases linearly with additional hydrogen bonds. Values for the change in enthalpy and entropy of helix nucleation and propagation are reported. Additionally the results obtained from the GB model are compared to explicit solvent simulations of two synthetic alanine-based peptides.

A synthetic peptide fragment derived from RANTES is a potent inhibitor of HIV-1 infectivity despite a surprising lack of CCR5 receptor affinity

CCR5 (CC-chemokine receptor 5) is a key co-receptor, in concert with CD4, for infectivity of HIV-1 (human immunodeficiency virus type-1) into healthy human cells, and RANTES, an endogenous ligand for CCR5, is a potent inhibitor of HIV-1 infectivity. In this structure-activity relationship (SAR) study, peptide fragments derived from RANTES were designed, synthesized and evaluated for their ability to inhibit HIV-1 infectivity. The goal was to determine the effect of peptide length on anti-HIV activity and to obtain an optimally sized RANTES peptide probe for further SAR studies. The analogue Ac[Ala10,11]RANTES-(1–14)NH2, AA14, was identified as an effective inhibitor of HIV-1 infectivity at 10 nM but despite the functional activity, surprisingly it did not exhibit any notable affinity for the CCR5 chemokine receptor. Further, increasing peptide size enhanced neither the inhibition of HIV-1 infectivity nor CCR5 receptor affinity. As a potent inhibitor of HIV-1 infectivity, the lead analogue most likely utilizes a different (and currently unknown) mechanism than interaction with CCR5 for anti-HIV activity.

A hydrophobicity scale for the lipid bilayer barrier domain from peptide permeabilities: nonadditivities in residue contributions.

Passive peptide transport across lipid membranes is governed by the energetics of partitioning into the ordered chain interior coupled with the rate of diffusion across this region. A hydrophobicity scale for peptide transfer into the barrier region of membranes derived from permeability coefficients would be useful to predict passive permeation of peptides across biomembranes and for determining the thermodynamics of peptide/protein insertion into the membrane interior. This study reports transport rates across large unilamellar vesicles (LUVs) composed of egg lecithin at 25 degrees C for a series of peptides having the general structure N-p-toluyl-(X)(n) (n =1-3), where X is glycine, alanine, or sarcosine. Apparent residue group contributions were calculated from permeability coefficients, P(RX), using the equation Delta(Delta G degrees )(X) = -RT ln(P(RX)/P(RH)). Multiple linear least-squares regression analysis performed for the set of 14 permeants yielded the best correlation (r(2) = 0.9993) when the following permeant descriptors were utilized: side-chain nonpolar surface area, number of -CONH- residues, number of toluyl-CON(Me)- residues, and number of other -CON(Me)- residues. The backbone -CONH- residue contribution in peptides, 4.6 kcal/mol, is significantly lower than that obtained for a single isolated -CONH- (>6 kcal/mol), suggesting a possible influence of intramolecular hydrogen bonding. Under closer scrutiny, Delta(Delta G degrees )(X) for the Ala and Gly residues decrease with increasing peptide length. The effect of N-methylation is also highly dependent on position and number of N-methyl groups on the molecule (Delta(Delta G degrees )(X) = -0.5 to -2.2 kcal/mol). These nonadditivities may be rationalized by considering the effects of peptide length and N-methylation on membrane-induced intramolecular hydrogen bonding leading to various folded conformations.

Binding affinity independent contribution of peptide length to the stability of peptide-HLA-DR complexes in live antigen presenting cells

The effect of peptide length on the stability of peptide-HLR-DR1 (DR1) complexes was analyzed using two peptide series of increasing length, each containing a 7mer core with five DR1-binding anchors, extended stepwise with A1a residues at the N- and C-terminus, respectively. The A1a extensions, although did not affect binding affinity, significantly increased the half lives of peptide-DR1 complexes (from 1.5 h up to 10 h) in live antigen presenting cells (APC). Flanking residues from position −2 to 0 and 8 to 11 were involved in the affinity-independent increase of complex stability. The shortest (8mer and 9mer) peptides, with in vivo half lives of <2.5 h, were unable to form stable complexes with DR1 in presence of HLA-DM (DM) molecules, and were poor competitors of antigen presentation. Longer peptides were resistant to DM-mediated unloading, and were efficient competitors of antigen presentation. Thus, DM appears to limit short peptides in establishing biologically relevant DR occupancy, despite their high binding affinity. In APC, stable complexes can form only with high affinity peptides of >9 residues, and the longevity of complexes seems to depend on full of occupation of the binding site.

Determination of Affinities for lck SH2 Binding Peptides Using a Sensitive Fluorescence Assay: Comparison between the pYEEIP and pYQPQP Consensus Sequences Reveals Context-Dependent Binding Specificity

The development of a sensitive fluorescence binding assay for evaluating the binding of phosphotyrosyl (pY) peptides to the recombinant SH2 domain of lck in solution is described. Several fluorescent peptides containing the consensus sequence of the viral hamster polyoma middle T antigen (pYEEI) were characterized. The peptides contained either the acetamido-anilino-naphthyl sulfonic acid (AANS), acrylodan, or dansyl groups as fluorophores. The spectral features of these probes were characterized in the presence and absence of the lck SH2 domain. The binding affinities (Kd) for the fluorescent peptides studied ranged from 40 to 500 nM. The fluorescent peptide containing the sequence FTATEC(AANS)QpYEEIP exhibited the highest binding affinity (Kd = 3.98 x 10(-8) M) and largest change in emission intensity (approximately 8.7-fold) upon binding the SH2 domain. This probe was subsequently used in competitive binding assays to study the interaction of the lck SH2 domain with a series of phosphopeptides related to the pYEEIP and pYQPQP (the pY505 C-terminal) consensus sequences. The effects of peptide length and substitutions of residues within the pYEEIP sequence are discussed in terms of binding affinities. Comparison between the two peptide series revealed that the contributions of individual substitutions to binding affinity are context-dependent. The data also led to the conclusion that the presence of P at +2 results in a functional "truncation" of the binding sequence; i.e., residues at positions higher than +2 do not participate significantly in binding. This implicit truncation may actually be a desired property for the autoregulatory nature of the pYQPQP sequence, since it retains specificity for the SH2 domain while adjusting the Kd to a value appropriate for maintaining the delicate balance of receptor-ligand interactions that are involved in signal transduction events.

High-performance liquid chromatography of amino acids, peptides and proteins: CXXII. Application of experimentally derived retention coefficients to the prediction of peptide retention times: studies with myohemerythrin

Amino acid retention coefficients were derived from the experimental retention data of 118 overlapping peptide heptamers related to the primary amino acid sequence of myohemerythrin. Individual retention coefficient values for each amino acid were derived by a multiple linear regression matrix approach. Retention data were derived for five different experimental conditions including different organic modifiers (acetonitrile, methanol or 2-propanol), different mobile phase additives (trifluoroacetic acid or potassium phosphate) and different silica-based stationary phase ligands (octadecyl or phenyl groups). A high degree of correlation was observed between these experimentally derived amino acid coefficients (EXP) and the coefficients (LIT) which we recently reported derived from the retention data of over 2000 peptides [M. C. J. Wilce et al., J. Chromatogr., 536 (1991) 165 and 548 (1991) 105]. These results demonstrated that the LIT and EXP coefficients can be used for the prediction of the retention of any peptide set. The effect of peptide length was also further investigated and the correlation results demonstrated the importance of peptide flexibility on the final value of the amino acid coefficient.

Parathyroid hormone-related protein stimulates prostaglandin E2 release from human osteoblast-like cells: modulating effect of peptide length.

Parathyroid hormone-related protein (PTHrP) is a potent bone-resorbing protein that frequently mediates the humoral hypercalcemia of malignancy syndrome. Since prostaglandins may mediate the bone-resorptive action of certain hormones, we examined the effect of PTHrP on prostaglandin E2 (PGE2) secretion by human osteoblast-like cells. There was low-level basal secretion of PGE2 by Saos-2 cells (8.1 +/- 0.6 pg/ml). Using four different preparations of PTHrP, it was observed that with increasing peptide length, from 36 to 141 amino acids, a significant increase in efficacy for PGE2 release was seen in these cells. All forms of PTHrP were agonists for PGE2 release, with effects seen at concentrations as low as 10(-12) M in 48 h conditioned media. The amino terminus of the molecule appeared critical for this effect since the truncated derivative PTHrP-(7-34) did not induce significant PGE2 secretion. However, the influence of peptide length could not be explained by differential activation of adenylate cyclase since [Tyr36]PTHrP-(1-36)amide was equipotent to the longest peptide preparation, PTHrP-(1-141), in stimulating cyclic AMP accumulation in the Saos-2 cells. In contrast, PTHrP-(1-141) was significantly more effective than [Tyr35]PTHrP-(1-36)-amide in inducing a rise in cytosolic calcium. Further, this effect was noted at concentrations lower than those that caused significant cyclic AMP accumulation in the Saos-2 cells. PTHrP-(1-141) induced the release of PGE2 from primary human bone cell cultures to levels entirely comparable to those seen in the Saos-2 cells. PTHrP-(1-141) also induced PGE2 release by cultured fetal rat long bones at 72 h. We conclude that the carboxy-terminal region of PTHrP has important effects on cellular signal transduction pathways and on the release of a potent bone-active cytokine, PGE2.

Peptide binding to HLA-A2 and HLA-B27 isolated from Escherichia coli. Reconstitution of HLA-A2 and HLA-B27 heavy chain/beta 2-microglobulin complexes requires specific peptides.

The specificity of peptide binding by human leukocyte antigen (HLA) class I molecules was investigated in a cell-free direct-binding assay. Peptides were assessed for binding to HLA-A2 and HLA-B27 by measuring the formation of heterotrimeric HLA complexes that consisted of iodinated beta 2-microglobulin, HLA heavy chain fragments isolated from the Escherichia coli cytoplasm, and peptide. In this system, no detectable HLA heavy chain-beta 2-microglobulin complexes were formed unless appropriate peptides were intentionally added to the reconstitution solution. Analysis with monoclonal antibodies demonstrated that these heterotrimeric complexes were correctly folded. Five nonhomologous peptides, known to form complexes with HLA-A2 or HLA-B27 from T-cell functional studies, were tested for their capacity to bind to HLA-A2 and HLA-B27 using the reconstitution assay. Four of the peptides bound to the appropriate class I molecule only. One peptide and some (but not all) substitution analogs of it bound to both HLA-A2 and HLA-B27. The effect of peptide length on binding to HLA-B27 was studied, and it was found that the optimal length was 9 or 10 amino acid residues; however, one peptide that bound to HLA-B27 was 15 amino acids long. All peptides that bound to HLA-B27 in the direct-binding assay also competed with antigenic peptides for binding to HLA-B27 on the surface of intact cells, as determined by a standard cytotoxic T-lymphocyte functional assay. Thus, we conclude that HLA-A2 and HLA-B27 bind distinct but partially overlapping sets of peptides and that, at least in vitro, the assembly of HLA heavy chain-beta 2-microglobulin complexes requires specific peptides.

Specific activation of open complex formation at an Escherichia coli promoter by oligo(N-methylpyrrolecarboxamide)s: effects of peptide length and identification of DNA target sites.

It has previously been shown that open complex formation at a promoter containing a block substitution of nonalternating A-T sequences in the spacer DNA separating the contacted -10 and -35 regions could be accelerated by distamycin. No stimulation was observed at a promoter with a substitution of alternating A-T base pairs in the same region or at the promoter with wild-type spacer. Here we compare the effect of distamycin [tris(N-methylpyrrolecarboxamide), formally a P3] with that of its extended homologues P4, P5, and P6. It is found that the stimulatory potential of these synthetic oligopeptides which bind in the minor groove of DNA ranks in the order P4 greater than (distamycin, P5) greater than P6. The interaction of these peptides with the three promoters was studied by monitoring the positions of the promoter DNA protected from MPE-Fe(II) cleavage in the presence of different concentrations of ligand. The results suggest that a higher affinity of oligopeptide for the spacer DNA than for the -10 and/or -35 region is a necessary, but not sufficient condition for stimulation. Different patterns of protected DNA regions are seen with each of the three promoters; with distamycin, P4, and P5, a unique arrangement of protected regions is observed for the variant containing nonalternating A-T base pairs in its spacer DNA. These data support the hypothesis that differences in the ways the minor-groove binders interact with each of the promoter variants account for the observed differential stimulation. We further postulate that it is a ligand-induced structural change in the nonalternating A-T DNA which is responsible for the activation of open complex formation at the promoter containing this substitution.