Helix termination and chain reversal: crystal and molecular structure of the alpha, beta-dehydrooctapeptide Boc-Val-DeltaPhe-Phe-Ala-Leu-Ala-DeltaPhe-Leu-OH

The crystal structure of the dehydro octapeptide Boc-Val-DeltaPhe-Phe-Ala-Leu-Ala-DeltaPhe-Leu-OH has been determined to atomic resolution by X-ray crystallographic methods. The crystals grown by slow evaporation of peptide solution in methanol/water are orthorhombic, space group P2(1)2(1)2(1). The unit cell parameters are a= 8.404(3), b= 25.598(2) and c= 27.946(3) Angstrom, Z=4. The agreement factor is R = 7.58% for 3636 reflections having (vertical bar Fo vertical bar) > or = 3sigma (vertical bar Fo vertical bar). The peptide molecule is characterised by a 3(10)-helix at the N-terminus and a pi-turn at the C-terminus. This conformation is exactly similar to the helix termination features observed in proteins. The pi-turn conformation observed in the octapeptide is in good agreement with the conformational features of pi-turns seen in some proteins. The alphaL-position in the pi-turn of the octapeptide is occupied by DeltaPhe7, which shows that even bulky residues can be accommodated in this position of the pi-turns. In proteins, it is generally seen that alphaL-position is occupied by glycine residue. No intermolecular head-to-tail hydrogen bonds are observed in solid state structure of the octapeptide. A water molecule located in the unit cell of the peptide molecule is mainly used to hold the peptide molecule together in the crystal. The conformation observed for the octapeptide might be useful to understand the helix termination and chain reversal in proteins and to construct helix terminators for denovo protein design.

Solution structure of dehydropeptides: a CD investigation

A CD investigation of eleven dehydropeptides is reported. The compounds investigated include tri-, tetra-, hepta-, and octapeptides and contain one, two, or three dehydro-phenylalanine (deltaPhe) residues. The peptides showed different CD profiles depending on chain length, position, and number of dehydro residues. The CD data very much complemented that provided by nmr studies, confirming the conformational preference for beta-bend structures in small peptides (tripeptides), and 3(10)-helical or alpha-helical structures in longer peptides. The secondary structures were stable in chloroform solution and were denatured by addition of trifluoroacetic acid. Solvent titration experiments performed by measuring CD as a function of solvent composition provided evidence that the order < or > disorder conformational changes occurred as cooperative transitions.

Carrier-induced epitope-specific regulation and its bypass in a protein-protein conjugate

In the course of clinical trials on a birth control vaccine, it was found that some of the immunized women responded poorly to booster immunizations. This vaccine consists of a dimer of the beta chain of human chorionic gonadotropin (beta hCG) and the alpha chain of ovine luteinizing hormone (alpha oLH), linked to tetanus toxoid (TT) as a carrier. Changing this carrier to diphtheria toxoid resulted in reversion to high anti-hCG antibody titers, indicating the extent to which the carrier influences anti-ligand responses in this system. The suppression of anti-hCG responses after booster immunizations was reminiscent of the phenomenon of carrier-induced, epitope-specific regulation. In a mouse model designed to test the effects of preimmunization with TT on anti-hCG responses, we found that a single preimmunization with TT causes reduced anti-hCG antibody responses in two out of four mouse strains, while anti-alpha oLH antibody responses were not affected by the preimmunization with TT. This is particularly interesting considering that beta hCG and alpha oLH were not presented when linked separately to TT. In an effort to devise a strategy to circumvent this carrier-induced, ligand-specific hyporesponsiveness, we investigated the effectiveness of a synthetic T helper epitope from TT as carrier. We show that preimmunization with TT causes a less profound reduction in anti-hCG titers if the preimmunized mice are subsequently injected with alpha oLH-beta hCG conjugated to a synthetic tetanus toxin peptide recognized by TT-induced and peptide-induced T cells.

Crystal and molecular structure of Boc-Phe-Val-OMe; comparison of the peptide conformation with its dehydro analogue

The crystal structure of the peptide Boc-Phe-Val-OMe determined by X-ray diffraction methods is reported in this paper. The crystals grown from aqueous methanol are orthorhombic, space group P2(1)2(1)2(1),a = 11.843(2), b = 21.493(4), c = 26.676(4) A3 and V = 6790 A3. Data were collected on a CAD4 diffractometer using MoK alpha radiation (lambda = 0.7107 A) up to Bragg angle theta = 26 degrees. The structure was solved by direct methods and refined by a least-squares procedure to an R value of 6.8% for 3288 observed reflections. There are three crystal-lographically independent peptide molecules in the asymmetric unit. All the three molecules exhibit extended conformation. The sidechain of the Val2 residue shows two different conformations. The conformation of the peptide Boc-Phe-Val-OMe is compared with the conformation of Ac-delta Phe-Val-OH. It is observed that while Boc-Phe-Val-OMe exhibits an extended conformation, Ac-delta Phe-Val-OH shows a folded conformation. The results of this comparison highlight the conformation constraining property of the delta Phe residue. Interestingly, even though Boc-Phe-Val-OMe and Ac-delta Phe-Val-OH are conformationally different, they exhibit similar packing patterns in the solid state.

A conserved peptide sequence of the Plasmodium falciparum circumsporozoite protein and antipeptide antibodies inhibit Plasmodium berghei sporozoite invasion of Hep-G2 cells and protect immunized mice against P. berghei sporozoite challenge

Minutes after injection into the circulation, malaria sporozoites enter hepatocytes. The speed and specificity of the invasion process suggest that it is receptor mediated. The region II sequence of Plasmodium falciparum circumsporozoite (CS) protein includes a nonapeptide (WSPCSVTCG) which is highly conserved in all of the CS proteins sequenced to data, including the one from Plasmodium berghei. We have found that two peptides based on the P. falciparum region II sequence, P18 (EWSPCSVTCGNGIQVRIK) and P32 (IEQYLKKIKNS ISTEWSPCSVTCGNGIQVRIK), significantly inhibited P. berghei sporozoite invasion into Hep-G2 cells in vitro. This inhibition was enhanced if either peptide was preincubated with Hep-G2 cells prior to sporozoite invasion. We confirm that region II is a sporozoite ligand for the hepatocyte receptor; moreover, despite the few differences between P. falciparum and P. berghei region II sequences around the nonapeptide sequence (66% homology), the functional characteristics of the motif sequences are not affected. Since the conserved motifs represent a crucial sequence involved in Plasmodium sporozoite invasion of hepatocytes, antibodies to region II should inhibit sporozite invasion into hepatocytes. Indeed, we found that polyclonal antibodies generated to the P. falciparum-based peptide P32 inhibited P. berghei sporozoite invasion of Hep-G2 cells. Furthermore, inbred mice (C57BL/6) immunized with P32 were protected against a lethal challenge of P. berghei sporozoites. Our results suggest that the conserved region II of the CS protein contains crucial B- and T-cell epitopes, that such peptide sequences from the human malaria parasite P. falciparum can be screened in the P. berghei rodent model, and, finally, that region II can be considered useful as one of the components of a malaria vaccine.

Assignment of disulphide bonds in the X protein (HBx) of hepatitis B virus

We have established the disulphide arrangement of cysteines in E. coli expressed HBx by chromatographic analysis of enzymatically cleaved protein and sequence analysis of cysteine containing fragments. Eight of the nine cysteines are disulphide linked in an interesting pattern. Each cysteine is linked to the fourth cysteine in a sequential manner and the last cysteine is free; the disulphide linkages are between Cys7 and Cys78, Cys17 and Cys115, Cys61 and Cys137, Cys69 and Cys143 while Cys148 is free.

Synthesis, and crystal and molecular structure of the 3(10)-helical alpha,beta-dehydro pentapeptide Boc-Leu-Phe-Ala-delta Phe-Leu-OMe

alpha,beta-Dehydro amino acid residues are known to constrain the peptide backbone to the beta-bend conformation. A pentapeptide containing only one alpha,beta-dehydrophenylalanine (delta Phe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc-Leu-Phe-Ala-delta Phe-Leu-OMe (C39H55N5O8, Mw = 721.9) was crystallized from aqueous methanol. Monoclinic space group was P2(1), a = 10.290(2) degrees, b = 17.149(2) degrees, c = 12.179(2) A, beta = 96.64(1) degrees with two molecules in the unit cell. The x-ray (MoK alpha, lambda = 0.7107A) intensity data were collected using a CAD4 diffractometer. The crystal structure was determined by direct methods and refined using least-squares technique. R = 4.4% and Rw = 5.4% for 4403 reflections having magnitude of F0 > or = 3 sigma(magnitude of F0). All the peptide links are trans and the pentapeptide molecule assumes 3(10)-helical conformation. The mean phi,psi values, averaged over the first four residues, are -64.4 degrees, -22.4 degrees respectively. There are three 4-->1 intramolecular hydrogen bonds, characteristic of 3(10)-helix. In the crystal, the peptide helices interact through two head-to-tail, N-H-O intermolecular hydrogen bonds. The peptide molecules related by 2(1) screw symmetry form a skewed assembly of helices.

Fine specificity of immune responses to epitopic sequences in synthetic peptides containing B and T epitopes from the conserved Plasmodium falciparum blood-stage antigens

Immunisation with two chemically synthesised, linear, multiple epitope peptides (MEP) containing B and T cell epitopes from two conserved blood-stage antigens of the human malaria parasite, Plasmodium falciparum, induced high levels of circulating antibodies without the use of a carrier protein. Immunisation of BALB/c mice with MEP constructs (P1 and P2) induced antibodies against the various epitope sequences included in their structures, although the immune response was focused more towards the N terminal and the middle portion of the peptides. In vitro T cell proliferation assays indicated that only one of the two Th epitopes included in P1 and P2 are functional. Both P1 and P2, based on P. falciparum sequences, cross-reacted with sera from P. yoelii-infected mice. Immunisation with P1 in CFA, but not with P2, provided partial protection to BALB/c mice against P. yoelii challenge infection. Peptide P1 was highly immunogenic in alum also, and a somewhat higher level of protection was observed as compared to CFA immunisation. We found that immunisation with P1 induced antibody responses in different strains of mice, although to different extents. These results suggest that linear, multiple epitope peptides may offer attractive alternatives as subunit vaccine candidate molecules, but at the same time highlight the fact that the design principles are far from being clear and have yet to be worked out.

Predicted conformation of poly(dehydroalanine): a preference for turns

Repetitive conformations of poly(dehydroalanine) were studied using molecular mechanics. An exhaustive search of the conformational space was carried out on a delta Ala octapeptide model, using the AMBER force field and the delta Ala parameters of Alagona et al [26], under three dielectric conditions, epsilon = 1 (vacuum), epsilon = r and epsilon = 4r (solvent). In all cases, two major groups of low-energy conformers were found, one corresponding to a regular 3/10 helix or type III turn, the other to an irregular conformation, phi = -157 to -170 degrees, psi = -1 to 15 degrees which however can be found in the i + 2 position of gamma-turns. The data confirm that delta Ala may induce turn-like structures in peptides and also indicate that it may confer flexibility to the peptide chain.

Hairpin formation in d-AAGCTTAAGCTT under high salt conditions shows unusual properties

The hairpin-duplex equilibria of the dodecamer d-AAGCTTAAGCTT and interaction of the duplex form with a pentapeptide, KGWGK, has been studied. UV thermal transitions are monophasic at low salt but biphasic at higher salt concentrations. At 10(-5) M or less oligomer concentration biphasic melting curves persist till 900 mM NaCl. The d(Tm)/d log(Na+) for the duplex form is 12 degrees C and for the hairpin is 18 degrees C. The delta H and delta S values for duplex formation are low (-25 K cal/mole and -59 Cal/mole respectively). KGWGK binds to the duplex form with a binding constant K = 3.4 x 10(5)M-1 measured from fluorescence quenching of tryptophan. These unusual results are markedly different from that reported for d-AGATCTAGATCT (Biochemistry 31, 6241-6245) and are discussed in terms of sequence dependence of loop folding and cruciform extrusion pathway of hairpin formation.

Cellular and humoral immune responses to well-defined blood stage antigens (major merozoite surface antigen) of Plasmodium falciparum in adults from an Indian zone where malaria is endemic

Conserved and variant regions of two blood stage vaccine candidate antigens of Plasmodium falciparum, merozoite surface antigen (MSA-1) and ring-infected erythrocyte surface antigen (Pf155/RESA), have been shown to be immunogenic. However, the relative immunogenicity of these immunogens in different populations has not been studied. The conserved N-terminal region of MSA-1 was investigated for its immunogenicity by studying cellular (T cell) and humoral (B cell) immune responses in P. falciparum-primed individuals, living in malaria-hyperendemic areas (Orissa State, India), where malaria presents an alarming situation. MSA-1-derived synthetic peptides contained sequences that activated T cells to proliferate and release gamma interferon in vitro. There was considerable variation in the responses to different peptides. However, the highest responses (51% [18 of 35] by proliferation and 34% [12 of 35] by gamma interferon release) were obtained with a synthetic hybrid peptide containing sequences from conserved N- and C-terminal repeat regions of MSA-1 and Pf155/RESA, respectively. Antibody reactivities in an enzyme immunoassay of plasma samples from these donors to different peptides used for T-cell activation were heterogeneous. In general, there was poor correlation between DNA synthesis and either gamma interferon release or antibody responses in individual donors, underlining the importance of examining several parameters of T-cell activation to assess the total T-cell responsiveness of a study population to a given antigen. However, the results from our studies suggest that synthetic constructs containing sequences from the N- and C-terminal regions of MSA-1 and Pf155/RESA representing different erythrocytic stages of the P. falciparum parasite are more immunogenic in humans living in malaria-hyperendemic areas of India who have been primed by natural infection.

The use of peptide ELISA in determining malaria endemicity

A study was undertaken with the objective to find out whether a reliable transmission index could be established by a simple peptide ELISA. This would be important to evaluate the success of the bioenvironmental malaria control programmes implemented in endemic areas like the Haldwani and Shankargarh districts of Uttar Pradesh, India. We have estimated antimalarial antibodies against three synthetic peptides derived from blood stage antigens of Plasmodium falciparum and against P. falciparum crude antigen by enzyme-linked immunosorbent assay (ELISA), in children and adults. We have found that while all the peptides react with serum antibodies, as does the whole crude blood stage antigen, a nonapeptide from RESA antigen gave the most uniform results. Our results suggest that synthetic peptides, which are easy to obtain and can be fully characterized, may offer a simple way to measure malaria endemicity.

Conformationally constrained formyl methionyl tripeptides: structure-function study of analogs containing alpha,beta-dehydrophenylalanine and dehydroleucine

In order to probe the role of peptide backbone conformation on the biological activity of chemotactic peptides through conformationally constrained peptides, we synthesized the following three analogs of N-formyl-Met-Leu-Phe-OH (fMLF) containing dehydrophenylalanine (delta ZPhe) and dehydroleucine (delta ZLeu): formyl-Met-delta ZPhe-Phe-OCH3 (1), formyl-Met-delta ZLeu-Phe-OCH3 (2) and formyl-Met-delta ZPhe-delta ZPhe-OCH3 (3) and studied their conformational behavior in solution by 1H NMR and IR spectroscopy. The conformation of (1) was also examined by x-ray diffraction methods. Biological activity of these analogs was assessed for their ability to induce the release of beta-glucosaminidase from rabbit neutrophils. In addition, the chemotactic activity of analog (2) was also determined. We found that, in the solid state, (1) favors a type II beta-turn structure, stabilized by a 4-->1 intramolecular hydrogen bond. A similar structure was reported recently for (2) also. 1H NMR studies in solution suggest that the Phe NH is solvent shielded in both (1) and (2) and that a major population of peptide molecule exists in an intramolecular hydrogen bond stabilized type II beta-turn conformation. None of the NH groups in (3) and another analog, formyl-Met-Phe-Phe-OCH3 (4), appear solvent shielded, favoring an extended structure for these analogs. Analogs (2) and (4) are highly active indicating that both extended and beta-turn backbone conformations may be compatible with high activity and that the phenylalanine ring in the middle position is well accepted. Highly reduced activities of (1) and (3) suggest that delta ZPhe residue in position 2, irrespective of the preferred peptide backbone conformation, is not acceptable for high bioactivity. These results suggest that an induced fit mechanism may possibly be the most relevant one, but the nature and the topography of the side chains, particularly the middle residue, may be crucial for appropriate receptor ligand interactions.

Co-dominant and reciprocal T-helper cell activity of epitopic sequences and formation of junctional B-cell determinants in synthetic T:B chimeric immunogens

The identification of defined T-helper (Th) cell determinants, particularly those recognized in the context of several MHC or HLA haplotypes, and their use to provide effective carrier help to short synthetic constructs representing a B-cell epitope have made it feasible to synthesize putatively potent immunogens. However, a number of crucial questions regarding immunogenicity of epitopic sequences need to be addressed before an optimally effective synthetic vaccine can be designed. The present study deals with the hybrid constructs incorporating a known B-cell epitope from the merozoite surface protein-1 (MSP-1) of a human malarial parasite, Plasmodium falciparum, and the promiscuous Th-cell epitope from tetanus toxin or from the circumsporozoite protein of P. falciparum. Here, we provide data which suggest that B- and T-cell determinants present in a hybrid construct could, in fact, provide reciprocal helper activity for antibody production; that antibodies to a Th-cell epitope may not necessarily block its helper function; and that junctional B-cell epitopes may be formed. All this may influence, in an unpredictable manner, the quality of protective immune response sought to be generated using the chimeric immunogens, with important implications for vaccine design.

Solution structure of GCCAAT recognition motif by 2D NMR, spectral simulation, molecular modeling, and distance geometry calculations

Solution conformation of a self-complementary 14-mer DNA duplex (d-GGATTGGCCAATCC) containing the GCCAAT recognition motif of several transcription factors has been investigated by NMR spectroscopy. Complete resonance assignment of all the protons (except H5',H5'' protons) has been obtained following standard procedures based on two-dimensional NMR techniques. Three-bond coupling constants have been determined by spectral simulation procedures. New strategies have been described and employed for quantifying NOE intensities from the structural point of view. Approximate ranges of gamma torsion angles have been obtained from a selective NOESY experiment, by estimating the J(4'-5'), J(4'-5''), or their sum in the H1'-H4' cross peaks of the spectrum. Likewise, ranges of epsilon torsion angles have been obtained by monitoring the H3' multiplicities in the H8/H6-H3' cross peaks in selective NOESY spectra. With the help of such a total of 73 coupling constraints, 79 NOE intensity constraints, and 108 H-bond constraints, model building has been carried out to obtain a structure which satisfies the constraints. Starting from such a structure, an expanded distance constraint set has been created which has been used for the distance geometry calculations using the program TANDY. In the best structure thus derived, interesting irregularities similar to a BI-BII transition have been observed in the center. The molecule exhibits a bend. The overall base stacking is different from that in either B- or A-DNA models. The base pairs are tilted with respect to the local helix axes. The observed structural features are likely to have important implications for the recognition mechanism of the GCCAAT motif.

Conformation of dehydropeptides. Synthesis and solution structure of model peptides containing (E) and (Z) dehydroaminobutyric acid residues

Six model dipeptide methylamides containing dehydroaminobutyric acid (delta Abu) of the type Boc-X-delta z Abu-NHCH3 and Box-X-delta E Abu-NHCH3, X = Ala, Val, Phe (Boc = tert-butoxycarbonyl), have been synthesized and their solution conformations explored using 300 MHz 1H NMR and IR spectroscopy. Studies based on delineation of intramolecularly hydrogen bonded NH groups in CDCl3 and (CD3)2SO revealed that none of the NH groups is appreciably solvent shielded. Difference NOE (Nuclear Overhauser Effect) studies have also failed to detect the presence of any discernible turn structure in these peptides. These studies indicate that the conformational preferences of peptides containing, alpha, beta-dehydroaminobutyric acid are different from those of delta ZPhe and delta ZLeu. It appears that steric interactions due to the beta-substituent in the dehydroamino acid moiety play an important role. Unlike delta ZPhe and delta ZLeu, which have relatively large beta-substituents, phenyl and isopropyl, respectively, and stabilize a beta-turn, the beta-methyl group of delta ZAbu or delta EAbu is readily accommodated in extended conformation. Clearly, the size of beta-substituent in dehydroamino acid crucially influences the conformational preferences. Thus, it may be possible to use different dehydroamino acids to introduce variable but definite constraints in synthetic peptides.

Synthetic peptides based on conserved Plasmodium falciparum antigens are immunogenic and protective against Plasmodium yoelii malaria

Two synthetic polypeptides containing multiple B- and T-cell epitopes derived from the conserved regions of two vaccine candidate antigens namely MSA-1 and RESA of human malarial parasite P. falciparum were studied for immunogenicity and protectivity. Both constructs elicited strong antibody and lymphocyte proliferation responses in BALB/c mice immunized with the carrier-free peptides. In an ELISA, these peptides also bound antibodies present in the sera from the P. vivax infected humans as well as from the P. yoelii infected mice. Significantly, our data showed that immunization of mice with these P. falciparum peptide could impart partial protection against P. yoelii challenge infection. Our finding that synthetic peptides representing portions of P. falciparum antigens were capable of stimulating protective immune responses against rodent malaria suggests that murine malaria model P. yoelii may provide a suitable system for primary screening of potentially protective synthetic immunogens.

Enhancing factor protein from mouse small intestines belongs to the phospholipase A2 family

Enhancing factor (EF), a growth regulatory molecule, isolated from mouse small intestines, has been well characterized in this laboratory. It increases the binding of epidermal growth factor in a unique manner via its own receptor. In the first 20 N-terminal amino acids sequenced, EF showed 50% homology to human Group II phospholipase A2 (PLA2). Here we propose that EF is yet another, unidentified isoform of PLA2 which regulates cell proliferation via modulation of EGF binding. To our knowledge, this is the first report implicating PLA2-II-like molecules in growth regulation.

Peptide design 3(10)-helical conformation of a linear pentapeptide containing two dehydrophenylalanines, Boc-Gly-delta ZPhe-Leu-delta ZPhe-Ala-NHCH3

alpha,beta-Dehydroamino acids are expected to provide conformational constraint to the peptide backbone. A pentapeptide containing two dehydrophenylalanines (delta ZPhe) separated by one L-amino acid has been synthesized and its solid state conformation determined. The pentapeptide, Boc-Gly-delta ZPhe-Leu-delta ZPhe-Ala-NHCH3, crystallizes from aqueous methanol in the orthorhombic space group P2(1)2(1)2(1). There are four formula units, C35H46N6O7, in a unit cell of dimensions a = 10.155(3), b = 15.175(1), and c = 23.447(2) A, at room temperature. The structure was solved by direct methods program, SIR88, and refined to a final R = 0.038 based on 3049 reflections with I > 2 sigma (I). All the peptide links are trans and the backbone conformation of the pentapeptide can be described as a 3(10)-helix, with mean phi,psi values of -65.1 degrees and -22.8 degrees (the value is averaged over the first four residues). There are four intramolecular 4-->1 type hydrogen bonds characteristic of 3(10)-type helices. In the crystal, the helices are held together by intermolecular N-H...O = C head-to-tail and lateral hydrogen bonding between symmetry related molecules. This mode of packing is similar to the packing motifs observed so often in other oligopeptides that adopt a 3(10)-helical structure.

Synthetic gonadotrophin-releasing hormone (GnRH) vaccines incorporating GnRH and synthetic T-helper epitopes

A vaccine against the gonadotrophin-releasing hormone (GnRH) is being developed as an immunological method for treatment of prostatic hypertrophy, based on the observation that active immunization against GnRH leads to the production of anti-GnRH antibodies which results in the shrinkage of the prostate gland. We have been investigating the regulation of anti-GnRH antibody responses by carrier molecules. In previous studies we showed that the use of large protein molecules as carriers limits the use of such a vaccine owing to potential problems of carrier-induced anti-haptenic suppression. In this report we show that synthetic T-helper epitopes can be used as carriers for the generation of anti-GnRH antibody responses.

Binding of oligopeptides to d-AGATCTAGATCT and d-AAGCTTAAGCTT: can tryptophan intercalate in DNA hairpins?

The interactions of three tryptophan-containing peptides, KWK, KGWK tert-butyl ester, and KGWGK, with two self-complementary dodecamers of the same base composition but different sequence were studied by UV, CD, and fluorescence spectroscopy. The oligonucleotides, d-AGATCTAGATCT and d-AAGCTTAAGCTT, contain tandem repeats of the recognition site for the restriction enzyme BglII in the former and HindIII in the latter. Thermal transition data in dilute solutions and in 0.01 M NaCl indicate these dodecamers to be present in hairpin forms. Binding of peptides to these hairpins was followed by tryptophan fluorescence quenching titrations at 10 mM Na+; the data suggest intercalation of the indole ring. The association constants for the peptide-oligonucleotide (PN) complexes are an order of magnitude higher (10(5) M) than those reported with polynucleotides [10(4) M; Rajeswari et al. (1987) Biochemistry 26, 6825]. The pentapeptide, KGWGK, discriminates between BglII and HindIII sequences with higher affinity for the HindIII dodecamer. The CD maximum of KGWGK, at 220 nm, is drastically diminished upon interaction with oligonucleotides. The ellipticity at 220 nm is halved at 10 times less P/N ratio with the HindIII dodecamer than the BglII dodecamer, suggesting stronger binding to the HindIII dodecamer. The results are discussed in terms of two different modes of binding of oligopeptides to the DNA hairpins.

Hairpin and duplex forms of a self-complementary dodecamer, d-AGATCTAGATCT, and interaction of the duplex form with the peptide KGWGK: can a pentapeptide destabilize DNA?

Ordered forms of a synthetic dodecamer, d-AGATCTAGATCT, a direct repeat of the BglII recognition sequence, have been investigated using UV, CD, and fluorescence spectroscopy. Complex hairpin-duplex equilibria are manifest in UV thermal transitions, which are monophasic in the presence of very low or high NaCl concentrations but distinctly biphasic at intermediate ionic strengths. In 100 mM NaCl, the 1/Tm vs 1n C curve has a reasonable positive slope, which yields delta H and delta S for duplex formation as -66.2 kcal/mol and -190 cal/mol, respectively. Interaction of the dodecamer in duplex form with a tryptophan-containing peptide, KGWGK, has also been investigated to test the "bookmark" hypothesis (Gabbay et al., 1976) under the uniform structural constraint of the oligonucleotide of defined sequence. CD spectra of the peptide (P), the oligonucleotide (N), and their mixtures at different P/N ratios show a dramatic change in peptide spectrum but little change in nucleic acid dichroism with peptide binding. The Tm of P-N complexes decreases with an increase in peptide binding and levels off at saturation binding of P/N = 2.0. The data are interpreted in terms of a groove-cum-intercalation mode of binding, where intercalation to the tryptophan side chain destabilizes the double helix. A Scatchard plot of the binding data is nonlinear, with best-fit values for an overall association constant K = 4.33 x 10(5) M-1, and the number of binding sites n = 3.23 when fitted to the site-exclusion model of binding.

"Universal" T helper cell determinants enhance immunogenicity of a Plasmodium falciparum merozoite surface antigen peptide

Synthetic peptide constructs containing a limited number of epitopes are being currently investigated as subunit vaccines against a variety of pathogens. However, because of widespread nonresponsiveness to most such constructs, possibly attributable to MHC restriction, the choice of appropriate carrier molecules to enhance immunogenicity of peptides constitutes an important and essential aspect of designing synthetic immunogens for human use. Widely used vaccines such as tetanus toxoid (TT) have not been uniformly effective as carrier proteins because of the phenomenon of epitope-specific suppression in which induction of an immune response against a synthetic peptide conjugated to TT is prevented by preexisting immunity to TT. Recently, T cell determinants that can be recognized in the context of several class II MHC molecules have been identified in tetanus toxin as well as in the circumsporozoite protein of a human malarial parasite, Plasmodium falciparum. Such determinants can be potentially used to circumvent the problem of epitope-specific suppression. In the present study we evaluated two such T cell determinants, viz., tt830-844 from tetanus toxin and CST3 from the malarial parasite, for their ability to help induce a boostable antibody response and to overcome genetic nonresponsiveness to a synthetic 20-residue construct containing a B cell and an overlapping T cell epitope from a major merozoite surface protein of P. falciparum. Our data provide support for the view that widely recognized T cell determinants may be used as universal carrier molecules for general vaccination.

Crystal structure and conformation of a highly constrained linear tetrapeptide Boc-Leu-dehydro Phe-Ala-Leu-OCH3

The conformation of a tetrapeptide containing a dehydro amino acid, delta ZPhe, in its sequence has been determined in the crystalline state using X-ray crystallographic techniques. The tetrapeptide, Boc-Leu-delta ZPhe-Ala-Leu-OCH3, crystallizes in the orthorhombic space group P2(1)2(1)2(1) with four molecules in a unit cell of dimensions a = 11.655(1) A, b = 15.698(6) A and c = 18.651(3) A V = 3414.9 A and Dcalc = 1.12 g/cm-3. The asymmetric unit contains one tetrapeptide molecule, C30H46N4O7, a total of 41 nonhydrogen atoms. The structure was determined using the direct methods program SHELXS86 and refined to an R-factor of 0.049 for 3347 reflections (I3.0(I). The linear tetrapeptide in the crystal exhibits a double bend of the Type III-I, with Leu1 (phi = -54.1 degrees, psi = -34.5 degrees) and delta ZPhe2 (phi = -59.9 degrees, psi = -17.1 degrees) as the corner residues of Type III turn and delta ZPhe2 (phi = -59.9 degrees, psi = -17.1 degrees) and Ala3 (phi = -80.4 degrees, psi = 0.5 degrees) residues occupying the corners of Type I turn, with delta ZPhe as the common residue in the double bend. The turn structures are further stabilized by two intramolecular 4----1 type hydrogen bonds.

"Universal" T helper cell determinants enhance immunogenicity of a Plasmodium falciparum merozoite surface antigen peptide

Synthetic peptide constructs containing a limited number of epitopes are being currently investigated as subunit vaccines against a variety of pathogens. However, because of widespread nonresponsiveness to most such constructs, possibly attributable to MHC restriction, the choice of appropriate carrier molecules to enhance immunogenicity of peptides constitutes an important and essential aspect of designing synthetic immunogens for human use. Widely used vaccines such as tetanus toxoid (TT) have not been uniformly effective as carrier proteins because of the phenomenon of epitope-specific suppression in which induction of an immune response against a synthetic peptide conjugated to TT is prevented by preexisting immunity to TT. Recently, T cell determinants that can be recognized in the context of several class II MHC molecules have been identified in tetanus toxin as well as in the circumsporozoite protein of a human malarial parasite, Plasmodium falciparum. Such determinants can be potentially used to circumvent the problem of epitope-specific suppression. In the present study we evaluated two such T cell determinants, viz., tt830-844 from tetanus toxin and CST3 from the malarial parasite, for their ability to help induce a boostable antibody response and to overcome genetic nonresponsiveness to a synthetic 20-residue construct containing a B cell and an overlapping T cell epitope from a major merozoite surface protein of P. falciparum. Our data provide support for the view that widely recognized T cell determinants may be used as universal carrier molecules for general vaccination.

Synthetic, immunological and structural studies on repeat unit peptides of Plasmodium falciparum antigens

Using solid phase methodology, we have synthesized five peptides (16-18 residues long) corresponding to repeat sequences of four antigens of a human malarial parasite, Plasmodium falciparum. Three of these antigens (RESA, FIRA, and ABRA) are found in the asexual blood-stages of the parasite, while the remaining one (CSP) is found in the sporozoites. The synthetic peptides, conjugated to bovine serum albumin, elicited high levels of antibodies in rabbits, and these antibodies were found to cross-react with the heterologous peptides. The degree of cross-reactivity, as estimated in an ELISA, was quite remarkable among all the peptides. The peptide corresponding to the RESA tetrapeptide repeat was found to be the most immunogenic and highly cross-reactive. For this reason this tetrapeptide repeat unit, peptide 1, may be a suitable candidate for inclusion in a multiple epitope polypeptide vaccine design. Conformational studies using circular dichroism spectroscopy show that these peptides have similar conformational characteristics with a common feature of approximately 30% and approximately 50% helical content water and TFE respectively. Theoretical predictions regarding conformation using the Chou-Fasman method have also been presented.

Synthesis, crystal structure, and molecular conformation of N-Boc-L-Phe-dehydro-Leu-L-Val-OCH3

The peptide N-Boc-L-Phe-dehydro-Leu-L-Val-OCH3 was synthesized by the usual workup procedure and finally by coupling the N-Boc-L-Phe-dehydro-Leu-OH to valine methyl ester. It was crystallized from its solution in methanol-water mixture at 4 degrees C. The crystals belong to the triclinic space group P1 with a = 5.972(5) A, b = 9.455(6) A, c = 13.101(6) A, alpha = 103.00(4) degrees, beta = 97.14(5) degrees, gamma = 102.86(5) degrees, V = 690.8(8) A, Z = 1, dm = 1.179(5) Mg m-3 and dc = 1.177(5) Mg m-3. The structure was determined by direct methods using SHELXS86. It was refined by block-diagonal least-squares procedure to an R value of 0.060 for 1674 observed reflections. The C alpha 2-C beta 2 distance of 1.323(9) A in dehydro-Leu is an appropriate double bond length. The bond angle C alpha-C beta-C gamma in the dehydro-Leu residue is 129.4(8) degrees. The peptide backbone torsion angles are theta 1 = -168.6(6) degrees, omega 0 = 170.0(6) degrees, phi 1 = -44.5(9) degrees, psi 1 = 134.5(6) degrees, omega 1 = 177.3(6) degrees, phi 2 = 54.5(9) degrees, psi 2 = 31.1(10) degrees, omega 2 = 171.7(6) degrees, phi 3 = 51.9(8) degrees, psi T3 = 139.0(6) degrees, theta T = -175.7(6) degrees. These values show that the backbone adopts a beta-turn II conformation. As a result of beta-turn, an intramolecular hydrogen bond is formed between the oxygen of the ith residue and NH of the (i + 3)th residue at a distance of 3.134(6) A.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthesis, crystal structure, and molecular conformation of peptide N-Boc-L-Pro-dehydro-Phe-L-Gly-OH

The peptide N-Boc-L-Pro-dehydro-Phe-L-Gly-OH was synthesized by the usual workup procedure and finally coupling the N-Boc-L-Pro-dehydro-Phe to glycine. The peptide crystallizes in monoclinic space group P2(1) with a = 8.951(4) A, b = 5.677(6) A, c = 21.192(11) A, beta = 96.97(4) degrees, V = 1069(1) A3, Z = 2, dm = 1.295(5) Mgm-3, and dc = 1.297(4) Mgm-3. The structure was determined by direct methods using SHELXS86. The structure was refined by the block-diagonal least-squares procedure to an R value of 0.074 for 1002 observed reflections. The C alpha 2-C beta 2 distance of 1.33(2) A is an appropriate double bond length. The angle C alpha 2-C beta 2-C gamma 2 is 133(1) degrees. The peptide backbone torsion angles are theta 1 = -167(1) degrees, omega 0 = 179(1) degrees, phi 1 = -48(1) degrees, psi 1 = 137(1) degrees, omega 1 = 175(1) degrees, phi 2 = 65(2) degrees, psi 2 = 15(2) degrees, omega 2 = -179(1) degrees, and phi 3 = -166(1) degrees. These values show that the Boc group has a trans-trans conformation while the peptide backbone adopts a beta-turn II conformation, which is stabilized by an intramolecular hydrogen bond of length of 3.05(1) A. The structures of dehydro-Phe containing peptides suggest that the dehydro-Phe promotes the beta-turn II conformation. The five-membered pyrrolidine ring of the Pro residue adopts an ideal C gamma-exo conformation with torsion angles chi 1(1) = -24(1) degrees, chi 2(1) = 34(1) degrees, chi 3(1) = -30(1) degrees, chi 4(1) = 15(1) degrees, and theta 0(1) = 6(1) degrees. The side-chain torsion angles in dehydro-Phe are chi 1(2) = -1(2) degrees, chi 2,1(2) = -176(1) degrees, and chi 2,2(2) = 8(2) degrees. The plane of C alpha 2-C beta 2-C gamma 2 is rotated with respect to the plane of the phenyl ring at 7(1) degrees, which indicates that the atoms of the side chain of dehydro-Phe are essentially coplanar. The molecules form a 2(1) screw axis related hydrogen-bonded rows along the b axis.

Synthetic and conformational studies on dehydroalanine-containing model peptides

Three model dipeptides containing a dehydroalanine residue (delta Ala) at the C-terminal, Boc-X-delta Ala-NHCH3 [X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by 1H-NMR, IR, and CD spectroscopy. NMR studies on these peptides in CDCl3 clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. This conclusion is supported by IR studies also. Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse gamma-turn-type of conformation that is characterized by conformational angles of phi approximately -70 degrees and psi approximately +70 degrees around the X residue, and a C alpha i + 1 H-Ni + 2H interproton distance of 2.5 A. It appears that unlike dehydrophenylalanine or dehydroleucine, which tend to stabilize beta-turn type of structures occupying the i + 2 position of the turn, dehydroalanine favors the formation of an inverse gamma-turn, centered at the preceding L-residue in such solvents as CDCl3 and (CD3)2SO. A comparison of solution conformation of Boc Val-delta Ala-NHCH3 with the corresponding saturated analogue, Boc-Val-Ala-NHCH3, is also presented and shows that dehydroalanine is responsible for inducing the turn structure. It may be possible to design peptides with different preferred conformations using the suitable dehydroamino acid.

Crystal structure and molecular conformation of the peptide N-Boc-L-Gly-dehydro-Phe-NHCH3

The peptide N-Boc-L-Gly-dehydro-Phe-NHCH3 was synthesized by the combination of N-Boc-L-Gly-dehydro-Phe azlactone and methylamine. The peptide crystallizes in orthorhombic space group P2(1)2(1)2(1) with a = 5.679(2) A, b = 16.423(9) A, c = 19.198(10) A, V = 1791(2) A3, Z = 4, dm = 1.212(5) Mg m-3, dc = 1.237(1) Mg m-3. The structure was determined by direct methods using SHELXS 86. The structure was refined by full-matrix least squares procedure to an R value of 0.049 for 1509 observed reflections. The molecular dimensions are, in general, in good agreement with the standard values. The bond angle C alpha-C beta-C gamma in the dehydro-Phe residue is 133.6(5) degrees. The peptide backbone torsion angles are theta 1 = -171.4(4) degrees, omega 0 = 178.2(4) degrees, phi 1 = -57.2(6) degrees, psi 1 = 141.2(4) degrees, omega 1 = -174.4(4) degrees, phi 2 = 71.5(6) degrees, psi 2 = 7.2(6) degrees, and omega 2 = -179.8(5) degrees. These values show that the backbone adopts the beta-bend type II conformation. The Boc group has a trans-trans conformation. The side-chain torsion angles in dehydro-Phe are chi 2 = 1.6(9) degrees, chi 2(2, 1) = 0.5(9) degrees, and chi 2(2, 2) = 179.8(6) degrees. The plane of C2 alpha-C2 beta-C2 gamma is rotated with respect to the plane of the phenyl ring at 0.5(6) degrees, which indicates that the atoms of the side chain of the dehydro-Phe residue are essentially coplanar.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformations of peptides containing Z-alpha,beta-dehydroleucine (delta ZLeu). A comparison of Boc-Pro-delta ZLeu-Gly-NHEt and Boc-Pro-delta ZPhe-Gly-NHEt

Two tripeptides of the type Boc-Pro-delta ZX-Gly-NHEt (where X = Leu, Phe) have been synthesized and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. These conformational studies indicated that delta ZLeu, similar to delta ZPhe, has a strong tendency to stabilize folded Type II beta-turn conformations when present at i + 2 position.

Conformations of dehydrophenylalanine containing peptides: nmr studies of an acyclic hexapeptide with two delta Z-Phe residues

The conformation of an acyclic dehydrophenylalanine (delta Z-Phe) containing hexapeptide, Boc-Phe-delta Z-Phe-Val-Phe-delta Z-Phe-Val-OMe, has been investigated in CDCl3 and (CD3)2SO by 270-MHz 1H-nmr. Studies of NH group solvent accessibility and observation of interresidue nuclear Overhauser effects (NOEs) suggest a significant solvent-dependent conformational variability. In CDCl3, a population of folded helical conformations is supported by the inaccessibility to solvent of the NH groups of residues 3-6 and the detection of several NiH----Ni + 1H NOEs. Evidence is also obtained for conformational heterogeneity from the detection of some Ci alpha H----Ni + 1H NOEs characteristic of extended strands. In (CD3)2SO, the peptide largely favors an extended conformation, characterized by five solvent-exposed NH groups and successive Ci alpha H----Ni + 1H NOEs for the L-residues and Ci beta H----Ni + 1H NOEs for the delta Z-Phe residues. The results suggest that delta Z-Phe residues do not provide compelling conformational constraints.

Conformations of dehydrophenylalanine containing peptides. Nuclear Overhauser effect study of two acyclic tetrapeptides

Two isomeric, acyclic tetrapeptides containing a Z-dehydrophenylalanine residue (delta Z-Phe) at position 2 or 3, Boc-Leu-Ala-delta Z-Phe-Leu-OMe (1) and Boc-Leu-delta Z-Phe-Ala-Leu-OMe (2), have been synthesized and their solution conformations investigated by 270 MHz 1H n.m.r. spectroscopy. In peptide 1 the Leu(4) NH group appears to be partially shielded from solvent, while in peptide 2 both Ala(3) and Leu(4) NH groups show limited solvent accessibility. Extensive difference nuclear Overhauser effect (n.O.e.) studies establish the occurrence of several diagnostic inter-residue n.O.e.s (Ci alpha H----Ni+1H and NiH----Ni+1H) between backbone protons. The simultaneous observation of "mutually exclusive" n.O.e.s suggests the presence of multiple solution conformations for both peptides. In peptide 1 the n.O.e. data are consistent with a dynamic equilibrium between an -Ala-delta Z-Phe- Type II beta-turn structure and a second species with delta Z-Phe adopting a partially extended conformation with psi values of +/- 100 degrees to +/- 150 degrees. In peptide 2 the results are compatible with an equilibrium between a highly folded consecutive beta-turn structure for the -Leu-delta Z-Phe-Ala- segment and an almost completely extended conformation.

Leprosy deformities. II. As parameters to monitor the effectivity of leprosy control programme

Leprosy deformities have been considered as the main reason for dehabilitation and social ostracism. Prevention of deformities is considered as one of the most important objectives of leprosy control programme. In present work based on deformity status, efforts have been made to evolve new parameters and their possible application in assessment of leprosy control programme.

Analogues of luteinizing hormone-releasing hormone (LH-RH) containing dehydroalanine in 6th position

(Phe5, delta Ala6)-LH-RH and des-Gly10(Phe5, delta Ala6)-LH-RH ethylamide, two analogues of luteinizing hormone-releasing hormone (LH-RH), have been synthesised using fragment condensation approach in solution phase with minimum protection of the side chains. The presence of dehydroalanine in peptide fragments was confirmed by 1H n.m.r. and chemical analysis. Both the analogues were found to be inactive in comparison to LH-RH, indicating that alpha,beta-dehydrogenation of alanine in 6th position is not tolerated and suggesting that flexibility at this position may be crucial for the retention of biological activity.

Leprosy deformities. I. An epidemiological study in a rural area of Rajasthan

Leprosy deformities have been the cause of dehabilitation, destitution and social ostracism. Present study was planned and conducted in a rural area situated in eastern districts of Rajasthan. Out of 426 cases of leprosy, ninety cases were found suffering with deformities. The influences of various host factors and disease factors, in causation of deformities have been discussed.

Solution conformation of poly(L-lysyl-L-glutamic acid) and poly(L-lysyl-L-glutamine)

Solution conformation of poly(L-lysyl-L-glutamic acid) (PLGU) and poly(L-lysyl-L-glutamine) (PLGN) was studied in water as a function of pH, added salt, detergents, methanol and trifluoroethanol (TFE). Both the polypeptides exhibit no ordered conformation in the pH range 1.5-12.5; salts and detergents did not have any marked effect. Replacement of side chain carboxyl by an amide group did not help in inducing PLGN to adopt a helical conformation even at pH as high as 12.0, unlike poly(L-lysine). The helicogenic solvents, methanol and TFE, induce formation of weak helices in PLGU as well as in PLGN. It is not unlikely that H-bonding between the side chains leads to stabilizing an unordered conformations.

Hydroxy- and amino-protection based on the 4-dimethylcarbamoylbenzyl group

0-4-Dimethylcarbamoylbenzyl-L-tyrosine, N (epsilon)-4-dimethylcarbamoylbenzyloxycarbonyl-L-lysine, and simple derivatives, have been prepared. The protecting groups are markedly more stable to trifluoroacetic acid than are the unsubstituted benzylanalogues. N-t-Butoxycarbonyl-O-4-dimethylcarbamoylbenzyl-L-serine (cyclohexylammonium salt) is also described.

Conformational characteristics of peptides containing alpha, beta-dehydroamino acid residues

The structural preferences of synthetic peptides containing alpha, beta-dehydroamino acid residues, as determined by theoretical studies, x-ray diffraction analyses, and spectroscopic studies, are reviewed. The role of delta ZPhe residues in stabilizing type II beta-turn structures in small peptides and in nucleating helical structure in longer peptides is exemplified by several crystal as well as solution structural studies. From the few studies reported so far it appears that delta ZLeu influences the peptide backbone, much like the delta ZPhe residue, whereas delta Ala prefers the extended conformation, suggesting that the nature of beta substituents might influence the conformation restriction behavior of the dehydroresidues. Conformational studies on synthetic peptides containing delta E, delta ZAbu, and delta Val have also been described.