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Biomedical subjects

R Nagaraj

Publications and source records attributed to R Nagaraj.

At least 37 records · Page 2Linked to original sources
PubMed2000

Norbornene-constrained cyclic peptides with hairpin architecture: design, synthesis, conformation, and membrane ion transport.

A novel family of hairpin cyclic peptides has been designed on the basis of the use of norbornene units as the bridging ligands. The design is flexible with respect to the choice of an amino acid, the ring size, and the nature of the second bridging ligand as illustrated here with the preparation of a large number of norborneno cyclic peptides containing a variety of amino acids in ring sizes varying from 12- to 29-membered, with the choice of the second bridging ligand being a rigid norbornene (11, 13a,b), an adamantane unit (7a,b and 8), or a flexible cystine residue (4a,b and 10). The presence of built-in handles (as protected COOH groups) permits the attachment of a variety of subunits as shown here with the ligation of Leu-Leu, Val-Val, or Aib-Aib pendants in 4b, 7b, and 13b, respectively. This novel class of constrained cyclic peptides are demonstrated to adopt beta-sheet- or hairpin-like conformation as shown by (1)H NMR and CD spectra. Membrane ion-transport studies have shown that the norborneno cyclic peptides 4b and 7b containing Leu-Leu or Val-Val pendants symmetrically placed on the exterior of the ring show high efficiency and selectivity in the transport of specifically monovalent cations. This property can be attributed to the hairpin-like architecture induced by the norbornene unit since the bis-adamantano peptide 15 containing two pairs of Leu-Leu pendants on the exterior is able to transport both monovalent (Na(+), K(+)) and divalent (Mg(2+)/Ca(2+)) cations.

Circular Dichroism↗
PubMed2000

Solid-phase synthesis of a modified 13-residue seminalplasmin fragment on 1,6-hexanediol diacrylate-crosslinked polystyrene support.

A novel 1,6-hexanediol diacrylate cross-linked resin was prepared that was subsequently functionalized by using chloromethyl methyl ether to afford a high-capacity resin. The resin exhibited good swelling and its application in the successful synthesis of a 13-residue peptide corresponding to the fragment of seminalplasmin has been illustrated. The resin was chemically inert at peptide synthetic conditions.

Acrylates↗
PubMed1999

Interaction of antimicrobial peptides with biological and model membranes: structural and charge requirements for activity.

Species right across the evolutionary scale from insects to mammals use peptides as part of their host-defense system to counter microbial infection. The primary structures of a large number of these host-defense peptides have been determined. While there is no primary structure homology, the peptides are characterized by a preponderance of cationic and hydrophobic amino acids. The secondary structures of many of the host-defense peptides have been determined by a variety of techniques. The acyclic peptides tend to adopt helical conformation, especially in media of low dielectric constant, whereas peptides with more than one disulfide bridge adopt beta-structures. Detailed investigations have indicated that a majority of these host-defense peptides exert their action by permeabilizing microbial membranes. In this review, we discuss structural and charge requirements for the interaction of endogenous antimicrobial peptides and short peptides that have been derived from them, with membranes.

Amino Acid Sequence↗
PubMed1999

A negatively charged region of the skeletal muscle ryanodine receptor is involved in Ca(2+)-dependent regulation of the Ca(2+) release channel.

The ryanodine receptor/Ca(2+) release channels from skeletal (RyR1) and cardiac (RyR2) muscle cells exhibit different inactivation profiles by cytosolic Ca(2+). D3 is one of the divergent regions between RyR1 (amino acids (aa) 1872-1923) and RyR2 (aa 1852-1890) and may contain putative binding site(s) for Ca(2+)-dependent inactivation of RyR. To test this possibility, we have deleted the D3 region from RyR1 (DeltaD3-RyR1), residues 1038-3355 from RyR2 (Delta(1038-3355)-RyR2) and inserted the skeletal D3 into Delta(1038-3355)-RyR2 to generate sD3-RyR2. The channels formed by DeltaD3-RyR1 and Delta(1038-3355)-RyR2 are resistant to inactivation by mM [Ca(2+)], whereas the chimeric sD3-RyR2 channel exhibits significant inactivation at mM [Ca(2+)]. The DeltaD3-RyR1 channel retains its sensitivity to activation by caffeine, but is resistant to inactivation by Mg(2+). The data suggest that the skeletal D3 region is involved in the Ca(2+)-dependent regulation of the RyR1 channel.

Amino Acid Sequence↗
PubMed1999

Biological activities of C-terminal 15-residue synthetic fragment of melittin: design of an analog with improved antibacterial activity.

Melittin, the 26-residue predominant toxic peptide from bee venom, exhibits potent antibacterial activity in addition to its hemolytic activity. The synthetic peptide of 15 residues corresponding to its C-terminal end (MCF), which encompasses its most amphiphilic segment, is now being shown to possess antibacterial activity about 5-7 times less compared to that of melittin. MCF, however, is 300 times less hemolytic. An analog of MCF, MCFA, in which two cationic residues have been transpositioned to the N-terminal region from the C-terminal region, exhibits antibacterial activity comparable to that of melittin, but is only marginally more hemolytic than MCF. The biophysical properties of the peptides, like folding and aggregation, correlate well with their biological properties.

Amino Acid Sequence↗
PubMed1999

Synthetic peptides corresponding to the beta-hairpin loop of rabbit defensin NP-2 show antimicrobial activity.

Mammalian defensins, a class of antibacterial peptides, are composed of 29-35 amino acids with six cysteines which form three disulfide bonds. Structural studies indicate a triple stranded beta-sheet structure with a well defined beta-hairpin loop at the C-terminal region. It is demonstrated in this report that 18 and 26 residue synthetic peptides corresponding to the beta-hairpin region, constrained by a single disulfide bond, have potent antimicrobial activity without hemolytic activity. Circular dichroism spectroscopy indicates that the single S-S bridge appears to constrain the peptides to a beta-structure. Peptides corresponding to the beta-hairpin region of defensins could thus be attractive candidates as therapeutic agents as well as good model compounds for investigation of the various physiological actions of defensins.

Amino Acid Sequence↗
PubMed1999

Consequences of introducing a disulfide bond into an antibacterial and hemolytic peptide.

The effect of introducing a disulfide bridge between the N- and C-terminal ends on the structure and biological activities of the 13-residue linear peptide PKLLKTFLSKWIG(SPFK), which has both antibacterial and hemolytic activity, have been investigated. The terminal amino acids P and G in SPFK were replaced by cysteines to form a disulfide bridge. The linear peptides C(Acm)KLLKTFLSKWIC(Acm) and C(Acm) KLLKTFLSKWIC(Acm)-amide, where Acm is acetamidomethyl group, showed antibacterial activity but did not possess hemolytic activity unlike SPFK. Introduction of an S-S bridge resulted in enhanced hemolytic activity compared with SPFK. The hemolytic activity was particularly pronounced in the cyclic peptide CKLLKTFLSKWIC-amide. Circular dichroism studies indicate that the cyclic peptides tend to adopt distorted helical structures. The cyclic peptides also have a greater affinity for lipid vesicles, which could be the reason for the effective perturbation of the erythrocyte membrane.

Amino Acid Sequence↗
PubMed1999

Addition and omission analogs of the 13-residue antibacterial and hemolytic peptide PKLLKTFLSKWIG: structural preferences, model membrane binding and biological activities.

The consequences of selective addition or deletion of polar amino acids in a 13-residue antibacterial peptide PKLLKTFLSKWIG on structure, membrane binding and biological activities have been investigated. The variants generated are (a) S and T residues replaced by K, (b) S and T residues deleted individually and together, (c) introduction of two additional K and (d) deletion of L and L with T. In the aqueous environment all the peptides were unordered. In trifluoroethanol, the spectra of peptides belonging to groups (a-c) suggest distorted helical conformation. Peptides in group (d) appear to adopt beta-sheet conformation. The peptides bind to zwitterionic and negatively charged lipid vesicles, although to different extents. With the exception of peptides in group (d), all the other peptides exhibited comparable antibacterial activity against Escherichia coli and Staphylococcus aureus. However, the changes made in the peptides in groups (a-c) resulted in reduction of hemolytic activity compared to the parent peptide. Extent of binding to lipid vesicles composed of phosphatidylcholine and cholesterol appears to correlate with hemolytic activity. It appears that polar and charged residues play a major role in modulating the biological activities of the 13-residue peptide PKLLKTFLSKWIG. The 11-residue peptide-like PKLLKFLKWIG has selective antibacterial activity. Thus, by judicious engineering it should be possible to generate short peptides with selective antibacterial activity.

Animals↗
PubMed1999

Role of the EGF receptor pathway in growth and patterning of the Drosophila wing through the regulation of vestigial.

Growth and patterning of the Drosophila wing disc depends on the coordinated expression of the key regulatory gene vestigial both in the Dorsal-Ventral (D/V) boundary cells and in the wing pouch. We propose that a short-range signal originating from the core of the D/V boundary cells is responsible for activating EGFR in a zone of organizing cells on the edges of the D/V boundary. Using loss-of-function mutations and ectopic expression studies, we show that EGFR signaling is essential for vestigial transcription in these cells and for making them competent to undergo subsequent vestigial-mediated proliferation within the wing pouch.

Animals↗
PubMed1999

Conformations of hydrophobic peptides in trifluoroethanol, water and in solid state: a circular dichroism and Fourier Transform Infrared study.

The conformations of peptides corresponding to KLLIALVLCFLPLAALG have been examined in trifluoroethanol (TFE), aqueous medium by circular dichroism spectroscopy and in the solid state by Fourier Transform Infra Red Spectroscopy (FTIR). The 17-residue parent peptide and peptides corresponding to shorter segments LVLCFLPLAALG and CFLPLAALG showed preference for helical conformation in TFE. Even the shorter hydrophobic peptides corresponding to KLLIA and LVL showed propensity for beta-turn conformations in TFE. However, peptides corresponding to the relatively polar segment FLPLAALG were unordered in TFE. In water, peptides that showed ordered conformation in TFE preferred beta-conformation. In solid-state, FTIR spectra indicated that the hydrophobic peptides adopt beta-structures with extensive hydrogen bonded network in the solid-state. The hydrophobic core segment thus appears to dictate the conformational propensity of the peptide.

Amino Acid Sequence↗
PubMed1998

Structural features of helical aggregates of antibacterial peptides via simulated annealing and molecular modeling.

A 27-residue stretch of amino acids encompassing two putative 13-residue amphiphilic helical segments is an important determinant of activity in the 47-residue antibacterial peptide bovine seminalplasmin. Synthetic peptides corresponding to the 27-residue stretch (P27) SLSRYAKLANRLANPKLLETFLSKWIG as well as the 13-residue segments PKLLETFLSKWIG (SPF),exhibit antimicrobial activity. An analog of SPF where E has been replaced by K(SPFK) showed improved antimicrobial properties as compared to SPF. The peptides have the ability to bind and permeabilize membranes. We have modeled helical bundles of P27 and the two 13-residue peptides SPF and SPFK using simulated annealing via molecular dynamics. Octameric but not hexameric aggregates of P27 can form channels which would allow the passage of ions. In the case of 13-residue peptides, aggregates formed by 6 monomers can conceivably form ion conducting channels. Since the ability to form channels which would allow the passage of ions across the membranes is an important determinant of the biological activities of these peptides, knowledge of the pore forming structures should help in the design of analogs with improved activities.

Amino Acid Sequence↗
PubMed1998

Insight into the environment of tryptophan in a hydrophobic model peptide upon aggregation and interaction with lipid vesicles: a steady state and time resolved fluorescence study.

Fluorescence spectroscopy is extensively used to monitor binding of peptides to lipid vesicles as well as orientation in the lipid bilayer. In steady-state fluorescence, the emission characteristics of intrinsic and extrinsic fluorophores, which are sensitive to environment are monitored. Life time measurements should yield useful information about the location and flexibility of fluorophores, as these factors have a significant effect on the life times. However, studies on protein structure and dynamics indicate that interpretation of life-time data is complicated (Beechem. J.M. and Brand, L. (1985) Annu. Rev. Biochem. 54, 43-71). Hence, simple well-defined systems should help in interpretation of life time data, especially in lipid-peptide interactions. In order to examine how fluorescence characteristics of tryptophan and anthroyl group would reflect molecular details of peptide aggregation and lipid-peptide interaction, studies have been carried out on a model hydrophobic peptide and its fatty acylated derivative. Steady-state fluorescence measurements suggest that: (1) the fatty acyl chain attached to an amino acid associates with the peptide chain in aqueous environment. (2) In the lipid bilayer, the acyl chain is oriented perpendicular to the lipid bilayer surface with the peptide chain at an angle to it. Analysis of the fluorescence decay of tryptophan indicates the predominance of a very short life-time component (<1ns) in aqueous environment and lipid-vesicles. Since the preexponentials were not negative, it is unlikely that this is due to extensive deactivation process. We attribute the observation of the low life time component to predominance of one rotamer around (C alpha-C beta)bond of tryptophan in aqueous and lipid environments. Our investigations suggest that fluorescence life time data need to be complemented with steady state measurements to get an insight into details of lipid-peptide interaction.

Amino Acid Sequence↗
PubMed1997

strawberry notch encodes a conserved nuclear protein that functions downstream of Notch and regulates gene expression along the developing wing margin of Drosophila.

The dorsal/ventral (D/V) boundary functions as an organizer in the growth and patterning of the Drosophila wing disc and gives rise to the wing margin in the adult fly. Here we show that strawberry notch (sno) is a downstream component of the Notch signaling pathway and is important for the specification of this organizer. sno encodes a novel nuclear protein conserved in C. elegans, mouse, and humans. Mutations in wing margin genes interact dominantly with sno and loss of sno function results in loss of expression of wingless, vestigial, cut, and E(spl)-m8 at the D/V boundary. In regulating these genes, sno functions in close cooperation with Suppressor of Hairless and Hairless. Finally, sno has no role in lateral inhibition suggesting that it may contribute to the specificity between lateral and inductive Notch signaling pathways.

Amino Acid Sequence↗
PubMed1997

Identification of the region that plays an important role in determining antibacterial activity of bovine seminalplasmin.

Seminalplasmin (SPLN) is a 47-residue protein isolated from bovine seminal plasma having potent antimicrobial activity against a broad spectrum of microorganisms. SPLN, also known as caltrin, acts as a calcium transport regulator in bovine sperms. Analysis of the sequence of SPLN reveals a 27-residue stretch with the sequence SLSRYAKLANRLANPKLLETFLSKWIG more hydrophobic than the rest of the protein. It is demonstrated that a synthetic peptide corresponding to this 27-residue segment has antimicrobial activity comparable to that of SPLN. It does not exhibit hemolytic activity at concentrations where antibacterial activity is observed. Since P27 can be conveniently obtained in large amounts by chemical synthesis, it could serve not only as a starting compound to obtain peptides with improved antibacterial activity but also to understand the role of SPLN in reproductive physiology.

Amino Acid Sequence↗
PubMed1997

Solution conformations of peptides representing the sequence of the toxin pardaxin and analogues in trifluoroethanol-water mixtures: analysis of CD spectra.

The cytolytic activities and conformational properties of pardaxin (GFFALIPKIISSPLFKTLLSAVGSALSSSGEQE), a 33-residue linear peptide that exhibits unusual shark repellent and cytolytic activities, and its analogues have been examined in aqueous environment and trifluoroethanol (TFE) using CD spectroscopy. A peptide corresponding to the 1-26 segment and an analogue where P7 has been changed to A show greater hemolytic activity than pardaxin. While the peptide corresponding to the N-terminal 18-residue segment does not exhibit hemolytic activity, its analogue where P7 is replaced by A is hemolytic. The secondary structural propensities of the peptides were inferred by deconvolution of the experimental spectra into pure components. Pardaxin, its variant where proline at position 7 was replaced by alanine, and shorter peptides corresponding to N-terminal segments exist in multiple conformations in aqueous medium that are comprised of beta-turn, beta-sheet, and distorted helical structures. With increasing proportions of TFE, while helical conformation predominates in all the peptides, both distorted and the regular alpha-helices appear to be populated. Analysis of CD spectra by deconvolution methods appears to be a powerful tool for delineating multiple conformations in peptides, especially membrane-active peptides that encounter media of different polarity ranging from aqueous environment to one of low dielectric constant in the hydrophobic interior of membranes. Our study provides further insights into the structural requirements for the biological activity of pardaxin and related peptides.

Amino Acid Sequence↗
PubMed1997

Antimicrobial and hemolytic activities of crabrolin, a 13-residue peptide from the venom of the European hornet, Vespa crabro, and its analogs.

The venom of insects like bee, hornet and wasp contain peptides that exhibit potent biological activities. Many of these peptides are composed of 13-26 residues and are thus accessible through chemical synthesis as well as amenable to studies directed toward structure-function correlations. In this report, we describe antibacterial and hemolytic activities of crabrolin: FLPLILRKIVTAL-NH2, a 13-residue-peptide present in the venom of the hornet Vespa crabro and related peptides. The analogs were chosen so that the role of proline and positively charged amino acids in modulating biological activities could be evaluated. Our results indicate that, although helical conformation is necessary for hemolytic activity, it is not a prerequisite for antibacterial activity. Appropriately positioned, charged and hydrophobic residues and overall hydrophobicity appear to determine antibacterial activity. The discovery of a large number of host-defense peptides in a variety of species in recent years offers a large repertoire of molecules that can be "engineered" based on biophysical principles to yield molecules with specific activities.

Animals↗
PubMed1996

Requirements for antibacterial and hemolytic activities in the bovine neutrophil derived 13-residue peptide indolicidin.

The antimicrobial and hemolytic activities of the 13-residue peptide indolicidin (ILPWKWPWWPWRR-NH2), present in bovine neutrophils, and its analogs have been determined with a view to gaining insight into the structural roles of tryptophan and proline. Peptides where proline was replaced by alanine and tryptophan by phenylalanine showed antibacterial activities comparable to that of indolicidin. The peptides do not exhibit a strong propensity to occur in either helical or beta-sheet conformation. The peptides also do not appear to exert their activity by permeabilizing the bacterial plasma membrane unlike other endogenous antibacterial peptides. The presence of tryptophan appears to be essential for hemolytic activity as the phenylalanine analog does not exhibit any hemolytic activity.

Animals↗