Biomedical subjects

P Balaram

Publications and source records attributed to P Balaram.

At least 109 records · Page 6Linked to original sources

PubMed1995

Contrasting solution conformations of peptides containing alpha,alpha-dialkylated residues with linear and cyclic side chains.

The conformational properties of alpha,alpha-dialkylated amino acid residues possessing acyclic (diethylglycine, Deg; di-n-propylglycine, Dpg; di-n-butylglycine, Dbg) and cyclic (1-aminocycloalkane-1-carboxylic acid, Acnc) side chains have been compared in solution. The five peptides studied by nmr and CD spectroscopy are Boc-Ala-Xxx-Ala-OMe, where Xxx = Deg (I), Dpg (II), Dbg (III), Ac6c (IV), and Ac7c (V). Delineation of solvent-shielded NH groups have been achieved by solvent and temperature dependence of NH chemical shifts in CDCl3 and (CD3)2SO and by paramagnetic radical induced line broadening in peptide III. In the Dxg peptides the order of solvent exposure of NH groups is Ala(1) > Ala(3) > Dxg(2), whereas in the Acnc peptides the order of solvent exposure of NH groups is Ala(1) > Acnc(2) > Ala(3). The nmr results suggest that Acnc peptides adopt folded beta-turn conformations with Ala(1) and Acnc(2) occupying i + 1 and i + 2 positions. In contrast, the Dxg peptides favor extended C5 conformations. The conformational differences in the two series are clearly borne out in CD studies. The solution conformations of peptides I-III are distinctly different from the beta-turn structure observed in crystals. Low temperature nmr spectra recorded immediately after dissolution of crystals of peptide II provide evidence for a structural transition. Introduction of an additional hydrogen-bonding function in Boc-Ala-Dpg-Ala-NHMe (VI) results in a stabilization of a consecutive beta-turn or incipient 3(10)-helix in solution.

Alkylation↗

PubMed1995

A nonhelical, multiple beta-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central alpha-aminoisobutyric acid residue.

The conformational properties of the protected seven-residue C-terminal fragment of the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl3 and (CD3)2SO by 1H-nmr. Evidence for a multiple beta-turn conformation [type I' at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I' at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline states. A structural transition to a frayed right-handed helix is observed in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides.

Amino Acid Sequence↗

PubMed1995

Stereochemical analysis of the antigenic tip of the V3 loop peptide of HIV-1 gp120.

A novel multiple turn conformation has been observed for a segment GPGRAFY in the crystal structure of a complex of HIV-1 gp120 V3 loop peptide with the Fab fragment of a neutralizing antibody [Ghiara et al. (1994) Science 264, 82-85]. A structural motif has been defined for the peptide segment, employing idealized backbone conformations characterized by ranges of virtual C alpha torsion angles and bond angles. A search of 122 high-resolution protein crystal structures has permitted identification of 24 examples of similar structural motifs. Two major conformational families have been identified, which differ primarily in the conformation at residue 3. The observed conformation at residue 3 in family 1 is left-handed helical (alpha L) and that in family 2 is right-handed helical (alpha R). Of the 10 examples in family 1, 9 examples have Gly residues at position 3. Of the 12 examples in family 2, 7 examples have Asn/Asp at position 3. Computer modeling of the V3 loop tip sequence using the two backbone conformational families as starting points leads to minimum-energy conformations in which antigenically important side-chains occupy similar spatial arrangements. This stereochemical analysis of the V3 loop tip sequence suggests a rational basis for the design of synthetic analog peptides for use as viral antagonists or synthetic antigens.

Amino Acid Sequence↗

PubMed1995

Variation of human papillomavirus type 6 (HPV-6) and HPV-11 genomes sampled throughout the world.

We examined the genomic diversity of human papillomavirus type 6 (HPV-6) and HPV-11 isolates from different parts of the world by comparing the nucleotide sequences of part of the long control region of three reference clones and 62 HPV-6 and 40 HPV-11 isolates from Africa, Europe, Asia, and North and South America. The genomic sequence of the HPV-6b reference type had to be amended by inclusion of a 94-bp segment, which is also present with minor differences in HPV-6a. Aside from two small inserts typical of all variants related to HPV-6a and three inserts found in HPV-11 variants, no major alterations to the size of the long control regions of these viruses were observed. This corrects the previous impression that these two HPV types are highly polymorphic. Altogether, 19 HPV-6 and 10 HPV-11 variant genomes could be distinguished, and most of the differences were due to point substitutions. The variants of either type were continuously connected in phylogenetic trees rather than clustered separately into subtype groups. Thirteen mutations, namely, the two HPV-6a inserts and 11 substitutions in HPV-6 or HPV-11 variants, reduced the dissimilarity between the types, but they bridged only a small fraction of the genetic distance between the two types. Genomes more obviously intermediate between HPV-6 and HPV-11 were not found and probably do not exist any more. A single HPV-11 variant was found in Africa, but otherwise, no significant correlations of HPV-6 or HPV-11 variants with geography or ethnicity of the patient cohort were found. Functional analysis of diverse enhancer variants showed activities that differed two-to threefold, and it must be considered that transcriptional differences may alter the biology or pathology of these viruses. Similar variants were found in lesions from anatomically different sites and in both benign and malignant lesions.

Base Sequence↗

PubMed1994

Incorporation of a potentially helix breaking D-Phe-Pro sequence into the center of a right handed 16 residue peptide helix.

Non protein amino acids with strong secondary structure preferences are potentially useful in peptide design. alpha-Aminoisobutyric acid (Aib) is a powerful 'stereochemical director' of polypeptide chain folding, stabilizing helical conformations in diverse oligopeptide sequences. In an approach to the de novo design of alpha,alpha motifs, the 16 residue peptides Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Xxx-Pro-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (Xxx = D-Phe 1; Xxx = L-Phe 2) have been spectroscopically studied in solution. Analysis of nuclear Overhauser effects, delineation of solvent shielded NH groups and circular dichroism spectra establish helical conformations in both the peptides. Despite the presence of a potentially helix breaking, central, (D)Phe-(L)Pro segment, peptide 1 is forced into a continuous helical fold presumably as a consequence of the overriding stereochemical dominance of the Aib residues.

Amino Acid Sequence↗

PubMed1994

Interaction of cationic amphiphilic drugs with lipid A: implications for development of endotoxin antagonists.

This report presents evidence for the interactions of several classes of cationic amphiphilic drugs including the phenothiazines, aminoquinolines, biguanides, and aromatic diamidines, with lipid A, the endotoxic principle of lipopolysaccharides. The interactions of the drugs were quantitatively assessed by fluorescence methods. The affinities of the drugs for lipid A parallel their endotoxin-antagonistic effects in the Limulus gelation assay. Dicationic compounds bind lipid A with greater affinity; the affinity of such molecules increases exponentially as a function of the distance between the basic moieties. The bis-amidine drug--pentamidine--examined in greater detail, binds lipid A with high affinity (apparent Kd: 0.12 microM), and LPS, probably due to simultaneous interactions of the terminal amidine groups with the anionic phosphates on lipid A. The sequestration of endotoxin by pentamidine reduces its propensity to bind to cells, and the complex exhibits attenuated toxicity in biological assays. These results have implications in the development of therapeutic strategies against endotoxin-related disease states.

Aminoquinolines↗

PubMed1994

Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion.

Thymidylate synthase (TS) from Lactobacillus casei has a 50 amino acid insert (residues 90-139) in the small domain that is found in only one other TS. A deletion mutant was constructed which lacked the entire insert, thereby reducing the small domain to the size found in Escherichia coli TS. This mutant did not catalyze the formation of dTMP. From the crystal structure of L. casei TS, we surmised that the loss of activity might have resulted from the exposure of residues of helices C and D, which were previously buried by the insert. To restore the local structure of helices C and D in the deletion mutants, we replaced several residues in this region by the corresponding residues found in E. coli TS. The mutant whose sequence most closely resembled that of E. coli TS carried six mutations and possessed partially restored TS activity. The mutant which had all those mutations except F87D did not catalyze any dTMP formation. The crucial role of F87D was proven in a deletion mutant which had only this change and showed greatly increased activity. All of the mutants catalyzed the debromination of BrdUMP in the absence of cofactor about as well as wild type TS. The kinetic parameters for dTMP formation of the active mutants show that the deletion has its major effect on kcat and binding of cofactor CH2H4folate, with less effect on binding of the substrate dUMP. Removal of residues 90-139 is believed to disorder helices C and D, which in turn decreases cofactor binding and catalysis.

Amino Acid Sequence↗

PubMed1994

Coexistence of folded and extended conformations of a tripeptide containing alpha, alpha -di-n-propylglycine in crystals.

The crystal structure of the tripeptide Boc-Leu-Dpg-Val-OMe (Dpg, alpha, alpha -di-n-propylglycine) reveals the coexistence of two distinct backbone conformations. In molecule A the Dpg residue adopts a fully extended conformation (phi = 76.0 degrees, psi = 180.0 degrees) while in molecule B a left handed helical conformation (phi = 62.8 degrees, psi = 39.6 degrees) is observed. Molecule B adopts a folded structure corresponding to a highly distorted Type II beta-turn conformation, which lacks an intramolecular 4 -> 1 hydrogen bond. In contrast, molecule A has an open, extended conformation. The results demonstrate that both fully extended and helical conformations are energetically accessible to the Dpg residue.

Models, Molecular↗

PubMed1994

Thermal stabilization of thymidylate synthase by engineering two disulfide bridges across the dimer interface.

Thermal inactivation of oligomeric enzymes is most often irreversible and is frequently accompanied by precipitation. We have engineered two symmetry related disulfide bridges (155-188' and 188-155') across the subunit interface of Lactobacillus casei thymidylate synthase, at sites chosen on the basis of an algorithm for the introduction of stereochemically unstrained bridges into proteins. In this communication, we demonstrate a remarkable enhancement in the thermal stability of the covalently cross-linked double disulfide containing dimeric enzyme. The mutant enzyme remains soluble and retains secondary structure even at 90 degrees C, in contrast to the wild-type enzyme which precipitates at 52 degrees C. Furthermore, the mutant enzyme has a temperature optimum of 55 degrees C and possesses appreciable enzymatic activity at 65 degrees C. Cooling restores complete activity, in the mutant protein, demonstrating reversible thermal unfolding. The results suggest that inter-subunit crosslinks can impart appreciable thermal stability in multimeric enzymes.

Amino Acid Sequence↗

PubMed1994

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage.

The membrane channel-forming polypeptide, Leu1-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile5-Thr-Aib-Leu-Aib-Hyp10-Gln-Aib-Hyp-Aib-P ro15-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximately 47 degrees. The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp (10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximately 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH2O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337(2) A, b = 28.387(7) A, c = 39.864(11) A, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma (F), resolution = 1.2 A.

Amino Acid Sequence↗

PubMed1994

Facile transition between 3(10)- and alpha-helix: structures of 8-, 9-, and 10-residue peptides containing the -(Leu-Aib-Ala)2-Phe-Aib- fragment.

A structural transition from a 3(10)-helix to an alpha-helix has been characterized at high resolution for an octapeptide segment located in 3 different sequences. Three synthetic peptides, decapeptide (A) Boc-Aib-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, nonapeptide (B) Boc-Trp-(Leu-Aib-Ala)2-Phe-Aib-OMe, and octapeptide (C) Boc-(Leu-Aib-Ala)2-Phe-Aib-OMe, are completely helical in their respective crystals. At 0.9 A resolution, R factors for A, B, and C are 8.3%, 5.4%, and 7.3%, respectively. The octapeptide and nonapeptide form ideal 3(10)-helices with average torsional angles phi(N-C alpha) and psi(C alpha-C') of -57 degrees, -26 degrees C and -60 degrees, -27 degrees for B. The 10-residue peptide (A) begins as a 3(10)-helix and abruptly changes to an alpha-helix at carbonyl O(3), which is the acceptor for both a 4-->1 hydrogen bond with N(6)H and a 5-->1 hydrogen with N(7)H, even though the last 8 residues have the same sequence in all 3 peptides. The average phi, psi angles in the decapeptide are -58 degrees, -28 degrees for residues 1-3 and -63 degrees, -41 degrees for residues 4-10. The packing of helices in the crystals does not provide any obvious reason for the transition in helix type. Fourier transform infrared studies in the solid state also provide evidence for a 3(10)- to alpha-helix transition with the amide I band appearing at 1,656-1,657 cm-1 in the 9- and 10-residue peptides, whereas in shorter sequences the band is observed at 1,667 cm-1.

Amino Acid Sequence↗

PubMed1994

Ultrastructure of oral squamous cell carcinoma: a comparative analysis of different histological types.

Twenty-five oral carcinomas and five normal oral epithelial specimens were studied using light and electron microscopy. All histological types (well differentiated squamous cell carcinoma, moderately differentiated squamous cell carcinoma, poorly differentiated squamous cell carcinoma, verrucous carcinoma and spindle cell carcinoma) were seen in the study sample. In addition, 1 case of carcinoma in situ was also present. The normal oral epithelium consisted of three keratinising types (gingiva) and two non-keratinising types (buccal mucosa). The ultrastructural features of oral carcinomas showed good correlation with the features seen in light microscopy. The differentiation status of the lesions showed a relationship with cell and nuclear size, tonofilament and keratin content as well as few other cellular abnormalities. It was also observed that the fine details revealed by electron microscopy were often a means of explaining the characteristic histopathological features of oral carcinoma.

Biopsy↗

PubMed1994

CD2 related immunoregulation in oral cancer.

Sera from 93 patients with carcinoma of the buccal mucosa were analysed for its regulatory effect on CD2 antigen expression using anti CD2 monoclonal antibodies and sheep erythrocyte rosetting assay. The sera from 55.5% of the patients showed an inhibitory effect (blocker sera) while sera from 44.5% showed an enhancing effect (enhancer sera) on the CD2 antigen expression. An interesting feature observed was the dominance of enhancer sera in the early stages of the cancer, well differentiated squamous cell carcinoma and verrucous carcinoma. The regulatory effect of the sera had no correlation to the concentration of circulating immune complexes (CIC), ferritin, and serum immunoglobulins on an individual basis. Taken as a whole, the concentration of CIC was higher in the enhancer sera while the concentration of IgG and IgM were higher in the blocker sera. The dominance of enhancer sera in groups with better prognosis in clinical practice suggest a correlation with the presence of serum enhancing factors to a good prognosis. The correlation of regulatory status to the prognosis of the patient is examined as the second phase of the study.

Animals↗

PubMed1994

Alterations in expression of basement membrane proteins during tumour progression in oral mucosa.

Expression of three basement membrane proteins--collagen IV, laminin and fibronectin--was studied in normal, hyperplastic, dysplastic and neoplastic conditions of the oral mucosa using immunohistochemistry. Collagen IV and laminin exhibited similar staining patterns, while fibronectin showed a different pattern of expression. The expression of collagen IV and laminin also demonstrated an inverse correlation between staining intensity, thickness and basement membrane continuity in various stages of tumour progression. In contrast to the continuous and intense staining of basement membrane in normal oral mucosa with collagen IV and laminin antibodies, severe dysplasia and carcinoma exhibited discontinuous, thin and weakly stained basement membrane. The expression of fibronectin showed a direct correlation with extent of tumour progression. In normal mucosa, expression of fibronectin was almost absent, whereas in carcinoma intense expression of fibronectin was evident in the basement membrane and basal cells. These results emphasize the value of basement membrane proteins as biological markers for assessing oral carcinogenesis.

Antibodies, Monoclonal↗

PubMed1994

Hydration and distortion of peptide helices in crystals. Alpha-helical structure of a dodecapeptide, Boc-(Ala-Leu-Aib)4-OMe.

The dodecapeptide Boc-(Ala-Leu-Aib)4-OMe crystallized with two independent helical molecules in a triclinic cell. The two molecules are very similar in conformation, with a 3(10)-helix turn at the N-terminus followed by an alpha-helix, except for an elongated N(7)...O(3) distance in both molecules. All the helices in the crystal pack in a parallel motif. Eleven water sites have been found in the head-to-tail region between the apolar helices that participate in peptide-water hydrogen bonds and a network of water-water hydrogen bonds. The crystal parameters are as follows: 2(C58H104N12O15)+ca. 10H2O, space group P1 with a = 12.946(2), b = 17.321(3), c = 20.465(4) A, alpha = 103.12(2), beta = 105.63(2), gamma = 107.50(2) degrees, Z = 2, R = 10.9% for 5152 data observed > 3 sigma (F), resolution 1.0 A. In contrast to the shorter sequences [Karle et al. (1988) Proc. Natl. Acad. Sci. USA 85, 299-303] and Boc-(Ala-Leu-Aib)2-OMe [Karle et al. (1989) Biopolymers 28, 773-781], no insertion of a water molecule into the helix is observed. However, the elongated N---O distance between Ala7 NH and Aib3 CO in both molecules (molecule A, 3.40 A; molecule B, 3.42 A) is indicative of an incipient break in the helices.

Amino Acid Sequence↗

PubMed1994

Conformational characteristics of asparaginyl residues in proteins.

Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed alpha-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi, psi) regions of left-handed alpha-helix right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha L, which seems to be characteristic of non-glycyl residues at that position. In the liners connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha L or alpha R conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein.

Asparagine↗

PubMed1994

Alterations in expression of terminal differentiation markers of keratinocytes during oral carcinogenesis.

Expression of cytoskeletal proteins has been shown to be dependent on the differentiation status of the tissue. In the present study, expression of two cytoskeletal proteins normally present in terminally differentiated keratinocytes, namely cytokeratin types 10/11 and involucrin, were studied in different stages of tumour progression in the oral mucosa. Results showed that cytokeratins 10/11 and involucrin strongly correlated with the differentiation status of cells. High expression was observed in non-dysplastic hyperplastic epithelium as compared to normal, dysplastic and neoplastic epithelium. In addition, various grades of dysplasia showed an inverse correlation with expression of these proteins. Statistical analysis of the results also showed a negative correlation between the differentiation of upper spinal cells and the stage of tumour progression. It therefore appears that the proteins studied may be useful as markers for epithelial carcinogenesis.

Biomarkers, Tumor↗

PubMed1994

Co-expression of ras p21 and epidermal growth factor receptor during various stages of tumour progression in oral mucosa.

Ras p21 and epidermal growth factor receptor (EGFR) have commonly been implicated in a variety of malignancies. The present study immunohistochemically analysed the relationship between the expression of ras p21 and EGFR in normal, premalignant and malignant lesions of the oral mucosa. Except for normal mucosa, all other lesions showed a more or less similar expression pattern of both ras p21 and EGFR. It was also observed that the expression of both proteins was mostly confined to the basal or basaloid cells of the leucoplakia and carcinoma lesions, respectively. Normal keratinizing type mucosa showed expression of ras p21 and EGFR in the basal and lower spinal cells. However, in non-keratinizing mucosa the expression of ras p21 was totally negative while EGFR was restricted to the basal cells. Statistical analysis revealed a good correlation between the expression of ras p21 and EGFR with the various histological stages of tumour progression. The presence of these proteins in immature dividing cells of premalignant and malignant lesions thus emphasizes their relationship with cell proliferation.

ErbB Receptors↗