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Biomedical subjects

P Balaram

Publications and source records attributed to P Balaram.

At least 127 records · Page 7Linked to original sources
PubMed1994

Differential expression of cytokeratin proteins during tumour progression in oral mucosa.

The expression pattern of cytokeratin filaments in epithelia has been shown to be dependent on their type and grade of differentiation. The type of expression of cytokeratin in a cell may also be altered during carcinogenesis or other pathological conditions. The present study examined the alterations in expression of various cytokeratin types during different stages of tumour progression in the oral mucosa. Six monoclonal anti-cytokeratin antibodies were used for the study. Conspicuous staining differences with these antibodies were evident between normal keratinizing and non-keratinizing mucosa. These differences can be correlated to the differentiation pattern of the normal mucosa types. Antibodies specific to cytokeratin types 10/11, 19 and 14 showed significant correlation with stage of tumour progression. In addition cytokeratin type 18 also showed prominent differences in expression between different stages of tumour progression. These alterations in cytokeratin expression suggest that the terminal differentiation pathway of keratinocytes is disturbed during oral carcinogenesis. The results of the present study also emphasize the potential of using cytokeratin filaments as markers in the biological staging of oral premalignant and malignant lesions.

Antibodies, Monoclonal↗
PubMed1994

Peptide-lanthanide interactions. Crystal structure of a europium(III)-triglycine complex.

Crystals of Eu-(Gly-Gly-Gly).(H2O)5.(ClO4)3 are triclinic, spacegroup P1 with a = 9.123 (2), b = 11.185 (5), c = 11.426 (2) A; alpha = 90.79 (2), beta = 98.08 (1), gamma = 98.57 (2) degrees; Z = 2. The europium cation is surrounded by four oxygens from three different peptide units and four oxygens from water molecules. The geometry around the metal is a distorted bi-capped trigonal prism. The peptide backbone conformation in this complex is compared with those in the free peptide and in various metal complexes. Considerable differences are observed between Eu(III) and Ca(II) complexes of triglycine.

Amino Acid Sequence↗
PubMed1993

Termination of right handed helices in proteins by residues in left handed helical conformations.

An analysis of 636 helical segments, ranging in length from 4 to 32 residues, from 123 independent protein crystal structures reveals that helix termination by residues in left handed (alpha 1) helical conformations is a common occurrence. Gly and Asn residues are the most frequent alpha L helix terminators, with the former having a very high propensity to adopt such conformations. The alpha R-alpha R-alpha R-alpha L segment at the C termini of protein helices often possesses a 6--> 1 (pi-type) hydrogen bond between the CO of residue i and the NH of residue i + 5 with residue i + 4 occurring in the alpha L conformation. A stereochemical analysis of 216 examples shows that in 62 cases the 6-->1 hydrogen bond is absent. The present analysis provides a quantitative measure of the propensity of the 20 amino acids to adopt alpha L helix terminating conformations.

Hydrogen Bonding↗
PubMed1993

Accommodation of a D-Phe residue into a right-handed 3(10)-helix: structure of Boc-D-Phe-(Aib)4-Gly-L-Leu-(Aib)2-OMe, an analogue of the amino terminal segment of antiamoebins and emerimicins.

The crystal structure of the nonapeptide Boc-D-Phe-Aib-Aib-Aib-Aib-Gly-Leu-Aib-Aib-OMe (I), which is an analogue of the N-terminal sequence of antiamoebins and emerimicins, establishes a completely 3(10)-helical conformation with seven successive intramolecular 4-->1 hydrogen bonds. The average, phi,psi values for residues 1-8 are -59 degrees and -32 degrees, respectively. Crystal parameters are C47H77N9O12, space group P1, a = 10.636 (4) A, b = 11.239 (4) A, c = 12.227 (6) A, alpha = 101.17 (4) degrees, beta = 97.22 (4) degrees, gamma = 89.80 (3) degrees, Z = 1, R = 5.95% for 3018 data with magnitude of F0 > 3 sigma(F), resolution 0.93 A. The use of the torsion angle kappa = C(i-1)N(i)C alpha(i)C beta(i), where kappa = 68 degrees for D-Phe and kappa = 164 degrees for L-Leu, confirms the opposite configurations of these residues. The phi,psi values of -62 degrees and -32 degrees at D-Phe are unusual, since this region is characteristic of residues with L configurations. Peptide I possesses only two chiral residues of opposing configuration. The observed right-handed 3(10)-helical structure suggests that helix sense has probably been determined by the stereochemical preferences of the Leu residue.

Amino Acid Sequence↗
PubMed1993

Unfolding of an alpha-helix in peptide crystals by solvation: conformational fragility in a heptapeptide.

The structure of the peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe has been determined in crystals obtained from a dimethylsulfoxide-isopropanol mixture. Crystal parameters are as follows: C38H69N7O10.H2O.2C3H7OH, space group P2(1), a = 10.350 (2) A b = 26.084 (4) A, c = 10.395 (2) A, beta = 96.87 (12), Z = 2, R = 8.7% for 2686 reflections observed > 3.0 sigma (F). A single 5-->1 hydrogen bond is observed at the N-terminus, while two 4-->1 hydrogen bonds characteristic of a 3(10)-helix are seen in the central segment. The C-terminus residues, Ala(6) and Leu(7) are extended, while Val(5) is considerably distorted from a helical conformation. Two isopropanol molecules make hydrogen bonds to the C-terminal segment, while a water molecule interacts with the N-terminus. The structure is in contrast to that obtained for the same peptide in crystals from methanol-water [I. L. Karle, J. L. Flippen-Anderson, K. Uma, and P. Balaram (1990) Proteins: Structure, Function and Genetics, Vol. 7, pp. 62-73] in which two independent molecules reveal an almost perfect alpha-helix and a helix penetrated by a water molecule. A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding. The fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDCl3 and (CD3)2SO. A helical conformation is supported in the apolar solvent CDCl3, whereas almost complete unfolding is observed in the strongly solvating medium (CD3)2SO.

Amino Acid Sequence↗
PubMed1993

Stereochemical constraints in peptide design: analysis of the influence of a disulfide bridge and an alpha-aminoisobutyryl residue on the conformation of a hexapeptide.

The competing effects of a disulfide bridge and an alpha-aminoisobutyryl residue (Aib) in determining the conformation of a hexapeptide have been investigated, by comparing the cyclic disulfide [sequence: see text] and the acylic peptide Boc-Cys (SBzl)-Val-Aib-Ala-Leu-Cys (SBzl)-NHMe (2). Previously published nmr and crystallographic studies [R. Kishore, S. Raghothama, and P. Balaram (1987) Biopolymers, Vol. 26, pp. 873-891; I. L. Karle, R. Kishore, S. Raghothama, & P. Balaram, (1988) Journal of the American Chemical Society Vol. 110, pp. 1958-1963] have established an antiparallel beta-hairpin structure for 1 with a central Aib-Ala beta-turn. A comparison of nmr data for 1 and 2 in chloroform and dimethylsulfoxide reveals that the acyclic peptide is conformationally labile. Evidence for a 3(10)-helical conformation in CDCl3 is obtained from sensitivity of NH chemical shifts to temperature and solvent perturbation and low JHNC alpha H values. Studies in solvent mixtures establish a conformational transition on going from CDCl3 to (CD3)2SO. The changes in NH nmr parameters, together with the observation of several interresidue C alpha i H-Ni+1H nuclear Overhauser effects support a conformation having a central beta-turn with extended arms in (CD3)2SO. A single Aib residue appears to stabilize a helix in apolar solvents, for the acyclic hexapeptide, while the disulfide bridge serves to lock the beta-hairpin conformation.

Amino Acid Sequence↗
PubMed1993

Ion channel formation by zervamicin-IIB. A molecular modelling study.

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomeric Zrv-IIB is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K+, Cl- and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are "optimized" in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.

Anti-Bacterial Agents↗
PubMed1993

Expression of lectin-specific cellular glycoconjugates during oral carcinogenesis.

The binding pattern of two lectins, concanavalin A (ConA) and peanut agglutin (PNA), in various phases of tumour progression in the oral epithelium was studied. These included non-dysplastic, dysplastic and neoplastic lesions as well as normal tissue. ConA and PNA showed intense staining in the basement membrane of all types of lesions. Little difference was observed in the staining patterns between different stages of oral carcinogenesis, either with ConA or PNA. ConA showed mild cytoplasmic and membrane staining in all types of lesions while PNA showed moderate to intense staining in both the cytoplasm and membrane of lower-layer cells in all histological groups. The present study therefore shows that these lectins have limited value in the elucidation of oral carcinogenesis and are of insignificant diagnostic value.

Carcinoma↗
PubMed1993

Ultrastructural variations and assessment of malignant transformation risk in oral leukoplakia.

Oral cancer is the most common malignancy in India, having a well defined precancerous state, leukoplakia. Various follow-up studies have shown that only 4 to 18% of oral leukoplakia lesions subsequently progress into invasive malignancy over a period of time. This study evaluates the potential of electron microscopy in the early detection of malignant changes in leukoplakia. The study revealed that of the 25 leukoplakia lesions examined, 7 showed changes akin to malignancy. Predominant ultrastructural alterations observed were reduplication and discontinuity of the basal lamina, basal cells with pleomorphic and bizarre nuclei containing perichromatin and interchromatin granules, prominent intercellular spaces and poorly formed desmosomes. Since none of these changes were evident under light microscopy the study demonstrates the value of electron microscopy in evaluating oral carcinogenesis. A long term follow-up of such patients is needed to understand the prognostic implications of these ultrastructural variation and how they can be used as a base line for better light microscopic evaluation.

Cell Transformation, Neoplastic↗
PubMed1993

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of alpha-conotoxin GI and endothelin I.

A general procedure for arriving at 3-D models of disulphide-rich polypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini, R., Srinivasan, N., Shoichet, B., Santi, D.V., Ramakrishnan, C. and Balaram, P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphide-rich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, alpha-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

Amino Acid Sequence↗
PubMed1993

Peptide mimics for structural features in proteins. Crystal structures of three heptapeptide helices with a C-terminal 6-->1 hydrogen bond.

The crystal structure determination of three heptapeptides containing alpha-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6-->1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z = 1, a = 9.903 A, b = 10.709 A, c = 11.969 A, alpha = 102.94 degrees, beta = 103.41 degrees, gamma = 92.72 degrees, R = 4.55%; (II) space group P21, Z = 2, a = 10.052 A, b = 17.653 A, c = 13.510 A, beta = 108.45 degrees, R = 4.49%; (III) space group P1, Z = 2 (two independent molecules IIIa and IIIb in the asymmetric unit), a = 10.833 A, b = 13.850 A, c = 16.928 A, alpha = 99.77 degrees, beta = 105.90 degrees, gamma = 90.64 degrees, R = 8.54%. In all cases the helices form 3(10)/alpha-helical (or 3(10)helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (hL) conformation with positive phi, psi values, resulting in 6-->1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4-->1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices proteins, with the terminal pi-type turn being formed by four residues adopting the hRhRhRhL conformation.

Amino Acid Sequence↗
PubMed1993

Immuno-pathological and immunological features of oral precancers.

Cancer of the oral cavity and oropharyngeal regions constitute about 30% of all cancers seen in India, with Trivandrum District in southern India having one of the highest incidence. Despite easy accessibility for examination and diagnosis, these tumours still cause high mortality, emphasizing the need for better methods of diagnosis and more importantly prognosis. Most oral carcinomas initially present as premalignant lesions and hence understanding their biology and behaviour is vital to the management and control of the disease. This review presents some of the clinico-pathological, immuno-pathological and immunological aspects of oral precancers.

Antibody Formation↗
PubMed1992

Analysis of the binding of polymyxin B to endotoxic lipid A and core glycolipid using a fluorescent displacement probe.

Dansylcadaverine, a cationic fluorescent probe binds to bacterial lipopolysaccharide and lipid A, and is displaced competitively by other compounds which possess affinity toward endotoxins. The binding parameters of dansylcadaverine for lipid A were determined by Scatchard analysis to be two apparently equivalent sites with apparent dissociation constants (Kd) ranging between 16 microM to 26 microM, while that obtained for core glycolipid from Salmonella minnesota Re595 yielded a Kd of 22 microM to 28 microM with three binding sites. The Kd of polymyxin B for lipid A was computed from dansylcadaverine displacement by the method of Horovitz and Levitzki (Horovitz, A., and Levitzki, A. (1987) Proc. Natl. Acad. Sci. USA 84, 6654-6658). The applicability of this method for analyzing fluorescence data was validated by comparing the Kds of melittin for lipid A obtained by direct Scatchard analysis, and by the Horovitz-Levitzki method. The displacement of dansylcadaverine from lipid A by polymyxin B was distinctly biphasic with Kds for polymyxin B-lipid A interactions corresponding to 0.4 microM and 1.5 microM, probably resulting as a consequence of lipid A being a mixture of mono- and di-phosphoryl species. This was not observed with core glycolipid, for which the Kd for polymyxin was estimated to range from 1.1 microM to 5.8 microM. The use of dansylcadaverine as a displacement probe offers a novel and convenient method of quantitating the interactions of a wide variety of substances with lipid A.

Binding, Competitive↗
PubMed1992

Differences in hydration and association of helical Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-(Val-Ala-Leu-Aib)2-OMe.xH2O in two crystalline polymorphs.

The 15-residue apolar peptide, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-(Val-Ala-Leu-Aib)2-OMe has been crystallized from 2-propanol-water (form I). The crystal parameters for I are as follows: C74H133N15O18.2H2O, space group P2(1), a = 9.185 (6) A, b = 47.410 (3) A, c = 10.325 (9) A, beta = 91.47 (2) degrees, Z = 2, R = 6.3% for 4532 reflections observed > 3 sigma (F), resolution 0.94 A. The structure is almost completely alpha-helical with eleven 5-->1 hydrogen bonds and one 4-->1 hydrogen bond near the N-terminus. The structure has been compared with a polymorph (form II) obtained from methanol-water (Karle, I. L.; Flippen-Anderson, J. L.; Uma, K.; Sukumar, M.; Balaram, P., J. Am. Chem. Soc. 1990, 112, 9350-9356). The two forms differ in the extent of hydration; form I contains two water molecules in the head-to-tail region of helical columns, while form II is more extensively solvated, with the equivalent of 7.5 water molecules. The three-dimensional packing of helices is completely parallel in I and antiparallel in II.

Amino Acid Sequence↗
PubMed1992

Zervamicins, a structurally characterised peptide model for membrane ion channels.

Voltage dependent membrane channels are formed by the zervamicins, a group of alpha-aminoisobutyric acid containing peptides. The role of polar residues like Thr, Gln and Hyp in promoting helical bundle formation is established by dramatically reduced channel lifetimes for a synthetic apolar analog. Crystal structures of Leu1-zervamicin reveal association of bent helices. Polar contacts between convex faces result in an 'hour glass' like arrangement of an aqueous channel with a central constriction. The structure suggests that gating mechanisms may involve movement of the Gln11 carboxamide group. Gln3 may play a role in modulating the size of the channel mouth.

Amino Acid Sequence↗
PubMed1992

Role of immune response in the prognosis of carcinoma of the uterine cervix: can in vitro analysis provide a better framework for more effective management?

Cancer of the uterine cervix is the single largest female malignancy in India and also remains a major problem facing oncologists in other parts of the world. While advances in radiation therapy and surgical techniques have made the treatment of cervical carcinoma impressive, limitations to successful management still remain. In fact, the 5-year survival rate, stage for stage, has not improved in the United States or world wide in the past 40 years. With an estimated half a million women developing this disease annually, this lack of improved survival poses an international unresolved health problem. Immune response has been shown to be a major factor involved in the course of the disease for this cancer. Immunologic monitoring was also shown to be of effective value in assessing the prognosis for cervical carcinoma. We studied the various immunologic abnormalities in cervical cancer, the effects of radiation therapy on immune function, prospects of an immunologic staging system, the relationship between human papillomavirus infection and the immune response, and the possibility of using in vitro immunologic assessment to provide a better framework for more effective management of cancer of the uterine cervix.

Antibody Formation↗
PubMed1992

Pathogenesis of oral submucous fibrosis. Relationship to risk factors associated with oral cancer.

Oral submucous fibrosis (OSF) is a chronic disease of the oral mucosa characterized by inflammation and a progressive fibrosis of the lamina propria and deeper connective tissues. It is a condition predominantly seen among people of Indian origin, and an epidemiologic survey done a decade ago showed no less than 250,000 cases in India, a figure that must have increased sharply. OSF is a condition with a high risk of malignant transformation; to date, no conclusive etiologic agent has been identified, although plenty of data have been generated on various aspects of the disease. These include genetic, carcinogenic, immunologic, viral, nutritional, and autoimmune possibilities, all of which also have been implicated in the development of oral cancer. This article reviews existing evidence on the pathogenesis of OSF and its relation to oral cancer and suggests a possible multifactorial model to explain the disease process.

Humans↗