Biomedical subjects

P Balaram

Publications and source records attributed to P Balaram.

At least 163 records · Page 9Linked to original sources

PubMed1990

Conformations of disulfide bridges in proteins.

The conformational characteristics of disulfide bridges in proteins have been analyzed using a dataset of 22 protein structures, available at a resolution of less than or equal to 2.0 A, containing a total of 72 disulfide crosslinks. The parameters used in the analysis include (phi, psi) values at Cys residues, bridge dihedral angles chi ss, chi i1, chi j1, chi i2, and chi j2, the distances C alpha i-C alpha j and C beta i-C beta j between the C alpha and C beta atoms of Cys(i) and Cys(j). Eight families of bridge conformations with three or more occurrences have been identified on the basis of these stereochemical parameters. The most populated family corresponds to the "left handed spiral" identified earlier by Richardson [1981) Adv. Protein Chem. 34, 167-330). Disulfide bridging across antiparallel extended strands is observed in alpha-lytic protease, crambin, and beta-trypsin and this structure is shown to be very similar to those obtained in small cystine peptides. Solvent accessible surface area calculations show that the overwhelming majority of disulfide bridges are inaccessible to solvent.

Cystine↗

PubMed1990

Clinical and prognostic significance of concanavalin-A-induced suppressor cell activity in malignant cervical neoplasia.

Peripheral blood lymphocytes from patients with different stages of cancer of the uterine cervix were analysed for concanavalin-A-induced suppressor cell activity. All cancer patients had high levels of suppressor activity, the increase corresponding to tumour load. Radiotherapy resulted in further increase of suppressor activity. About six months after radiotherapy, patients who remained disease free returned to pretreatment levels of suppressor cell activity and later showed even lewer levels of suppression. On the other hand, patients who developed recurrent disease maintained sustained high levels of suppression and for all stages they always had higher suppressor activity than the patients who remained disease free in the corresponding stage. These results stress the importance of a possible deranged immune system in these patients and also shows the clinical and prognostic significance of the assay.

Female↗

PubMed1990

Radiation associated eosinophilia and monocytosis in carcinoma of the uterine cervix: a simple reliable clinical and prognostic indicator.

Clinical and prognostic significance of radiation associated eosinophilia (RAE) and radiation associated monocytosis (RAM) was evaluated in 176 patients with squamous cell carcinoma of the uterine cervix followed up after radiotherapy. Significant RAE was noticed in patients with Stages I/IIA and IIB who remained disease-free after treatment. On the contrary, patients belonging to these two stages but who developed recurrent disease showed absence of RAE. These patients as well as those belonging to Stage III showed considerably higher levels of RAM as compared to those patients remaining disease-free. These observations showed the usefulness of these two simple inexpensively carried out parameters in prognosticating disease course in malignant cervical neoplasia.

Carcinoma, Squamous Cell↗

PubMed1990

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac).

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.

Amino Acid Sequence↗

PubMed1989

Immunocompetence in lung cancer. Relationship to extent of tumor burden and histologic type.

In vitro assays of immunocompetence were done in 60 patients with differing extents of tumor load and various histologic types of lung cancer and were compared to values obtained for 60 normal controls. Profound alterations in monoclonal antibody-defined T-lymphocytes and circulating B-cells were seen. All patients showed impaired blastogenic response to the mitogens used with the exception of a normal response to pokeweed mitogen (PWM) in patients with localized disease. Increase levels of serum IgG were seen in patients with localized disease whereas high levels of IgA was seen in patients with more advanced disease. Distant metastases were associated with low IgM levels. All patients studied regardless of stage and histologic type had elevated levels of circulating immunocomplexes. These findings indicate gross immunologic abnormalities in these patients.

Adenocarcinoma↗

PubMed1989

Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals.

The incorporation of alpha-aminoisobutyryl (Aib) residues into peptide sequences facilitates helical folding. Aib-containing sequences have been chosen for the design of rigid helical segments in a modular approach to the construction of a synthetic protein mimic. The helical conformation of the synthetic peptide Boc-Aib-(Val-Ala-Leu-Aib)3-OMe in crystals is established by X-ray diffraction. The 13-residue apolar peptide adopts a helical form in the crystal with seven alpha-type hydrogen bonds in the middle and 3(10)-type hydrogen bonds at either end. The helices stack in columns, zigzag rather than linear, by means of direct NH...OC head to tail hydrogen bonds. Leucyl side chains are extended on one side of the helix and valyl side chains on the other side. Water molecules form hydrogen bonds with several backbone carbonyl oxygens that also participate in alpha-helix hydrogen bonds. There is no apparent distortion of the helix caused by hydration. The space group is P2(1)2(1)2(1), with a = 9.964 (3) A, b = 20.117 (3) A, c = 39.311 (6) A, Z = 4, and dx = 1.127 g/cm3 for C64H106N13O16.1.33H2O. The final agreement factor R was 0.089 for 3667 data observed greater than 3 sigma(F) with a resolution of 0.9 A.

Crystallization↗

PubMed1989

Conformational analysis of cyclolinopeptide A, a cyclic nonapeptide: nuclear Overhauser effect and energy minimization studies.

The conformation of cyclolinopeptide A [cyclo(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val)], a naturally occurring cyclic nonapeptide has been investigated in dimethylsulfoxide solution by 270 MHz 1H-nmr. A complete assignment of all C alpha H and NH resonances has been accomplished using two-dimensional correlated spectroscopy and nuclear Overhauser effects (NOEs). Analysis of interresidue NOEs and JHNC alpha H values permit construction of a molecular model for the cyclic peptide backbone. The crude model derived from nmr has been used as a starting point for energy minimization, which yields a refined structure largely compatible with nmr observations. The major features of the conformation of cyclolinopeptide A are a Type VI beta-turn centered at Pro(1)-Pro(2), with a cis peptide bond between these residues and a gamma-turn (C7 structure) centered at Ile(6). Two intramolecular hydrogen bonds Val(9) CO--Phe(3)NH (4----1) and Leu(5) CO--Ile(7)NH (3----1) are observed in the low-energy conformation. The limited solvent accessibility observed for the Val(9) and Leu(5) NH groups in the nmr studies are rationalized in terms of steric shielding.

Magnetic Resonance Spectroscopy↗

PubMed1989

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.

Magnetic Resonance Spectroscopy↗

PubMed1989

Solvated helical backbones: x-ray diffraction study of Boc-Ala-Leu-Aib-Ala-Leu-Aib-OMe.H2O.

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc-Aib-(Ala-Leu-Aib)3-OMe. The backbone of the title compound assumes an approximate 3(10)-helical form with three 4----1 hydrogen bonds. In the place of a fourth 4----1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) ... W(1) (2.95 A) and W(1) ... O(1) (2.81 A). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) ... O(4) (2.91 A). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P2(1)2(1)2(1) with a = 12.024(4) A, b = 15.714(6) A, c = 21.411(7) A, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9.H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities greater than 3 sigma(F) and the resolution is 0.90 A.

Models, Molecular↗

PubMed1989

Immune reactive proteins as prognostic and clinical markers in malignant cervical neoplasia.

The significance of immune reactive proteins in malignant cervical neoplasia, with particular reference to its prognostic and clinical relevance, was studied in 229 patients. All stages of the disease showed elevated levels of circulating immune complexes (CIC). Patients with stages I/IIA showed elevated levels of IgG, whereas those with stages III and IV showed depressed IgM levels. In the case of IgA, the situation was reversed: patients with advanced disease showed increased levels. Radiotherapy resulted in highly elevated levels of CIC, IgG, and IgA. However, in patients who remained disease-free after radiation treatment, levels of these proteins came down, often falling below pretreatment levels. On the other hand, patients developing recurrent disease showed sustained, high levels of CIC and IgA, with IgG as an isolated case in stage I/IIA. The present study therefore shows that although these increases were non-tumour-specific, patients with persistent elevation of CIC and IgA levels were at much greater risk of developing recurrent disease, thereby proving the merit of these substances as markers in prognosticating the course of disease in malignant cervical neoplasia.

Antigen-Antibody Complex↗

PubMed1989

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.

Leucine↗

PubMed1989

Interleukin 2 production in lymphocyte cultures: a rapid test for cancer-associated immunodeficiency in malignant cervical neoplasia.

Peripheral blood lymphocytes of patients with malignant cervical neoplasia were studied for their capacity to produce interleukin-2 (IL-2) upon in vitro mitogen stimulation. Patients with early disease (Stage I/IIA) showed levels comparable to normal controls but those with advanced disease showed reduced levels, the reduction increasing with tumour load. These findings excellently correlated with our previous observations on a depressed cellular immunity in these patients. On follow up of the patients it was noticed that those who developed recurrent disease showed sustained lower levels of IL-2 production compared to those who remained disease free. These results stress the importance of a deranged immune system in these patients and also shows the clinical and prognostic value of such an assay.

Carcinoma, Squamous Cell↗

PubMed1989

Alpha-helix and mixed 3(10)/alpha-helix in cocrystallized conformers of Boc-Aib-Val-Aib-Aib-Val-Val-Val-Aib-Val-Aib-OMe.

Two molecules of Boc-Aib-Val-Aib-Aib-Val-Val-Val-Aib-Val-Aib-OMe (where Boc is t-butoxycarbonyl and Aib is alpha-aminoisobutyryl) cocrystallize in a triclinic cell with different helical conformations. One molecule is completely alpha-helical with seven 5----1 intramolecular hydrogen bonds. It forms three head-to-tail NH...O = C hydrogen bonds to other molecules of the same conformation. The second molecule has a mixed 3(10)/alpha-helix conformation with three 4----1 hydrogen bonds and four 5----1 hydrogen bonds; furthermore, there is a helix reversal at both termini. The second molecule forms only two head-to-tail hydrogen bonds with molecules of the same type, and the N(3)H group does not participate in any hydrogen bonding. The two different types of helices occur in alternate sheets in the crystal, where each sheet is composed of adjacent rods of helices formed by head-to-tail hydrogen bonding. Within each sheet, containing helices of only one type of conformation, the helices aggregate in a parallel mode. Between the sheets of different helices, the aggregation is antiparallel. The peptide, with formula C51H92N10O13, crystallizes in space group P1 with Z = 2 and cell parameters a = 10.047 +/- 0.002 A, b = 16.684 +/- 0.003 A, c = 19.198 +/- 0.004 A, alpha = 80.30 degrees +/- 0.01 degrees, beta = 85.74 degrees +/- 0.01 degrees, and gamma = 83.03 degrees +/- 0.01 degrees; overall agreement factor R = 6.7% for 6053 data ([F0] greater than 3 sigma) and 0.96-A resolution.

Aminoisobutyric Acids↗

PubMed1989

Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.

A computer modeling procedure for assessing the stereochemical suitability of pairs of residues in proteins as potential sites for introduction of cystine disulfide crosslinks has been developed. Residue pairs with C alpha-C alpha distances of less than or equal to 6.5 A and C beta-C beta distances of less than or equal to 4.5 A are chosen for geometrical fixation of S atoms using the program MODIP. The stereochemistry of the modeled disulfides is evaluated using limits for the structural parameters of the various torsion angles and S-S bond length in the disulfide bridge. The ability of the procedure to correctly model disulfides has been checked with examples of cystine peptides of known crystal structures and 103 disulfide bridges from 25 available protein crystal structures determined at less than or equal to 2 A resolution. An analysis of results on three proteins with engineered disulfides, T4 lysozyme, dihydrofolate reductase and subtilisin, is presented. Two positions for the introduction of 'stereochemically optimal' disulfides are identified in subtilisin.

Disulfides↗

PubMed1989

Cystine peptides. Antiparallel beta-sheet conformation of the cyclic biscystine peptide [Boc-Cys-Ala-Cys-NHCH3]2.

The crystal structure analysis of the cyclic biscystine peptide [Boc-Cys1-Ala2-Cys3-NHCH3]2 with two disulfide bridges confirms the antiparallel beta-sheet conformation for the molecule as proposed for the conformation in solution. The molecule has exact twofold rotation symmetry. The 22-membered ring contains two transannular NH...OC hydrogen bonds and two additional NH...OC bonds are formed at both ends of the molecule between the terminal (CH3)3COCO and NHCH3 groups. The antiparallel peptide strands are distorted from a regularly pleated sheet, caused mainly by the L-Ala residue in which phi = -155 degrees and psi = 162 degrees. In the disulfide bridge C alpha(1)-C beta(1)-S(1)-S(3')-C beta(3')-C alpha(3'), S--S = 2.030 A, angles C beta SS = 107 degrees and 105 degrees, and the torsional angles are -49, -104, +99, -81, -61 degrees, respectively. The biscystine peptide crystallizes in space group C2 with a = 14.555(2) A, b = 10.854(2) A, c = 16.512(2) A, and beta = 101.34(1) with one-half formula unit of C30H52N8O10S4.2(CH3)2SO per asymmetric unit. Least-squares refinement of 1375 reflections observed with magnitude of F greater than 3 sigma(F) yielded an R factor of 7.2%.

Amino Acid Sequence↗

PubMed1989

Interleukin 2 and alpha interferon induced in vitro modulation of spontaneous cell mediated cytotoxicity in patients with cancer of the uterine cervix undergoing radiotherapy.

In vitro modulation of spontaneous cell mediated cytotoxicity by interferon and interleukin 2 was carried out using peripheral blood lymphocytes from patients with cancer of the uterine cervix before and at different intervals after commencement of radiation treatment. A total of 150 patients with various stages of the disease were included and cytotoxicity was measured using the single cell cytotoxic assay. These results indicate a beneficial effect in vitro of interleukin 2 and interferon in augmenting spontaneous cell mediated cytotoxicity, a possibly vital antitumour immune mechanism in patients with relatively early cervix cancer. Natural killer cell, lymphokine activated killer cell and interferon activated killer cell activity was depressed immediately following radiotherapy. The activity of these cell types later on increased above pretreatment levels in patients with stages I, IIA and IIB. A similar rebound above pretreatment levels was not observed in patients with stages III and IV.

Carcinoma, Squamous Cell↗

PubMed1989

Adrenal carcinoma with reactive plasmacytosis.

An 18 year old boy presented with anaemia, congestive cardiac failure and a 'renal mass'. Preoperative and post-operative investigations demonstrated "reactive plasmacytosis" with antibodies directed against a non-functioning adrenal carcinoma. Existing literature on reactive plasmacytosis and anti-tumour antibodies is summarised.

Adolescent↗

PubMed1988

Synthetic peptide models for the redox-active disulfide loop of glutaredoxin. Conformational studies.

Two cyclic peptide disulfides (Sequence: see text). (X = L-Tyr or L-Phe) have been synthesized as models for the 14-membered redox-active disulfide loop of glutaredoxin. 1H NMR studies at 270 MHz in chloroform solutions establish a type I beta-turn conformation for the Pro-X segment in both peptides, stabilized by a 4----1 hydrogen bond between the Cys(1) CO and Cys(4) NH groups. Nuclear Overhauser effects establish that the aromatic ring in the X = Phe peptide is oriented over the central peptide unit. In dimethyl sulfoxide solutions two conformational species are observed in slow exchange on the NMR time scale, for both peptides. These are assigned to type I and type II beta-turn structures with -Pro-Tyr(Phe)- as the corner residues. The structural assignments are based on correlation of NMR parameters with model 14-membered cyclic cystine peptides with Pro-X spacers. Circular dichroism studies based on the -S-S- n-omega* transition suggest a structural change in the disulfide bridge with changing solvent polarity, establishing conformational coupling between the peptide backbone and the disulfide linkage in these systems.

Bacterial Proteins↗