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Biomedical subjects

M Sukumar

Publications and source records attributed to M Sukumar.

At least 19 recordsLinked to original sources
PubMed2006

Aspiration versus tube drainage in primary spontaneous pneumothorax: a randomised study.

This randomised study was designed to compare clinical outcomes for simple aspiration versus tube thoracostomy, in the treatment of the first primary spontaneous pneumothorax (PSP) attack. A randomised trial, comparing simple aspiration with tube thoracostomy, in 137 patients with a first episode of PSP was carried out. Immediate success was obtained in 40 out of the 65 patients (62%) randomly assigned to undergo simple aspiration and in 49 out of the 72 patients (68%) who had been randomly assigned to undergo tube thoracostomy. The 1-week success rates were: 58 (89%) patients in the intention-to-treat simple aspiration group and 63 (88%) patients in the tube thoracostomy group. In the aspiration group, there were more recurrences during the 3-month follow-up period (15 versus 8%), though the difference was not significant. Recurrence rates at 1 and 2 yrs were 16 (22%) and 20 (31%) for patients who had undergone simple aspiration, respectively, and 17 (24%) and 18 (25%) for patients who had undergone tube thoracostomies, respectively. Complications occurred in 5 (7%) patients who had undergone a tube thoracostomy and 1 (2%) patient who had undergone simple aspiration. Analgesia was required in 22 (34%) patients of the simple aspiration group versus 40 (56%) patients of the tube thoracostomy group. These findings suggest that simple aspiration could be an acceptable alternative to tube thoracostomy in the treatment of primary spontaneous pneumothorax.

Adult↗
PubMed2000

Dynamics of cellular retinoic acid binding protein I on multiple time scales with implications for ligand binding.

Cellular retinoic acid binding protein I (CRABPI) belongs to the family of intracellular lipid binding proteins (iLBPs), all of which bind a hydrophobic ligand within an internal cavity. The structures of several iLBPs reveal minimal structural differences between the apo (ligand-free) and holo (ligand-bound) forms, suggesting that dynamics must play an important role in the ligand recognition and binding processes. Here, a variety of nuclear magnetic resonance (NMR) spectroscopy methods were used to systematically study the dynamics of both apo and holo CRABPI at various time scales. Translational and rotational diffusion constant measurements were used to study the overall motions of the proteins. Both apo and holo forms of CRABPI tend to self-associate at high (1.2 mM) concentrations, while at low concentrations (0.2 mM), they are predominantly monomeric. Rapid amide exchange rate and laboratory frame relaxation rate measurements at two spectrometer field strengths (500 and 600 MHz) were used to probe the internal motions of the individual residues. Several residues in the apo form, notably within the ligand recognition region, exhibit millisecond time scale motions that are significantly arrested in the holo form. In contrast, no significant differences in the high-frequency motions were observed between the two forms. These results provide direct experimental evidence for dynamics-induced ligand recognition and binding at a specifically defined time scale. They also exemplify the importance of dynamics in providing a more comprehensive understanding of how a protein functions.

Apoproteins↗
PubMed1998

High-frequency partial liquid ventilation in respiratory distress syndrome: hemodynamics and gas exchange.

Partial liquid ventilation using conventional ventilatory schemes improves lung function in animal models of respiratory failure. We examined the feasibility of high-frequency partial liquid ventilation in the preterm lamb with respiratory distress syndrome and evaluated its effect on pulmonary and systemic hemodynamics. Seventeen lambs were studied in three groups: high-frequency gas ventilation (Gas group), high-frequency partial liquid ventilation (Liquid group), and high-frequency partial liquid ventilation with hypoxia-hypercarbia (Liquid-Hypoxia group). High-frequency partial liquid ventilation increased oxygenation compared with high-frequency gas ventilation over 5 h (arterial oxygen tension 253 +/- 21.3 vs. 17 +/- 1.8 Torr; P < 0.001). Pulmonary vascular resistance decreased 78% (P < 0.001), pulmonary blood flow increased fivefold (P < 0.001), and aortic pressure was maintained (P < 0.01) in the Liquid group, in contrast to progressive hypoxemia, hypercarbia, and shock in the Gas group. Central venous pressure did not change. The Liquid-Hypoxia group was similar to the Gas group. We conclude that high-frequency partial liquid ventilation improves gas exchange and stabilizes pulmonary and systemic hemodynamics compared with high-frequency gas ventilation. The stabilization appears to be due in large part to improvement in gas exchange.

Animals↗
PubMed1997

A Gs-selective analog of the receptor-mimetic peptide mastoparan binds to Gs alpha in a kinked helical conformation.

Mastoparan, a 14-residue peptide, stimulates GDP/GTP exchange on G proteins in a manner strikingly analogous to that of agonist-bound receptors. Presumably, the peptide structurally mimics a receptor's G protein-binding domain. We previously reported that mastoparan-X binds to alpha-subunits of Gi and Go in a predominantly alpha-helical conformation [Sukumar, M., & Higashijima, T. (1992) J. Biol. Chem. 267, 21421-21424]. We have now developed an analogous peptide, INWKGIASM-alpha-aminoisobutyryl (Aib)-RQVL-NH2 (MP-S), which is a selective activator of Gs. We report the conformation of MP-S when it is bound to Gs alpha, determined from distance geometry calculations based on transferred nuclear Overhauser effects (TRNOEs). The Gs-bound conformation of MP-S is an alpha-helix that is kinked at residue 9. The conformations of MP-S when bound to Gi alpha or Go alpha are similar to the Gs alpha-bound conformation. In contrast, the lipid-bound conformation of MP-S is a straight helix. On the basis of the Gs-bound conformation of MP-S, directions for the design of Gs-selective peptidergic mimics of receptors are suggested.

Drug Design↗
PubMed1997

Atraumatic gastric transposition after transhiatal esophagectomy.

Transhiatal esophagectomy using the stomach for esophageal replacement requires that the gastric "neoesophagus" be transferred from the peritoneal cavity through the posterior mediastinum into the neck under blind conditions. This process is associated with stretching, tearing, and hematoma formation in the most critical portion of the gastric tube, that to be used for the anastomosis. A technique is described for this procedure that is simple to perform and, most importantly, completely atraumatic to the gastric conduit.

Anastomosis, Surgical↗
PubMed1997

Local interactions in a Schellman motif dictate interhelical arrangement in a protein fragment.

BACKGROUND: As an approach to understanding the role of local sequence in determining protein tertiary structure, we have examined the conformation of a 23-residue peptide fragment corresponding to the structurally conserved helix-Schellman motif-helix (H-Sm-H) domain (residue 10-32) of cellular retinoic acid binding protein, along with variants designed to probe the contributions of the helix-terminating Gly23 and the hydrophobic interactions between Leu 19 and Val24 in stabilizing the Schellman motif and hence helix termination. RESULTS: In aqueous solution, NMR data for the H-Sm-H peptide show that it samples a largely helical conformation with a break in the helix at the point of the turn in the protein. The data also establish the presence of local hydrophobic interactions and intramolecular hydrogen bonds characteristic of a Schellman motif. Absence of helix termination in trifluoroethanol, a solvent known to disrupt hydrophobic interactions, along with an analysis of H alpha chemical shifts and NOEs in the variant peptides, suggest a major role for glycine in terminating the helix, with local hydrophobic interactions further stabilizing the Schellman motif. CONCLUSIONS: The presence of a Schellman motif in this isolated fragment in water is governed by local interactions and specifies the interspatial arrangement of the helices. This observation underlines the structure predictive value of folding motifs. As proposed for a Schellman motif, helix termination in this fragment is dictated by the local distribution of polar/apolar residues, which is reminiscent of the binary code for protein folding.

Amino Acid Sequence↗
PubMed1995

Biradicals as ESR probes of conformations in model beta-turn peptides.

Electron spin-spin exchange interaction in biradicals has been examined for its potential usefulness in the conformational analysis of peptides in solution. Three peptides with high propensity to adopt beta-turn conformations in solution, Boc-Cys-Pro-Xxx-Cys-NHMe (Xxx = Leu, 1; Xxx = Aib, 2; Xxx = Tyr, 3), have been modified into biradicals by spin labeling the thiols groups. Analysis of electron spin resonance spectra of these peptides in a variety of solvents and at different temperatures suggests that the population of folded conformations follows the order 2 > 1 > 3.

Amino Acid Sequence↗
PubMed1995

The structure of Escherichia coli heat-stable enterotoxin b by nuclear magnetic resonance and circular dichroism.

The heat-stable enterotoxin b (STb) is secreted by enterotoxigenic Escherichia coli that cause secretory diarrhea in animals and humans. It is a 48-amino acid peptide containing two disulfide bridges, between residues 10 and 48 and 21 and 36, which are crucial for its biological activity. Here, we report the solution structure of STb determined by two- and three-dimensional NMR methods. Approximate interproton distances derived from NOE data were used to construct structures of STb using distance-geometry and simulated annealing procedures. The NMR-derived structure shows that STb is helical between residues 10 and 22 and residues 38 and 44. The helical structure in the region 10-22 is amphipathic and exposes several polar residues to the solvent, some of which have been shown to be important in determining the toxicity of STb. The hydrophobic residues on the opposite face of this helix make contacts with the hydrophobic residues of the C-terminal helix. The loop region between residues 21 and 36 has another cluster of hydrophobic residues and exposes Arg 29 and Asp 30, which have been shown to be important for intestinal secretory activity. CD studies show that reduction of disulfide bridges results in a dramatic loss of structure, which correlates with loss of function. Reduced STb adopts a predominantly random-coil conformation. Chromatographic measurements of concentrations of native, fully reduced, and single-disulfide species in equilibrium mixtures of STb in redox buffers indicate that the formation of the two disulfide bonds in STb is only moderately cooperative. Similar measurements in the presence of 8 M urea suggest that the native secondary structure significantly stabilizes the disulfide bonds.

Amino Acid Sequence↗
PubMed1993

The mechanism of aluminum-independent G-protein activation by fluoride and magnesium. 31P NMR spectroscopy and fluorescence kinetic studies.

With magnesium present, fluoride and aluminum ions activate heterotrimeric G-proteins by forming AlFx complexes that mimic the gamma phosphate of a GTP. We report compelling evidence for a newly proposed process of G-protein activation by fluoride and magnesium, without Al3+. With millimolar Mg2+ and F-, Gs and Gt activate adenylylcyclase and cGMP-phosphodiesterase, respectively. In 31P NMR, addition of magnesium to Gi1 alpha GDP or Gt alpha GDP solutions containing fluoride, but no Al3+, modifies the chemical shift of the GDP beta phosphorus, suggesting that magnesium interacts with the beta phosphate. Titration of this effect indicates that two Mg2+ are bound per G alpha. Biphasic activation kinetics, monitored by G alpha tryptophan fluorescence, suggests the rapid binding of one Mg2+ to G alpha GDP and the slow association of another Mg2+, in correlation with fluoride binding and G alpha activation. The deactivation rate upon fluoride dilution shows a second order dependence with respect to the residual F- concentration, suggesting the sequential release of at least three F-/G alpha. Thus, in millimolar Mg2+ and F-, and without Al3+, two Mg2+ and three F- bind sequentially to G alpha GDP and induce the switch to an active G alpha (GDP-MgF3)Mg state, which is structurally analogous to G alpha (GDP-AlFx)Mg and to G alpha (GTP)Mg.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed1992

G protein-bound conformation of mastoparan-X, a receptor-mimetic peptide.

Mastoparans are a family of 14-residue peptide toxins from wasp venom which have been proposed to stimulate secretion from a variety of cells, by directly activating GTP-binding regulatory proteins (G proteins). In vitro studies have shown that mastoparans activate G proteins by a mechanism remarkably similar to that used by agonist-bound receptors (Higashijima, T., Uzu, S., Nakajima, T., and Ross, E. M. (1988) J. Biol. Chem. 263, 6491-6494). Here, we report the conformation of mastoparan-X (INWKGIAAMAKKLL-NH2) when it is bound to the alpha subunits of recombinant G(i) and G(o), derived from an analysis of transferred nuclear Overhauser effects in a two-dimensional 1H NMR spectrum of mastoparan-X obtained in the presence of these G proteins. Restrained molecular dynamic simulations with NMR-derived distance constraints were used to determine conformations consistent with NMR data. The G(i)- and G(o)-bound conformations of mastoparan-X are very similar, and in both cases, a major part of the molecule adopts an amphiphilic alpha-helical conformation. The lysine residues are known to be crucial for activity, and it is thus likely that at least the polar face of the amphiphilic helix is in contact with the G proteins. These conclusions should be useful in the design of potent and selective analogs of mastoparan and in the development of models for receptor-G protein interaction.

Amino Acid Sequence↗
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

Helix packing of leucine-rich peptides: a parallel leucine ladder in the structure of Boc-Aib-Leu-Aib-Aib-Leu-Leu-Leu-Aib-Leu-Aib-OMe.

The packing of peptide helices in crystals of the leucine-rich decapeptide Boc-Aib-Leu-Aib-Aib-Leu-Leu-Leu-Aib-Leu-Aib-OMe provides an example of ladder-like leucylleucyl interactions between neighboring molecules. The peptide molecule forms a helix with five 5----1 hydrogen bonds and two 4----1 hydrogen bonds near the C terminus. Three head-to-tail NH ... O = C hydrogen bonds between helices form continuous columns of helices in the crystal. The helicial columns associate in an antiparallel fashion, except for the association of Leu ... Leu side chains, which occurs along the diagonal of the cell where the peptide helices are parallel. The peptide, with formula C56H102N10O13, crystallizes in space group P2(1)2(1)2(1) with Z = 4 and cell parameters a = 16.774(3) A, b = 20.032(3) A and c = 20.117(3) A; overall agreement factor R = 10.7% for 2014 data with magnitude of F(obs) greater than 3 sigma (F); resolution 1.0 A.

Amino Acid Sequence↗
PubMed1992

The properties of ion channels formed by zervamicins.

The zervamicins (Zrv) are a family of 16 residue peptaibol channel formers, related to the 20 residue peptaibol alamethicin (Alm), but containing a higher proportion of polar sidechains. Zrv-IIB forms multi-level channels in planar lipid (diphytanoyl phosphatidylcholine) bilayers in response to cis positive voltages. Analysis of the voltage and concentration dependence of macroscopic conductances induced by Zrv-IIB suggests that, on average, channels contain ca. 13 peptide monomers. Analysis of single channel conductance levels suggests a similar value. The pattern of successive conductance levels is consistent with a modified helix bundle model in which the higher order bundle are distorted within the plane of the bilayer towards a "torpedo" shaped cross-section. The kinetics of intra-burst switching between adjacent conductance levels are shown to be approximately an order of magnitude faster for Zrv-IIB than for Alm. The channel forming properties of the related naturally occurring peptaibols, Zrv-Leu and Zrv-IC, have also been demonstrated, as have those of the synthetic apolar analogue Zrv-Al-16. The experimental studies on channel formation are combined with the known crystallographic structures of Zrv-Al-16 and Zrv-Leu to develop a molecular model of Zrv-IIB channels.

Alamethicin↗
PubMed1991

Stereochemistry of peptides containing 1-aminocycloheptane-1-carboxylic acid (Ac7c).

The crystal structures of four peptides incorporating 1-aminocycloheptane-1-carboxylic acid (Ac7c) are described. Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe adopt beta-turn conformations stabilized by an intramolecular 4----1 hydrogen bond, the former folding into a type-I/III beta-turn and the latter into a type-II beta-turn. In the dipeptide esters, Boc-Aib-Ac7c-OMe and Boc-Pro-Ac7c-OMe, the Ac7c and Aib residues adopt helical conformations, while the Pro residue remains semi-extended in both the molecules of Boc-Pro-Ac7c-OMe found in the asymmetric unit. The cycloheptane ring of Ac7c residues adopts a twist-chair conformation in all the peptides studied. 1H-NMR studies in CDCl3 and (CD3)2SO and IR studies in CDCl3 suggest that Boc-Aib-Ac7c-NHMe and Boc-Pro-Ac7c-Ala-OMe maintain the beta-turn conformations in solution.

Amino Acid Sequence↗
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↗
PubMed1988

Monoclinic polymorph of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe(anhydrous). Parallel packing of 3(10)-/alpha-helices and a transition of helix type.

The structures of two crystal forms of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe have been determined. The triclinic form (P1, Z = 1) from DMSO/H2O crystallizes as a dihydrate (Karle, Sukumar & Balaram (1986) Proc, Natl, Acad. Sci. USA 83, 9284-9288). The monoclinic form (P2(1), Z = 2) crystallized from dioxane is anhydrous. The conformation of the peptide is essentially the same in both crystal system, but small changes in conformational angles are associated with a shift of the helix from a predominantly alpha-type to a predominantly 3(10)-type. The r.m.s. deviation of 33 atoms in the backbone and C beta positions of residues 2-8 is only 0.29 A between molecules in the two polymorphs. In both space groups, the helical molecules pack in a parallel fashion, rather than antiparallel. The only intermolecular hydrogen bonding is head-to-tail between helices. There are no lateral hydrogen bonds. In the P2(1) cell, a = 9.422(2) A, b = 36.392(11) A, c = 10.548(2) A, beta = 111.31(2) degrees and V = 3369.3 A for 2 molecules of C60H97N11O13 per cell.

Amino Acid Sequence↗