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K Rajagopal

Publications and source records attributed to K Rajagopal.

15 recordsLinked to original sources

A model for the formation and lysis of blood clots.

Both biochemical and mechanical factors have to be taken into account if a meaningful model for the formation, growth, and lysis of clots in flowing blood is to be developed. Most models that are currently in use neglect one or the other of these factors. We have previously reported a model [J Theoret Med 2003;5:183-218] that we believe is a step in this direction, incorporating many of the crucial biochemical and rheological factors that play a role in the formation, growth, and lysis of clots. While this model takes into account the extrinsic pathway of coagulation, it largely ignores the intrinsic pathway. Here, we discuss some of the general issues with respect to mathematical modeling of thrombus formation and lysis, as well as specific aspects of the model that we have developed.

Blood Coagulation↗

Enforced electrical neutrality of the color-flavor locked phase.

We demonstrate that quark matter in the color-flavor locked phase of QCD is rigorously electrically neutral, despite the unequal quark masses, and even in the presence of an electron chemical potential. As long as the strange quark mass and the electron chemical potential do not preclude the color-flavor locked phase, quark matter is automatically neutral. No electrons are required and none are admitted.

Journal Article↗

Antifungal and cytotoxic effects of methanol extracts of three marine molluscs.

Methanol extracts of whole body (Melampus ceylonicus), blood (Anadara rhombea) and hepatopancreas (Sepiella inermis) were screened for antifungal and cytotoxic activity. Blood of A. rhombea and hepatopancreas of S. inermis strongly inhibited Candida albicans, Mucor racemosus and Penicillium expansum. A. rhombea appear to exert strong cytotoxic activity against vertebrate erythrocytes. The bacterial pathogens (Escherichia coli and Vibrio cholarae) were not inhibited by any of the three tested methanol extracts.

Animals↗

Gapless color superconductivity

We present the dispersion relations for quasiparticle excitations about the color-flavor locked ground state of QCD at high baryon density. In the presence of condensates which pair light and strange quarks there need not be an energy gap in the quasiparticle spectrum. This raises the possibility of gapless color superconductivity, with a Meissner effect but no minimum excitation energy. Analysis within a toy model suggests that gapless color superconductivity may occur only as a metastable phase.

Journal Article↗

Lack of predictive value of the Epworth Sleepiness Scale in patients after uvulopalatopharyngoplasty.

The Epworth Sleepiness Scale (ESS) has been recognized as a valid measure of sleep propensity. Statistically significant correlations between ESS scores, the respiratory disturbance index (RDI), and the lowest arterial oxygen saturation (LSAT) have been described in patients with surgically untreated obstructive sleep apnea (OSA). We investigated whether the same relationships hold true after uvulopalatopharyngoplasty (UPPP). Forty-two adults with documented OSA treated by UPPP were reevaluated with the ESS questionnaire and 8-hour diagnostic nocturnal polysomnography (nPSG). We found no significant correlation between the ESS scores and the RDI or LSAT in patients after UPPP. Because postoperative ESS scores do not correlate with the RDI or LSAT, we conclude that the ESS is not a reliable surrogate for nPSG testing.

Adult↗

RIBP, a novel Rlk/Txk- and itk-binding adaptor protein that regulates T cell activation.

A novel T cell-specific adaptor protein, RIBP, was identified based on its ability to bind Rlk/Txk in a yeast two-hybrid screen of a mouse T cell lymphoma library. RIBP was also found to interact with a related member of the Tec family of tyrosine kinases, Itk. Expression of RIBP is restricted to T and natural killer cells and is upregulated substantially after T cell activation. RIBP-disrupted knockout mice displayed apparently normal T cell development. However, proliferation of RIBP-deficient T cells in response to T cell receptor (TCR)-mediated activation was significantly impaired. Furthermore, these activated T cells were defective in the production of interleukin (IL)-2 and interferon gamma, but not IL-4. These data suggest that RIBP plays an important role in TCR-mediated signal transduction pathways and that its binding to Itk and Rlk/Txk may regulate T cell differentiation.

Adaptor Proteins, Signal Transducing↗

Function of the central domain of streptokinase in substrate plasminogen docking and processing revealed by site-directed mutagenesis.

The possible role of the central beta-domain (residues 151-287) of streptokinase (SK) was probed by site-specifically altering two charged residues at a time to alanines in a region (residues 230-290) previously identified by Peptide Walking to play a key role in plasminogen (PG) activation. These mutants were then screened for altered ability to activate equimolar "partner" human PG, or altered interaction with substrate PG resulting in an overall compromised capability for substrate PG processing. Of the eight initial alanine-linker mutants of SK, one mutant, viz. SK(KK256.257AA) (SK-D1), showed a roughly 20-fold reduction in PG activator activity in comparison to wild-type SK expressed in Escherichia coli (nSK). Five other mutants were as active as nSK, with two [SK(RE248.249AA) and SK(EK281.282AA), referred to as SK(C) and SK(H), respectively] showing specific activities approximately one-half and two-thirds, respectively, that of nSK. Unlike SK(C) and SK(H), however, SK(D1) showed an extended initial delay in the kinetics of PG activation. These features were drastically accentuated when the charges on the two Lys residues at positions 256 and 257 of nSK were reversed, to obtain SK(KK256.257EE) [SK(D2)]. This mutant showed a PG activator activity approximately 10-fold less than that of SK(D1). Remarkably, inclusion of small amounts of human plasmin (PN) in the PG activation reactions of SK(D2) resulted in a dramatic, PN dose-dependent rejuvenation of its PG activation capability, indicating that it required pre-existing PN to form a functional activator since it could not effect active site exposure in partner PG on its own, a conclusion further confirmed by its inability to show a "burst" of p-nitrophenol release in the presence of equimolar human PG and p-nitrophenyl guanidino benzoate. The steady-state kinetic parameters for HPG activation of its 1:1 complex with human PN revealed that although it could form a highly functional activator once "supplied" with a mature active site, the Km for PG was increased nearly eightfold in comparison to that of nSK-PN. SK mutants carrying simultaneous two- and three-site charge-cluster alterations, viz., SK(RE24249AA:EK281.282AA) [SK(CH)], SK(EK272.273AA;EK281.282AA) [SK(FH)], and SK(RE248.249AA;EK272.273AA:EK281.282AA+ ++) [SK(CFH)], showed additive/synergistic influence of multiple charge-cluster mutations on HPG activation when compared to the respective "single-site" mutants, with the "triple-site" mutant [SK(CFH)] showing absolutely no detectable HPG activation ability. Nevertheless, like the other constructs, the double- and triple-charge cluster mutants retained a native like affinity for complexation with partner PG. Their overall structure also, as judged by far-ultraviolet circular dichroism, was closely similar to that of nSK. These results provide the first experimental evidence for a direct assistance by the SK beta-domain in the docking and processing of substrate PG by the activator complex, a facet not readily evident probably because of the flexibility of this domain in the recent X-ray crystal structure of the SK-plasmin light chain complex.

Amino Acid Sequence↗

Biology of the inner space: voids in biopolymers

Dynamic states of biopolymers are associated with appearance and disappearance of spaces, or voids, to an extent larger than what is hitherto recognized. Current awareness of the existence of free space in biopolymers is by and large restricted in terms of (i) essentially small pores obeying Boltzman distribution of sizes and energy and (ii) rigid structures dictated by structural constraints, whose volume merely exhibits fluctuations within the thermal limits. Interconnectivity of these spaces within biopolymers such as membranes give rises to new possibilities in addressing some of the long standing problems in understanding catalysis, transport and the derived biological phenomena. Given the a priori recognition that other kinds of space can exist in biopolymers, which are dynamic, predominantly inducible and possibly larger, a new kind of experimentation becomes possible as also a new set of constraints for the acceptability of molecular models of interactions in the explanation of biological phenomena. The theory of adsorption of liquids and presence of structural cavities as exemplified by zeolites competently accounts for much of the current thinking in our understanding of cavities in biopolymers. Induction of (larger) voids requires approaches that are significantly different. We suggest that it is necessary to consider a reservoir of inner space as a specific contribution to the energetics of polymer dynamics. We outline a methodological approach that helps identify these voids as well as biological phenomena in which the notion of dynamics of voids would bring novel insights. Copyright 1998 Academic Press

Journal Article↗

Role of the amino-terminal region of streptokinase in the generation of a fully functional plasminogen activator complex probed with synthetic peptides.

The mechanism whereby fragments of streptokinase (SK) derived from its N terminus (e.g., SK1-59 or SK1-63) enhance the low plasminogen (PG)-activating ability of other fragments, namely SK64-386, SK60-414, SK60-387, and SK60-333 (reported previously), has been investigated using a synthetic peptide approach. The addition of either natural SK1-59, or chemically synthesized SK16-59, at saturation (about 500-fold molar excess) generated amidolytic and PG activation capabilities in equimolar mixtures of human plasminogen (HPG) and its complementary fragment (either SK60-414 or SK56-414, prepared by expression of truncated SK gene fragments in Escherichia coli) that were approximately 1.2- and 2.5-fold, respectively, of that generated by equimolar mixtures of native SK and HPG. Although in the absence of SK1-59 equimolar mixtures of SK56-414 and HPG could generate almost 80% of amidolytic activity, albeit slowly, less than 2% level of PG activation could be observed under the same conditions, indicating that the contribution of the N-terminal region lay mainly in imparting in SK56-414 an enhanced ability for PG activation. The ability of various synthetic peptides derived from the amino-terminal region (SK16-51, SK16-45, SK37-59, SK1-36, SK16-36, and SK37-51) to (1) complement equimolar mixtures of SK56-414 and HPG for the generation of amidolytic and PG activation functions, (2) inhibit the potentiation of SK56-414 and HPG by SK16-59, and (3) directly inhibit PG activation by the 1:1 SK-HPG activator complex was tested. Apart from SK16-59, SK16-51, and 16-45, the ability to rapidly generate amidolytic potential in HPG in the presence of SK56-414 survived even in the smaller SK-peptides, viz., SK37-59 and SK37-51. However, this ability was abolished upon specifically mutating the sequence -LTSRP-, present at position 42-46 in native SK. Although SK16-51 retained virtually complete ability for potentiation of PG activation in comparison to SK16-59 or SK1-59, this ability was reduced by approximately fourfold in the case of SK16-45, and completely abolished upon further truncation of the C-terminal residues to SK16-36 or SK1-36. Remarkably, however, these peptides not only displayed ability to bind PG, but also showed strong inhibition of PG activation by the native activator complex in the micromolar range of concentration; the observed inhibition, however, could be competitively relieved by increasing the concentration of substrate PG in the reaction, suggesting that this region in SK contains a site directed specifically toward interaction with substrate PG. This conclusion was substantiated by the observation that the potentiation of PG activating ability was found to be considerably reduced in a peptide (SK25-59) in which the sequence corresponding to this putative locus (residues 16-36) was truncated at the middle. On the other hand, fragments SK37-51 and SK37-59 did not show any inhibition of the PG activation by native activator complex. Taken together, these findings strongly support a model of SK action wherein the HPG binding site resident in the region 37-51 helps in anchoring the N-terminal domain to the strong intermolecular complex formed between HPG and the region 60-414. In contrast, the site located between residues 16 and 36 is qualitatively more similar to the previously reported PG interacting site (SK254-273) present in the core region of SK, in being involved in the relatively low-affinity enzyme-substrate interactions of the activator complex with PG during the catalytic cycle.

Amidohydrolases↗