Search PubMed⌕ Search

Biomedical subjects

S Sastry

Publications and source records attributed to S Sastry.

At least 19 recordsLinked to original sources
PubMed2006

Glass transition in biomolecules and the liquid-liquid critical point of water.

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.

Computer Simulation↗
PubMed2006

Troponin T after endoscopic retrograde cholangiopancreatography: no evidence of harm.

BACKGROUND AND STUDY AIMS: It is well recognized that myocardial ischemia can occur during endoscopic retrograde cholangiopancreatography (ERCP). Acute arrhythmias and ST segment changes have been reported by a number of authors, but the longer-term sequelae with regard to permanent myocardial damage are not known. The aim of this study was to determine the presence or absence of significant injury to the heart muscle. PATIENTS AND METHODS: Sixty-two patients undergoing therapeutic ERCP were assessed clinically and with electrocardiography (ECG) for the presence of ischemic heart disease before the procedure. Extensive intraprocedural monitoring was carried out, postprocedural ECGs were recorded, and serum troponin T levels were measured. The ECGs were evaluated blindly by a single cardiologist. RESULTS: In 61 of the 62 patients, no changes were observed between the ECGs before and after the procedure. One patient had postprocedural T wave inversion but a normal troponin T level, excluding myocardial damage. One patient with mild renal insufficiency and treated heart failure had borderline troponin T elevation (0.05 microg/l) but no ECG changes. No complications of ERCP occurred. CONCLUSIONS: Whilst ECG and rhythm changes indicating transient myocardial ischemia do occur during ERCP, there is no evidence that myocardial damage takes place as a consequence of this.

Adult↗
PubMed2005

Multivariate prediction of major adverse cardiac events after 9914 percutaneous coronary interventions in the north west of England.

OBJECTIVE: To develop a multivariate prediction model for major adverse cardiac events (MACE) after percutaneous coronary interventions (PCIs) by using the North West Quality Improvement Programme in Cardiac Interventions (NWQIP) PCI Registry. SETTING: All NHS centres undertaking adult PCIs in north west England. METHODS: Retrospective analysis of prospectively collected data on 9914 consecutive patients undergoing adult PCI between 1 August 2001 and 31 December 2003. A multivariate logistic regression analysis was undertaken, with the forward stepwise technique, to identify independent risk factors for MACE. The area under the receiver operating characteristic (ROC) curve and the Hosmer-Lemeshow goodness of fit statistic were calculated to assess the performance and calibration of the model, respectively. The statistical model was internally validated by using the technique of bootstrap resampling. MAIN OUTCOME MEASURES: MACE, which were in-hospital mortality, Q wave myocardial infarction, emergency coronary artery bypass graft surgery, and cerebrovascular accidents. RESULTS: Independent variables identified with an increased risk of developing MACE were advanced age, female sex, cerebrovascular disease, cardiogenic shock, priority, and treatment of the left main stem or graft lesions during PCI. The ROC curve for the predicted probability of MACE was 0.76, indicating a good discrimination power. The prediction equation was well calibrated, predicting well at all levels of risk. Bootstrapping showed that estimates were stable. CONCLUSIONS: A contemporaneous multivariate prediction model for MACE after PCI was developed. The NWQIP tool allows calculation of the risk of MACE permitting meaningful risk adjusted comparisons of performance between hospitals and operators.

Adult↗
PubMed2002

Changes in the corrected QT interval and corrected QT dispersion during haemodialysis.

The link between increased QT dispersion and cardiac death in subjects with diabetes and arterial disease is well recognised. Corrected QT dispersion was studied in subjects with end stage renal failure on haemodialysis. Thirty one stable, chronic subjects on haemodialysis had 12-lead electrocardiograms (ECGs) taken before and after a single haemodialysis session. The QT interval was measured manually in each and the corrected QT and corrected QT dispersion calculated. Serum concentrations of potassium, calcium, and magnesium were measured at the same time as ECG acquisition. Corrected QT dispersion increased from a mean (SEM) 90.6 (5.8) to 117.7 (10.2) ms (p=0.002). Serum potassium and magnesium decreased from 5.0 (0.14) to 3.5 (0.09) mmol/l and 0.95 (0.04) to 0.89 (0.09) mmol/l respectively, while serum calcium increased from 2.56 (0.04) to 2.77 (0.04) mmol/l. Intradialytic weight fell by a mean of 2.1 kg. There was no significant correlation between the change in QTc dispersion and the changes in measured serum anions or the subjects' weight during dialysis. Corrected QT dispersion was higher in subjects on haemodialysis than previously suggested normal values, and was significantly increased by haemodialysis. This reflects increased inhomogeneous ventricular repolarisation, which may lead to an increased risk of arrhythmias and sudden death. Studies looking at QT dispersion in subjects on dialysis should standardise the timing of ECG recordings taken with respect to dialysis.

Adult↗
PubMed2001

A fluorescence-based assay for transcription using a novel fluorescent GTP analogue.

A new fluorescent analogue of GTP (Cm-GTP) was synthesized, which contained a coumarin fluorophore attached to the gamma phosphorus. This compound was tested in transcription assays using T7 RNA polymerase as a model system. The fluorescent nucleotide was incorporated specifically at the 5' end of nascent RNA synthesized in two different modes of transcription initiation. In the first mode, with only Cm-GTP (+GTP), reiterative slippage synthesis occurred and poly rG ladders of up to 14 nucleotides were synthesized. In the second mode, with Cm-GTP (+GTP)+ATP+CTP, abortive transcripts of up to seven or eight nucleotides were synthesized. The fluorescence properties of the two types of RNA were studied in detail. There was greater reduction in fluorescence intensity in G-ladders than in abortive transcripts. Steady-state anisotropy and anisotropy decay indicated that the fluorophore motion was constrained in G-ladder RNAs as compared to abortive RNAs. Quenching experiments by using extraneous quenchers showed that the excited state of fluorophore at the 5' end of G-ladder RNA was less efficiently quenched as compared to the free fluorophore. These studies suggested that the fluorescent GTP analogue sensed the structural features that distinguished G-ladder RNAs from abortive RNAs. The results suggested that G-ladder RNAs adapt unusual conformations such as G-quartets. Thus, the new fluorescent probe can be useful for structural studies on RNA.

Fluorescence↗
PubMed2001

Spectral statistics of instantaneous normal modes in liquids and random matrices.

We study the statistical properties of eigenvalues of the Hessian matrix H (matrix of second derivatives of the potential energy) for a classical atomic liquid, and compare these properties with predictions for random matrix models. The eigenvalue spectra (the instantaneous normal mode or INM spectra) are evaluated numerically for configurations generated by molecular dynamics simulations. We find that distribution of spacings between nearest-neighbor eigenvalues, s, obeys quite well the Wigner prediction s exp(-s(2)), with the agreement being better for higher densities at fixed temperature. The deviations display a correlation with the number of localized eigenstates (normal modes) in the liquid; there are fewer localized states at higher densities that we quantify by calculating the participation ratios of the normal modes. We confirm this observation by calculating the spacing distribution for parts of the INM spectra with high participation ratios, obtaining greater conformity with the Wigner form. We also calculate the spectral rigidity and find a substantial dependence on the density of the liquid.

Journal Article↗
PubMed2001

Thermodynamic and structural aspects of the potential energy surface of simulated water.

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition is a topic of considerable interest. The potential energy surface of model liquids has been increasingly studied, since it provides a connection between the configurational component of the partition function on the one hand, and the system dynamics on the other. This connection is most obvious at low temperatures, where the motion of the system can be partitioned into vibrations within a basin of attraction and infrequent interbasin transitions. In this work, we present a description of the potential energy surface properties of supercooled liquid water. The dynamics of this model have been studied in great detail in recent years. We locate the minima sampled by the liquid by "quenches" from equilibrium configurations generated via molecular dynamics simulations, and then calculate the temperature and density dependence of the basin energy, degeneracy, and shape. The temperature dependence of the energy of the minima is qualitatively similar to simple liquids, but has anomalous density dependence. The unusual density dependence is also reflected in the configurational entropy, the thermodynamic measure of degeneracy. Finally, we study the structure of simulated water at the minima, which provides insight on the progressive tetrahedral ordering of the liquid on cooling.

Journal Article↗
PubMed2001

Biophysical analysis of the endoplasmic reticulum-resident chaperone/heat shock protein gp96/GRP94 and its complex with peptide antigen.

Animals vaccinated with heat shock protein (HSP)--peptide complexes develop specific protective immunity against cancers from which the HSPs were originally isolated. This autologous specific immunity has been demonstrated using a number of HSP--peptide antigen complexes. A prototypical HSP-based cancer vaccine is the gp96--peptide antigen complex, which is currently undergoing human clinical trials. Here, we analyzed the structure of a recombinant wild-type and a mutant gp96 protein and their peptide complexes using a number of biophysical techniques. Gel filtration chromatography, dynamic light scattering, and equilibrium analytical ultracentrifugation demonstrated that both a wild-type gp96 and a gp96 mutant lacking a dimerization domain formed higher order structures. More detailed analysis using scanning transmission electron microscopy indicated that both the wild-type and dimerization deletion mutant gp96 protein were organized, unexpectedly, into large aggregates. Size distributions ranged from dimers to octamers and higher. Circular dichroism and intrinsic Trp fluorescence suggested that the gp96 dimerization domain deletion mutant protein was more compact than the wild-type gp96. A fluorescent peptide antigen was synthesized, and the peptide-binding properties of wild-type and the dimerization domain deletion mutant gp96 were studied. Fluorescence lifetime and anisotropy decay showed that the bound antigenic peptide was located in a hydrophobic pocket, with considerable free space for the rotation of the probe. Deletion of the dimerization domain affected the peptide-binding microenvironment, although peptide-binding affinity was reduced by only a small extent. Peptide--gp96 complexes were extremely stable, persisting for many days in the cold. The extraordinary stability of peptide--gp96 complexes and the plasticity of the peptide-binding pocket support the proposed relay of diverse peptides to MHC and/or other molecules via molecular recognition.

Animals↗
PubMed2001

The relationship between fragility, configurational entropy and the potential energy landscape of glass-forming liquids.

Glass is a microscopically disordered, solid form of matter that results when a fluid is cooled or compressed in such a manner that it does not crystallize. Almost all types of materials are capable of glass formation, including polymers, metal alloys and molten salts. Given such diversity, general principles by which different glass-forming materials can be systematically classified are invaluable. One such principle is the classification of glass-formers according to their fragility. Fragility measures the rapidity with which a liquid's properties (such as viscosity) change as the glassy state is approached. Although the relationship between the fragility, configurational entropy and features of the energy landscape (the complicated dependence of energy on configuration) of a glass-former have been analysed previously, a detailed understanding of the origins of fragility is lacking. Here I use simulations to analyse the relationship between fragility and quantitative measures of the energy landscape for a model liquid whose fragility depends on its bulk density. The results reveal that fragility depends on changes in the vibrational properties of individual energy minima in addition to their total number and spread in energy. A thermodynamic expression for fragility is derived, which is in quantitative agreement with kinetic fragilities obtained from the liquid's diffusivity.

Journal Article↗
PubMed2001

Binding of antigenic peptide to the endoplasmic reticulum-resident protein gp96/GRP94 heat shock chaperone occurs in higher order complexes. Essential role of some aromatic amino acid residues in the peptide-binding site.

Vaccination with heat shock protein gp96-antigenic peptide complexes produces a powerful specific immune response against cancers and infectious diseases in some experimental animal models, and gp96-peptide complexes are now being tested in human clinical trials. gp96 appears to serve as a natural adjuvant for chaperoning antigenic peptides into the immune surveillance pathways. A fundamental issue that needs to be addressed is the mechanism of binding of antigenic peptide to gp96. Here, we show using scanning transmission electron microscopy that recombinant gp96 binds peptide in stable multimeric complexes, which may have biological significance. To open the possibility for genetically engineering gp96 for improved immunogenicity and to understand if molecular recognition plays a role in the binding of antigenic peptide, we mutagenized some specific aromatic amino acids in the presumed peptide-binding pocket. Replacement of Tyr-667 or Tyr-678 to Ala reduced affinity for peptide whereas conversion of Trp-654 to Tyr increased peptide binding. Similarly, changing Trp-621 to Phe or Leu or Ala or Ile negatively affected peptide binding whereas changing Trp-621 to Tyr or Val positively affected peptide binding. Probing the peptide microenvironment in gp96-peptide complexes, suggested that hydrophobic interactions (and perhaps hydrogen bonding/stacking interactions) may play a role in peptide loading by gp96.

Antigens, Neoplasm↗
PubMed2000

Liquid limits: glass transition and liquid-gas spinodal boundaries of metastable liquids.

The liquid-gas spinodal and the glass transition define ultimate boundaries beyond which substances cannot exist as (stable or metastable) liquids. The relation between these limits is analyzed via computer simulations of a model liquid. The results obtained indicate that the liquid-gas spinodal and the glass transition lines intersect at a finite temperature, implying a glass-gas mechanical instability locus at low temperatures. The glass transition lines obtained by thermodynamic and dynamic criteria agree very well with each other.

Journal Article↗
PubMed2000

Identification of the peptide-binding site in the heat shock chaperone/tumor rejection antigen gp96 (Grp94).

Heat shock protein (HSP)-peptide complexes from tumor cells elicit specific protective immunity when injected into inbred mice bearing the same specific type of tumor. The HSP-mediated specific immunogenicity also occurs with virus-infected cells. The immune response is solely due to endogenous peptides noncovalently bound to HSP. A vesicular stomatitis virus capsid-derived peptide ligand bearing a photoreactive azido group was specifically bound by and cross-linked to murine HSP glycoprotein (gp) 96. The peptide-binding site was mapped by specific proteolysis of the cross-links followed by analysis of the cross-linked peptides using a judicious combination of SDS-gel electrophoresis, mass spectrometry, and amino acid sequencing. The minimal peptide-binding site was mapped to amino acid residues 624-630 in a highly conserved region of gp96. A model of the peptide binding pocket of gp96 was constructed based on the known crystallographic structure of major histocompatibility complex class I molecule bound to a similar peptide. The gp96-peptide model predicts that the peptide ligand is held in a groove formed by alpha-helices and lies on a surface consisting of antiparallel beta-sheets. Interestingly, in this model, the peptide binding pocket abuts the dimerization domain of gp96, which may have implications for the extraordinary stability of peptide-gp96 complexes, and for the faithful relay of peptides to major histocompatibility complex class I molecule for antigen presentation.

Amino Acid Sequence↗
PubMed1999

Molecular mechanisms of peptide loading by the tumor rejection antigen/heat shock chaperone gp96 (GRP94).

Complexes of gp96/GRP94 and peptides have been shown to elicit immunogenicity. We used fluorescence to understand peptide association with gp96. A pyrene-peptide conjugate was complexed with gp96 under a variety of conditions. At room temperature in low salt (20 mM NaCl), the peptide binds gp96 with a strong affinity (approximately 100-150 nM) and forms pyrene excimers, suggesting that the peptides were assembled as dimers. In high salt (2.2 M NaCl), although peptide binding was stronger (Ka approximately 55 nM) than in low salt, pyrene excimers were absent, implying that peptides were farther apart in the complex. Heat shock-activated peptide binding exhibited characteristics of both low salt and high salt modes of binding. Anisotropy and average lifetime of the bound pyrene suggested that peptides were probably located in a solvent-accessible hydrophobic binding pocket in low salt, whereas in high salt, the peptide may be buried in a less hydrophobic (more hydrophilic) environment. These results suggested that peptide-gp96 complexes were assembled in several different ways, depending on the assembly conditions. Resonance energy transfer between the intrinsic tryptophan(s) in gp96 and pyrene suggested that one or more tryptophan residues were within the critical Forster distance of 27-30 A from the pyrene in the bound peptide. It is proposed that peptides are assembled within higher order gp96 complexes (dimers, etc.) in a hydrophobic pocket and that there may be a conformational change in gp96 leading to an open configuration for peptide loading.

Amino Acid Sequence↗
PubMed1999

Probing the interaction of T7 RNA polymerase with promoter.

Transcription is the fundamental process by which RNA is synthesized by RNA polymerases on double-stranded DNA templates. One structurally simple RNA polymerase is encoded by bacteriophage T7. T7 RNA polymerase is an excellent candidate for studying structural aspects of transcription, because unlike the eucaryotic and bacterial RNA polymerases, it is a single subunit enzyme and does not require additional factors to carry out the entire process of transcription from start to finish. An important advantage of studying transcription using this enzyme is that the high-resolution crystal structure of T7 RNA polymerase has been solved. However, a cocrystal structure of the polymerase complexed with promoter has not yet been published. Here, we have used cross-linking techniques to understand the interaction of promoter with T7 RNA polymerase. We constructed promoters that were substituted with the photo-cross-linkable nucleotide 5-iodo uracil at every dT in the promoter from -17 to -1. This substitution replaces the 5-methyl in dT with an iodine atom. The substituted promoters were photo-cross-linked to T7 RNAP, and the efficiency of cross-linking was quantitated at every position. In the melting domain, the strongest contacts occurred at -3 and at -1 on the template strand while very weak cross-linking was seen at -2 and at -4 on the nontemplate strand. In the binding domain, the strongest contacts were seen at -16, -15, and -13 and at -10 on the template strand while at -17 and -14 on the nontemplate strand very weak cross-linking was observed. Cross-linking was poor in the intervening region between the binding and the melting domains. These results suggested that, in the T7 RNA polymerase-promoter complex, the polymerase molecule mainly contacts the template bases in the TATA box while the upstream contacts are used as an anchor for DNA binding. For a systematic study designed to probe the nature of base-specific interactions in the polymerase-promoter complex, we used neutral salts from the Hofmeister series. In general, the order of perturbation was sulfate > citrate > acetate for anions and ammonium > magnesium > potassium for cations. Using acrylamide, a neutral hydrophobic agent to probe for nonionic contacts, we observed that at -2, -4, and -17 the contacts had a hydrophobic component, while at many other positions there was no significant effect, suggesting that the contacts in the promoter-polymerase complexes were predominantly ionic but at certain positions nonionic interactions also existed. To localize a specific interaction in the melting domain, we proteolyzed the cross-linked T7 RNAP and analyzed the fragments using gel electrophoresis, mass spectrometry, and amino acid composition. High-resolution mapping indicated that amino acid residues 614-627 may be in the vicinity of the melting domain. Specifically, Y623 may contact -3 on the template strand.

Bacteriophage T7↗
PubMed1999

Solution of lattice gas models in the generalized ensemble on the Bethe lattice.

We present the exact Bethe lattice solution for a lattice gas Potts model defined in the generalized ensemble which was previously studied in elucidating the anomalous thermodynamic properties of water. For this model the locus of density maxima (TMD), the locus of isothermal compressibility extrema, (TEC), the spinodal curve, and the percolation curve for four hydrogen bonded molecules are calculated using the Bethe lattice solution. The results confirm qualitative relationships between the TMD, the TEC, and the percolation curve obtained previously from a mean field calculation.

Journal Article↗
PubMed1998

The native form of alpha-synuclein is not found in the cerebrospinal fluid of patients with Parkinson's disease or normal controls.

Alpha-synuclein has recently been shown to be a major constituent of Lewy bodies in Parkinson's disease (PD). This observation led us to investigate the possibility that its detection in the cerebrospinal fluid (CSF) could be used as a marker for Lewy bodies in the central nervous system. In this study we determined the pattern of expression of alpha-synuclein in patients with sporadic Parkinson's disease (PD) and normal controls, using western immunoblotting in conjunction with an antibody that recognizes the carboxyl terminal of alpha-synuclein protein. The native 19 kDa band normally seen in brain homogenates was not found in the CSF of either parkinsonian patients or control subjects. However, a novel band was observed, which migrated at a position in the range of 42 kDa in CSF from both patients and controls. We conclude that alpha-synuclein cannot be used as a biomarker for Lewy bodies during life. However, further characterization of the 42 kDa protein may be of interest.

Blotting, Western↗