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At least 433 records · Page 24Linked to original sources
PubMed2002

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation.

Protein G is folded with an all-atom Monte Carlo simulation by using a Gō potential. When folding is monitored by using burial of the lone tryptophan in protein G as the reaction coordinate, the ensemble kinetics is single exponential. Other experimental observations, such as the burst phase and mutational data, are also reproduced. However, more detailed analysis reveals that folding occurs over three distinct, three-state pathways. We show that, because of this tryptophan's asymmetric location in the tertiary fold, its burial (i) does not detect certain intermediates and (ii) may not correspond to the folding event. This finding demonstrates that ensemble averaging can disguise the presence of multiple pathways and intermediates when a non-ideal reaction coordinate is used. Finally, all observed folding pathways eventually converge to a common rate-limiting step, which is the formation of a specific nucleus involving hydrophobic core residues. These residues are conserved in the ubiquitin superfamily and in a phage display experiment, suggesting that fold topology is a strong determinant of the transition state.

Binding Sites↗
PubMed1990

Long-range electron exchange measured in proteins by quenching of tryptophan phosphorescence.

Ten proteins that span a wide range of phosphorescence lifetimes were examined for sensitivity to quenching by four agents of disparate chemical nature. The results show that quenching efficiency is relatively independent of the quencher and is highly correlated with depth of burial of the phosphorescent tryptophan. The bimolecular quenching rate constants (kq) measured for the different proteins, spanning 5 orders of magnitude in kq, are found to decrease exponentially with the distance (r) of the tryptophan in angstroms from the protein surface--i.e., kq = Aexp(-r/rho), where A contains a geometrical factor dependent on tryptophan burial and surface geometry [corrected]. Theoretical analysis shows that this behavior can be expected for an electron-exchange reaction between the buried tryptophans and quenchers in solution in the rapid diffusion limit. Therefore, the results obtained provide evidence for an exponential dependence of electron-transfer rate on distance in a protein environment and evaluate the distance parameter, rho, for electron transfer through the general protein matrix at 1.0 A. For a unimolecular donor-acceptor pair with ket = koexp(-r/rho), ko approximately 10(9) sec-1.

Enzymes↗
PubMed1995

A general model of invariant chain association with class II major histocompatibility complex proteins.

The binding of invariant chain to major histocompatibility complex (MHC) proteins is an important step in processing of MHC class II proteins and in antigen presentation. The question of how invariant chain can bind to all MHC class II proteins is central to understanding these processes. We have employed molecular modeling to predict the structure of class II-associated invariant chain peptide (CLIP)-MHC protein complexes and to ask whether the predicted mode of association could be general across all MHC class II proteins. CLIP fits identically into the MHC class II alleles HLA-DR3, I-Ak, I-Au, and I-Ad, with a consistent pattern of hydrogen bonds, contacts, and hydrophobic burial and without bad contacts. Our model predicts the burial of CLIP residues Met-91 and Met-99 in the deep P1 and P9 anchor pockets and other detailed interactions, which we have compared with available data. The predicted pattern of I-A allele-specific effects on CLIP binding is very similar to that observed experimentally by alanine-scanning mutations of CLIP. Together, these results indicate that CLIP may bind in a single, general way across products of MHC class II alleles.

Alleles↗
PubMed1999

Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate.

On exposure to mildly acidic conditions, apomyoglobin forms a partially folded intermediate, I. The A, B, G, and H helices are significantly structured in this equilibrium intermediate, whereas the remainder of the protein is largely unfolded. We report here the effects of mutations at helix pairing sites on the stability of I in three classes of mutants that: (i) truncate hydrophobic side chains in native helix packing sites, (ii) truncate hydrophobic side chains not involved in interhelical contacts, and (iii) extend hydrophobic side chains at residues not involved in interhelical contacts. Class I mutants significantly decrease the stability and cooperativity of folding of the intermediate. Class II and III mutants show smaller effects on stability and have little effect on cooperativity. Qualitatively similar results to those found in I were obtained for all three classes of mutants in native myoglobin (N), demonstrating that hydrophobic burial is fairly specific to native helix packing sites in I as well as in N. These results suggest that hydrophobic burial along native-like interhelical contacts is important for the formation of the cooperatively folded intermediate.

Amino Acid Sequence↗
PubMed2000

Epilepsy and catalepsy in Anglo-American literature between romanticism and realism: Tennyson, Poe, Eliot and Collins.

Epilepsy and catalepsy were not clearly separated in the minds of people in the early 19th century, and catalepsy may have been used as a diagnostic euphemism for epilepsy. Tennyson, in "The Princess" describes, under the diagnosis of catalepsy, probable temporal lobe epileptic dreamy states with derealization which serve as a metaphor of sexual and moral ambivalence, the poem's central theme. It seems that Tennyson knew such seizures from his own father who had been given a diagnosis of catalepsy. Poe gave his Berenice in the novella of the same title a diagnosis of epilepsy as a reason for a premature burial. However, there was a good deal of unlikelyhood in this, and when he came to this theme in "The Fall of the House of Usher" and in "The Premature Burial" he chose instead a diagnosis of catalepsy which fitted better with the plot. The fits of the title character in George Eliot's Silas Marner, diagnosed as catalepsy, would today rather be seen as epileptic twilight states. It would seem that this author drew from contemporary dictionary descriptions which described conditions similar to Marner's fits under the heading of catalepsy. In Eliot's "legend with a realistic treatment", the twilight states are a central factor in the plot and explain Marner's reclusion and passivity. In Poor Miss Finch by English realist Wilkie Collins, the post-traumatic seizures of Oscar, one of the main characters, their cause, their treatment with silver nitrate, and the subsequent discoloration of his skin are central supporting elements of a perfectly constructed plot. Collins gives an exact description of a right versive seizure with secondary generalisation, and how to deal with it. In none of these works seizures are seen in a negative light. They rather evoke reactions of sympathy and support.

Catalepsy↗
PubMedDate not supplied

Human population dynamics.

Time-series analysis of parish register series can be used to study human population dynamics at three different levels: (i) The metapopulation of preindustrial rural England. A short wavelength, exogenous oscillation in the burials series of 404 parishes can be detected which, it is suggested, was driven by a cycle of malnutrition associated with wheat prices. (ii) Individual populations, where long-term endogenous oscillations in baptisms and burials of wavelength 30-32 years or 43-44 years can be detected. Their characteristics and causes are explored and elucidated by matrix modelling. (iii) The separate neonatal, post-neonatal, child and adult mortalities in an individual population each show an exogenous short wavelength oscillation and a model is presented to show how these cycles were driven by an oscillation in grain prices and how they interacted. Together, they formed the feedback in a saturated, density-dependent population which was fundamental in controlling the characteristics of the longer wavelength endogenous oscillations in the population dynamics described above.

England↗
PubMed1984

Microdistribution and localized dosimetry of 241Am in bones of beagle dogs.

The microdistribution of 241Am in selected bones of seven beagle dogs was analysed using a computer controlled microscope photometer. Four of the animals receiving between 102.5 and 165 kBq/kg were killed between 7 and 20 days after injection, and three animals receiving 32.9-34.0 kBq/kg were killed between 1300 and 1569 days. Using the photometric scanning technique, the concentrations of 241Am in several anatomical regions, as well as the specific surface activities and their variations, dose rates, accumulated radiation doses, burial depths and morphometric parameters, were derived. Dose rates to the 0-10 micron marrow band adjacent to surfaces were found to be between 8.6 and 15.7 times higher than the average skeletal dose. Accumulated radiation doses from initial deposits to lining cells were estimated to be between 87 and 252 Gy. The average burial depth in the animals killed at later times was around 8 micron. Morphometric parameters showed that radiation damage occurred in these animals, resulting in abnormal trabecular architecture. A positive correlation between specific surface activity and local turnover rates was established.

Americium↗
PubMed2006

Microbial survival rates of Escherichia coli and Deinococcus radiodurans under low temperature, low pressure, and UV-Irradiation conditions, and their relevance to possible Martian life.

Viability rates were determined for microbial populations of Escherichia coli and Deinococcus radiodurans under the environmental stresses of low temperature (-35 degrees C), low-pressure conditions (83.3 kPa), and ultraviolet (UV) irradiation (37 W/m(2)). During the stress tests the organisms were suspended in saltwater soil and freshwater soil media, at variable burial depths, and in seawater. Microbial populations of both organisms were most susceptible to dehydration stress associated with low-pressure conditions, and to UV irradiation. However, suspension in a liquid water medium and burial at larger depths (5 cm) improved survival rates markedly. Our results indicate that planetary surfaces that possess little to no atmosphere and have low water availability do not constitute a favorable environment for terrestrial microorganisms.

Atmospheric Pressure↗
PubMed2005

The impact of avalanche transceivers on mortality from avalanche accidents.

Rapid extrication is the most important determinant of survival in avalanche victims. To facilitate rapid localization of avalanche victims by uninjured companions, avalanche transceivers are widely used during off-piste and backcountry activities. Despite their widespread use, the influence of transceivers on survival probability in avalanche accidents is controversial. The aim of this retrospective study was to analyze the influence of transceivers on the mortality of avalanche victims. There were 194 accidents in Austria from 1994 to 2003, involving 278 totally buried victims, which were analyzed. Avalanche transceivers were used by 156 (56%) victims and were associated with a significant reduction in median burial time from 102 to 20 min (p < 0.001), as well as a significant reduction in mortality from 68.0% to 53.8% (p = 0.011). This reduction was due to a decrease in mortality during backcountry activities involving ski tourers in free alpine areas (from 78.9% to 50.4%, p < 0.001). Transceivers did not reduce mortality during off-piste activities beside or near organized ski slopes (67.7% with versus 58.5% without transceiver, not significant). Mortality of persons using a transceiver is significantly higher if burial depth exceeds 1.5 m. Despite a significant reduction, mortality still exceeds 50% even with the use of transceivers. Therefore, in addition to the use of emergency equipment like transceivers, avalanche avoidance measures are critically important. The fairly modest influence of the use of transceivers on survival probability may be due to the highly efficient mountain rescue service in the Austrian Alps. In remote areas the reduction in mortality will probably be far more pronounced.

Accident Prevention↗
PubMed1984

Distinct structures of ATP and GTP complexes in the myosin ATPase.

The active site of the myosin subfragment-1 ATPase was affinity-labeled with ribose-modified fluorescent analogs of ADP, dADP, CDP, UDP, IDP, and GDP in combination with vanadate, forming a stable myosin-nucleoside diphosphate-vanadate complex that is analogous to the normal myosin-ADP-Pi intermediate [Hiratsuka, T. (1984) J. Biochem. 96, 147-154]. Labeled enzyme was isolated free of unbound analog and vanadate, and fluorescent properties of the fluorophore at the active site were examined. Fluorescence emission and acrylamide quenching studies revealed that the hydrophobicity of environment around the fluorophore and the degree of its burial in the protein vary with the base structure of NDP. It was found that the fluorophore of ADP analog is most buried into the protein, while that of the GDP analog is least buried. The results suggest that the deep burial of ATP into the myosin active site is essential for muscle contraction.

Acrylamides↗
PubMed1999

The bottom line for prediction of residue solvent accessibility.

A simple method of predicting residue solvent accessibilities in proteins is described, with the intention that it should be used as a baseline by which more sophisticated approaches to prediction can be judged. Comparison with existing methods of predicting residue burial reveals that their performance is often little better than that of the baseline method. The problem of comparing different prediction methods is shown to be complicated by the proliferation of different schemes for classifying residue burial.

Algorithms↗
PubMed2000

Disulfide recognition in an optimized threading potential.

An energy potential is constructed and trained to succeed in fold recognition for the general population of proteins as well as an important class which has previously been problematic: small, disulfide-bearing proteins. The potential is modeled on solvation, with the energy a function of side chain burial and the number of disulfide bonds. An accurate disulfide recognition algorithm identifies cysteine pairs which have the appropriate orientation to form a disulfide bridge. The potential has 22 energy parameters which are optimized so the Protein Data Bank (PDB) structure for each sequence in a training set is the lowest in energy out of thousands of alternative structures. One parameter per amino acid type reflects burial preference and a single parameter is used in an overpacking term. Additionally, one optimized parameter provides a favorable contribution for each disulfide identified in a given protein structure. With little training, the potential is >80% accurate in ungapped threading tests using a variety of proteins. The same level of accuracy is observed in a threading test of small proteins which have disulfide bonds. Importantly, the energy potential is also successful with proteins having uncrosslinked cysteines.

Algorithms↗
PubMed1986

Determination of 241Pu in low-level radioactive wastes from reactors.

Plutonium-241 is unique in low-level radioactive wastes (LLW) from nuclear power plants because it is the only significant beta-emitting transuranic nuclide in LLW, has a relatively short half-life of 14.4 y, and has a fairly high allowable concentration for shallow land burial. Radiochemical separation of Pu followed by liquid scintillation analysis was used to quantitate 241Pu in a wide range of solid, semi-solid, and liquid LLW samples from two nuclear plants in Michigan. The 241Pu concentrations varied considerably by sample type and reactor operational period as did their correlation with 137Cs, 144Ce, 239Pu and 240Pu concentrations in the same sample. These patterns were also found in reported data for 241Pu in LLW from other reactors, raising the difficulty of accurately determining the inventory (or source term) in a LLW shallow land burial site and its implications for predicting and controlling the future environmental and public health impacts of such disposal.

Cerium Radioisotopes↗
PubMed1997

Carbon cartridge standards for 125I and suggested applications.

Carbon cartridge standards were prepared to assess the activity of 125I incident on, and adsorbed in, cartridge samples during air sampling. Each cartridge standard consisted of an 125I-spiked filter paper at a known depth, ranging from 0 to 19 mm, embedded in approximately 34 g of 20-30 mesh activated carbon contained within a 6.35 cm diameter by 2.22 cm deep metal cartridge with screened openings. The total counting efficiency values range from 17.8 to 20.8% for cartridges counted at 3.2 mm from a thin-crystal NaI(Tl) detector. The standards were analyzed using a front/back counting technique, and fitting functions were developed relating the front/back net counts ratio and counting efficiency to the 125I depth of burial. A method for determining sample activity that accounts for exponential radioiodine loading in cartridge samples is compared to a less complicated technique that assumes all the radioiodine is located at an equivalent depth of burial that is based on the sample front/back net counts ratio. In addition, methods are presented for determining airborne 125I activity for constant and variable concentrations. Variable concentrations are assumed to occur in a fume hood duct by one or more bulk releases as a result of iodinations that are performed during a given sampling interval. The two methods are shown to have maximum relative deviations ranging from -16 to +16%.

Air Pollutants, Radioactive↗
PubMed2005

Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling.

In a fire tragedy in Manila in December 1998, one of the worst tragic incidents which resulted in the reported death of 23 children, identity could not be established initially resulting in the burial of still unidentified bodies. Underscoring the importance of identifying each of the human remains, the bodies were exhumed 3 months after the tragedy. We describe here our work, which was the first national case handled by local laboratories wherein conventional and molecular-based techniques were successfully applied in forensic identification. The study reports analysis of DNA obtained from skeletal remains exposed to conditions of burning, burial, and exhumation. DNA typing methods using autosomal and Y-chromosomal short tandem repeat (Y-STR) markers reinforced postmortem examinations using conventional identification techniques. The strategy resulted in the identification of 18 out of the 21 human remains analyzed, overcoming challenges encountered due to the absence of established procedures for the recovery of mass disaster remains. There was incomplete antemortem information to match the postmortem data obtained from the remains of 3 female child victims. Two victims were readily identified due to the availability of antemortem tissues. In the absence of this biologic material, parentage testing was performed using reference blood samples collected from parents and relatives. Data on patrilineal lineage based on common Y-STR haplotypes augmented autosomal DNA typing, particularly in deficiency cases.

Autopsy↗
PubMed2003

Evidence for rapid climate change in the Mesozoic-Palaeogene greenhouse world.

The best-documented example of rapid climate change that characterized the so-called 'greenhouse world' took place at the time of the Palaeocene-Eocene boundary: introduction of isotopically light carbon into the ocean-atmosphere system, accompanied by global warming of 5-8 degrees C across a range of latitudes, took place over a few thousand years. Dissociation, release and oxidation of gas hydrates from continental-margin sites and the consequent rapid global warming from the input of greenhouses gases are generally credited with causing the abrupt negative excursions in carbon- and oxygen-isotope ratios. The isotopic anomalies, as recorded in foraminifera, propagated downwards from the shallowest levels of the ocean, implying that considerable quantities of methane survived upward transit through the water column to oxidize in the atmosphere. In the Mesozoic Era, a number of similar events have been recognized, of which those at the Triassic-Jurassic boundary, in the early Toarcian (Jurassic) and in the early Aptian (Cretaceous) currently carry the best documentation for dramatic rises in temperature. In these three examples, and in other less well-documented cases, the lack of a definitive time-scale for the intervals in question hinders calculation of the rate of environmental change. However, comparison with the Palaeocene-Eocene thermal maximum (PETM) suggests that these older examples could have been similarly rapid. In both the early Toarcian and early Aptian cases, the negative carbon-isotope excursion precedes global excess carbon burial across a range of marine environments, a phenomenon that defines these intervals as oceanic anoxic events (OAEs). Osmium-isotope ratios ((187)Os/(188)Os) for both the early Toarcian OAE and the PETM show an excursion to more radiogenic values, demonstrating an increase in weathering and erosion of continental crust consonant with elevated temperatures. The more highly buffered strontium-isotope system ((87)Sr/(86)Sr) also shows relatively more radiogenic signatures during the early Toarcian OAE, but the early Aptian and Cenomanian-Turonian OAEs show the reverse effect, implying that increased rates of sea-floor spreading and hydrothermal activity dominated over continental weathering in governing sea-water chemistry. The Cretaceous climatic optimum (late Cenomanian to mid Turonian) also shows evidence for abrupt cooling episodes characterized by episodic invasion of boreal faunas into temperate and subtropical regions and changes in terrestrial vegetation; drawdown of CO(2) related to massive marine carbon burial (OAE) may be implicated here. The absence of a pronounced negative carbon-isotope excursion preceding the Cenomanian-Turonian OAE indicates that methane release is not necessarily connected to global deposition of marine organic carbon, but relative thermal maxima are common to all OAEs. 'Cold snaps' have also been identified from the Mesozoic record but their duration, causes and effects are poorly documented.

Carbon↗
PubMed2006

The carbon cycle and associated redox processes through time.

Earth's biogeochemical cycle of carbon delivers both limestones and organic materials to the crust. In numerous, biologically catalysed redox reactions, hydrogen, sulphur, iron, and oxygen serve prominently as electron donors and acceptors. The progress of these reactions can be reconstructed from records of variations in the abundance of 13C in sedimentary carbonate minerals and organic materials. Because the crust is always receiving new CO2 from the mantle and a portion of it is being reduced by photoautotrophs, the carbon cycle has continuously released oxidizing power. Most of it is represented by Fe3+ that has accumulated in the crust or been returned to the mantle via subduction. Less than 3% of the estimated, integrated production of oxidizing power since 3.8 Gyr ago is represented by O2 in the atmosphere and dissolved in seawater. The balance is represented by sulphate. The accumulation of oxidizing power can be estimated from budgets summarizing inputs of mantle carbon and rates of organic-carbon burial, but levels of O2 are only weakly and indirectly coupled to those phenomena and thus to carbon-isotopic records. Elevated abundances of 13C in carbonate minerals ca 2.3 Gyr old, in particular, are here interpreted as indicating the importance of methanogenic bacteria in sediments rather than increased burial of organic carbon.

Atmosphere↗
PubMed2004

Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims.

This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration.

Base Sequence↗