Kinetic and Structural Analysis of the Mg2+ -binding Site of the Guanine Nucleotide-binding Protein p21 H-ras.

The coordination and binding of the Mg2+ ion in the nucleotide−binding site of p21 have been investigated using site−directed mutagenesis, kinetic methods, and phosphorous NMR. Mg2+ in the p21.nucleotide.Mg2+ complex appears to be in fast equilibrium with the solvent. The dissociation constant between Mg2+ and the p21.GDP complex was determined to be 2.8 microM. It decreases 30− or 16−fold on substituting Ser−17 or Asp−57 with alanine, respectively, whereas the T35A mutation has no effect. All three mutations influence the dissociation constants and the association and dissociation rate constants of the interaction between guanine nucleotides and p21, but to a different degree. We conclude that Thr−35 is only complexed to Mg2+ in the GTP conformation and both Asp−57 and Ser−17 appear to be critical for both GDP and GTP binding. 31P NMR spectra of the GDP and Gpp(NH)p (guanosine−5'−(beta,gamma−imido)triphosphate) complexes of mutated p21 show a remarkable perturbation of the guanine nucleotide− binding site compared to wild−type protein. The mutant proteins show reduced GTPase rates, which are not stimulated by the GTPase−activating protein GAP. p21(S17A) has been reported to function just as p21(S17N) as a dominant negative inhibitor of normal p21. We find that it inhibits oncogenic p21−induced survival of primary neuron

ICT literacy: a technical or a non-technical issue?

In this short reply to Riis’ paper I first deal with his perceptive defence of ICT literacy, to which I fully subscribe, showing how his ideas might gain from highlighting the ‘technical’ dimensions involved in literacy practices. Second, this will allow me to make some comments regarding the curricular and organizational aspects of contemporary (school) education, which forms the largest part of his paper. My main line of criticism towards Riis’ paper is that I defend a ‘technical’ rather than a ‘non-technical’ account of digital literacy

The pre-hydrolysis state of p21ras in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins

AbstractBackground: In numerous biological events the hydrolysis of guanine triphosphate (GTP) is a trigger to switch from the active to the inactive protein form. In spite of the availability of several high-resolution crystal structures, the details of the mechanism of nucleotide hydrolysis by GTPases are still unclear. This is partly because the structures of the proteins in their active states had to be determined in the presence of non-hydrolyzable GTP analogues (e.g. GppNHp). Knowledge of the structure of the true Michaelis complex might provide additional insights into the intrinsic protein hydrolysis mechanism of GTP and related nucleotides.Results: The structure of the complex formed between p21ras and GTP has been determined by X-ray diffraction at 1.6 Å using a combination of photolysis of an inactive GTP precursor (caged GTP) and rapid freezing (100K). The structure of this complex differs from that of p21ras–GppNHp (determined at 277K) with respect to the degree of order and conformation of the catalytic loop (loop 4 of the switch II region) and the positioning of water molecules around the γ-phosphate group. The changes in the arrangement of water molecules were induced by the cryo-temperature technique.Conclusions: The results shed light on the function of Gln61 in the intrinsic GTP hydrolysis reaction. Furthermore, the possibility of a proton shuffling mechanism between two attacking water molecules and an oxygen of the γ-phosphate group can be proposed for the basal GTPase mechanism, but arguments are presented that render this protonation mechanism unlikely for the GTPase activating protein (GAP)-activated GTPase

Different Ways of Reading, or Just Making the Right Noises?

What does reading look like? Can learning to read be reduced to the acquisition of a set of isolable skills, or proficiency in reading be equated with the independence of the solitary, silent reader of prose fiction? These conceptions of reading and reading development, which figure strongly in educational policy, may appear to be simple common sense. But both ethnographic data and evidence from literary texts suggest that such paradigms offer, at most, a partial and ahistorical picture of reading. An important dimension, neglected in the dominant paradigms, is the irreducibly social quality of reading practices

K. Schwarzschild's problem in radiation transfer theory

We solve exactly the problem of a finite slab receiving an isotropic radiation on one side and no radiation on the other side. This problem - to be more precise the calculation of the source function within the slab - was first formulated by K. Schwarzschild in 1914. We first solve it for unspecified albedos and optical thicknesses of the atmosphere, in particular for an albedo very close to 1 and a very large optical thickness in view of some astrophysical applications. Then we focus on the conservative case (albedo = 1), which is of great interest for the modeling of grey atmospheres in radiative equilibrium. Ten-figure tables of the conservative source function are given. From the analytical expression of this function, we deduce 1) a simple relation between the effective temperature of a grey atmosphere in radiative equilibrium and the temperature of the black body that irradiates it, 2) the temperature at any point of the atmosphere when it is in local thermodynamical equilibrium. This temperature distribution is the counterpart, for a finite slab, of Hopf's distribution in a half-space. Its graphical representation is given for various optical thicknesses of the atmosphere.Comment: 21 pages, 2 figures, JQSRT, accepted 16 May 200

Warming the early Earth - CO2 reconsidered

Despite a fainter Sun, the surface of the early Earth was mostly ice-free. Proposed solutions to this so-called "faint young Sun problem" have usually involved higher amounts of greenhouse gases than present in the modern-day atmosphere. However, geological evidence seemed to indicate that the atmospheric CO2 concentrations during the Archaean and Proterozoic were far too low to keep the surface from freezing. With a radiative-convective model including new, updated thermal absorption coefficients, we found that the amount of CO2 necessary to obtain 273 K at the surface is reduced up to an order of magnitude compared to previous studies. For the late Archaean and early Proterozoic period of the Earth, we calculate that CO2 partial pressures of only about 2.9 mb are required to keep its surface from freezing which is compatible with the amount inferred from sediment studies. This conclusion was not significantly changed when we varied model parameters such as relative humidity or surface albedo, obtaining CO2 partial pressures for the late Archaean between 1.5 and 5.5 mb. Thus, the contradiction between sediment data and model results disappears for the late Archaean and early Proterozoic.Comment: 53 pages, 4 tables, 11 figures, published in Planetary and Space Scienc

The Maximal Runaway Temperature of Earth-like Planets

We generalize the problem of the semi-gray model to cases in which a non-negligible fraction of the stellar radiation falls on the long-wavelength range, and/or that the planetary long-wavelength emission penetrates into the transparent short wavelength domain of the absorption. Second, applying the most general assumptions and independently of any particular properties of an absorber, we show that the greenhouse effect saturates and any Earth-like planet has a maximal temperature which depends on the type of and distance to its main-sequence star, its albedo and the primary atmospheric components which determine the cutoff frequency below which the atmosphere is optically thick. For example, a hypothetical convection-less planet similar to Venus, that is optically thin in the visible, could have at most a surface temperature of 1200-1300K irrespective of the nature of the greenhouse gas. We show that two primary mechanisms are responsible for the saturation of the runaway greenhouse effect, depending on the value of the wavelength above which the atmosphere becomes optically thick. Unless this wavelength is small and resides in the optical region, saturation is achieved by radiating the thermal flux of the planet through the short wavelength tail of the thermal distribution. This has the observational implication, the radiation from such a planet should be skewed towards the NIR. Otherwise, saturation takes place by radiating through windows in the FIR.Comment: 13 pages 14 figure

Methane in the atmosphere of the transiting hot Neptune GJ436b?

We present an analysis of seven primary transit observations of the hot Neptune GJ436b at 3.6, 4.5 and $8~\mu$m obtained with the Infrared Array Camera (IRAC) on the Spitzer Space Telescope. After correcting for systematic effects, we fitted the light curves using the Markov Chain Monte Carlo technique. Combining these new data with the EPOXI, HST and ground-based $V, I, H$ and $K_s$ published observations, the range $0.5-10~\mu$m can be covered. Due to the low level of activity of GJ436, the effect of starspots on the combination of transits at different epochs is negligible at the accuracy of the dataset. Representative climate models were calculated by using a three-dimensional, pseudo-spectral general circulation model with idealised thermal forcing. Simulated transit spectra of GJ436b were generated using line-by-line radiative transfer models including the opacities of the molecular species expected to be present in such a planetary atmosphere. A new, ab-initio calculated, linelist for hot ammonia has been used for the first time. The photometric data observed at multiple wavelengths can be interpreted with methane being the dominant absorption after molecular hydrogen, possibly with minor contributions from ammonia, water and other molecules. No clear evidence of carbon monoxide and dioxide is found from transit photometry. We discuss this result in the light of a recent paper where photochemical disequilibrium is hypothesised to interpret secondary transit photometric data. We show that the emission photometric data are not incompatible with the presence of abundant methane, but further spectroscopic data are desirable to confirm this scenario.Comment: 19 pages, 10 figures, 1 table, Astrophysical Journal in pres