Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

Transit and Eclipse Analyses of Exoplanet HD 149026b Using BLISS Mapping

The dayside of HD 149026b is near the edge of detectability by the Spitzer Space Telescope. We report on eleven secondary-eclipse events at 3.6, 4.5, 3 x 5.8, 4 x 8.0, and 2 x 16 microns plus three primary-transit events at 8.0 microns. The eclipse depths from jointly-fit models at each wavelength are 0.040 +/- 0.003% at 3.6 microns, 0.034 +/- 0.006% at 4.5 microns, 0.044 +/- 0.010% at 5.8 microns, 0.052 +/- 0.006% at 8.0 microns, and 0.085 +/- 0.032% at 16 microns. Multiple observations at the longer wavelengths improved eclipse-depth signal-to-noise ratios by up to a factor of two and improved estimates of the planet-to-star radius ratio (Rp/Rs = 0.0518 +/- 0.0006). We also identify no significant deviations from a circular orbit and, using this model, report an improved period of 2.8758916 +/- 0.0000014 days. Chemical-equilibrium models find no indication of a temperature inversion in the dayside atmosphere of HD 149026b. Our best-fit model favors large amounts of CO and CO2, moderate heat redistribution (f=0.5), and a strongly enhanced metallicity. These analyses use BiLinearly-Interpolated Subpixel Sensitivity (BLISS) mapping, a new technique to model two position-dependent systematics (intrapixel variability and pixelation) by mapping the pixel surface at high resolution. BLISS mapping outperforms previous methods in both speed and goodness of fit. We also present an orthogonalization technique for linearly-correlated parameters that accelerates the convergence of Markov chains that employ the Metropolis random walk sampler. The electronic supplement contains light-curve files and supplementary figures.Comment: Accepted for publication in Ap

Protein structures and optimal folding emerging from a geometrical variational principle

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is found that, irrespective of the sequence, the native state of a protein has exceedingly large number of conformations with a given amount of structural overlap compared to other compact artificial backbones; moreover the conformational entropies of unrelated proteins of the same length are nearly equal at any given stage of folding. These results are suggestive of an extremality principle underlying protein evolution, which, in turn, is shown to be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure

Infrared Eclipses of the Strongly Irradiated Planet WASP-33b, and Oscillations of its Host Star

We observe two secondary eclipses of the strongly irradiated transiting planet WASP-33b in the Ks band, and one secondary eclipse each at 3.6- and 4.5 microns using Warm Spitzer. This planet orbits an A5V delta-Scuti star that is known to exhibit low amplitude non-radial p-mode oscillations at about 0.1-percent semi-amplitude. We detect stellar oscillations in all of our infrared eclipse data, and also in one night of observations at J-band out of eclipse. The oscillation amplitude, in all infrared bands except Ks, is about the same as in the optical. However, the stellar oscillations in Ks band have about twice the amplitude as seen in the optical, possibly because the Brackett-gamma line falls in this bandpass. We use our best-fit values for the eclipse depth, as well as the 0.9 micron eclipse observed by Smith et al., to explore possible states of the exoplanetary atmosphere, based on the method of Madhusudhan and Seager. On this basis we find two possible states for the atmospheric structure of WASP-33b. One possibility is a non-inverted temperature structure in spite of the strong irradiance, but this model requires an enhanced carbon abundance (C/O>1). The alternative model has solar composition, but an inverted temperature structure. Spectroscopy of the planet at secondary eclipse, using a spectral resolution that can resolve the water vapor band structure, should be able to break the degeneracy between these very different possible states of the exoplanetary atmosphere. However, both of those model atmospheres absorb nearly all of the stellar irradiance with minimal longitudinal re-distribution of energy, strengthening the hypothesis of Cowan et al. that the most strongly irradiated planets circulate energy poorly. Our measurement of the central phase of the eclipse yields e*cos(omega)=0.0003 +/-0.00013, which we regard as being consistent with a circular orbit.Comment: 23 pages, 9 figures, 3 tables, accepted for the Astrophysical Journa

The TRAPPIST survey of southern transiting planets. I. Thirty eclipses of the ultra-short period planet WASP-43 b

We present twenty-three transit light curves and seven occultation light curves for the ultra-short period planet WASP-43 b, in addition to eight new measurements of the radial velocity of the star. Thanks to this extensive data set, we improve significantly the parameters of the system. Notably, the largely improved precision on the stellar density (2.41+-0.08 rho_sun) combined with constraining the age to be younger than a Hubble time allows us to break the degeneracy of the stellar solution mentioned in the discovery paper. The resulting stellar mass and size are 0.717+-0.025 M_sun and 0.667+-0.011 R_sun. Our deduced physical parameters for the planet are 2.034+-0.052 M_jup and 1.036+-0.019 R_jup. Taking into account its level of irradiation, the high density of the planet favors an old age and a massive core. Our deduced orbital eccentricity, 0.0035(-0.0025,+0.0060), is consistent with a fully circularized orbit. We detect the emission of the planet at 2.09 microns at better than 11-sigma, the deduced occultation depth being 1560+-140 ppm. Our detection of the occultation at 1.19 microns is marginal (790+-320 ppm) and more observations are needed to confirm it. We place a 3-sigma upper limit of 850 ppm on the depth of the occultation at ~0.9 microns. Together, these results strongly favor a poor redistribution of the heat to the night-side of the planet, and marginally favor a model with no day-side temperature inversion.Comment: 14 pages, 6 tables, 11 figures. Accepted for publication in A&

Spitzer observations of the thermal emission from WASP-43b

WASP-43b is one of the closest-orbiting hot Jupiters, with a semimajor axis of a = 0.01526 +/- 0.00018 AU and a period of only 0.81 days. However, it orbits one of the coolest stars with a hot Jupiter (Tstar = 4520 +/- 120 K), giving the planet a modest equilibrium temperature of Teq = 1440 +/- 40 K, assuming zero Bond albedo and uniform planetary energy redistribution. The eclipse depths and brightness temperatures from our jointly fit model are 0.347% +/- 0.013% and 1670 +/- 23 K at 3.6 {\mu}m and 0.382% +/- 0.015% and 1514 +/- 25 K at 4.5 {\mu}m. The eclipse timings improved the estimate of the orbital period, P, by a factor of three (P = 0.81347436 +/- 1.4*10-7 days) and put an upper limit on the eccentricity (e = 0.010+0.010 -0.007). We use our Spitzer eclipse depths along with four previously reported ground-based photometric observations in the near-infrared to constrain the atmospheric properties of WASP-43b. The data rule out a strong thermal inversion in the dayside atmosphere of WASP-43b. Model atmospheres with no thermal inversions and fiducial oxygen-rich compositions are able to explain all the available data. However, a wide range of metallicities and C/O ratios can explain the data. The data suggest low day-night energy redistribution in the planet, consistent with previous studies, with a nominal upper limit of about 35% for the fraction of energy incident on the dayside that is redistributed to the nightside.Comment: 11 pages, 9 figure

Possible thermochemical disequilibrium in the atmosphere of the exoplanet GJ 436b

The nearby extrasolar planet GJ 436b--which has been labelled as a 'hot Neptune'--reveals itself by the dimming of light as it crosses in front of and behind its parent star as seen from Earth. Respectively known as the primary transit and secondary eclipse, the former constrains the planet's radius and mass, and the latter constrains the planet's temperature and, with measurements at multiple wavelengths, its atmospheric composition. Previous work using transmission spectroscopy failed to detect the 1.4-\mu m water vapour band, leaving the planet's atmospheric composition poorly constrained. Here we report the detection of planetary thermal emission from the dayside of GJ 436b at multiple infrared wavelengths during the secondary eclipse. The best-fit compositional models contain a high CO abundance and a substantial methane (CH4) deficiency relative to thermochemical equilibrium models for the predicted hydrogen-dominated atmosphere. Moreover, we report the presence of some H2O and traces of CO2. Because CH4 is expected to be the dominant carbon-bearing species, disequilibrium processes such as vertical mixing and polymerization of methane into substances such as ethylene may be required to explain the hot Neptune's small CH4-to-CO ratio, which is at least 10^5 times smaller than predicted

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

Suppressed Far-UV stellar activity and low planetary mass-loss in the WASP-18 system

WASP-18 hosts a massive, very close-in Jupiter-like planet. Despite its young age (R′HK activity parameter lies slightly below the basal level; there is no significant time-variability in the log R′HK value; there is no detection of the star in the X-rays. We present results of far-UV observations of WASP-18 obtained with COS on board of HST aimed at explaining this anomaly. From the star’s spectral energy distribution, we infer the extinction (E(B − V) ≈ 0.01mag) and then the ISM column density for a number of ions, concluding that ISM absorption is not the origin of the anomaly. We measure the flux of the four stellar emission features detected in the COS spectrum (C II, C III, C IV, Si IV). Comparing the C II/C IV flux ratio measured for WASP-18 with that derived from spectra of nearby stars with known age, we see that the far-UV spectrum of WASP-18 resembles that of old (>5Gyr), inactive stars, in stark contrast with its young age. We conclude that WASP-18 has an intrinsically low activity level, possibly caused by star-planet tidal interaction, as suggested by previous studies. Re-scaling the solar irradiance reference spectrum to match the flux of the Si IV line, yields an XUV integrated flux at the planet orbit of 10.2 erg s−1 cm−2. We employ the rescaled XUV solar fluxes to model of the planetary upper atmosphere, deriving an extremely low thermal mass-loss rate of 10−20MJ Gyr−1. For such high-mass planets, thermal escape is not energy limited, but driven by Jeans escape