The charybdotoxin receptor of a Shaker K+ channel: peptide and channel residues mediating molecular recognition.

Charybdotoxin (CTX) is a peptide of known structure that inhibits Shaker K+ channels by a pore-blocking mechanism. Point mutagenesis of all 30 solvent-exposed residues identified the part of the CTX molecular surface making contact with the receptor in the K+ channel. All close-contact residues are clustered in a well-defined interaction surface; the shape of this surface implies that the outer opening of the Shaker channel conduction pore abruptly widens to a 25 x 35 A plateau. A mutagenic scan of the S5-S6 linker sequence of the Shaker K+ channel identified those channel residues influencing CTX binding affinity. The Shaker residues making the strongest contribution to toxin binding are located close to the pore-lining sequence, and more distant residues on both sides of this region influence CTX binding weakly, probably by an electrostatic mechanism. Complementary mutagenesis of both CTX and Shaker suggests that Shaker-F425 contacts a specific area near T8 and T9 on the CTX molecular surface. This contact point constrains Shaker-F425 to be located at a 20 A radial distance from the pore axis and 10-15 A above the "floor" of the CTX receptor

A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

We describe a novel coarse grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a viscoelastic continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations

Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity

BACKGROUND: With the advent of affordable and comprehensive sequencing technologies, access to molecular genetics for clinical diagnostics and research applications is increasing. However, variant interpretation remains challenging, and tools that close the gap between data generation and data interpretation are urgently required. Here we present a transferable approach to help address the limitations in variant annotation. METHODS: We develop a network of Bayesian logistic regression models that integrate multiple lines of evidence to evaluate the probability that a rare variant is the cause of an individual's disease. We present models for genes causing inherited cardiac conditions, though the framework is transferable to other genes and syndromes. RESULTS: Our models report a probability of pathogenicity, rather than a categorisation into pathogenic or benign, which captures the inherent uncertainty of the prediction. We find that gene- and syndrome-specific models outperform genome-wide approaches, and that the integration of multiple lines of evidence performs better than individual predictors. The models are adaptable to incorporate new lines of evidence, and results can be combined with familial segregation data in a transparent and quantitative manner to further enhance predictions. Though the probability scale is continuous, and innately interpretable, performance summaries based on thresholds are useful for comparisons. Using a threshold probability of pathogenicity of 0.9, we obtain a positive predictive value of 0.999 and sensitivity of 0.76 for the classification of variants known to cause long QT syndrome over the three most important genes, which represents sufficient accuracy to inform clinical decision-making. A web tool APPRAISE [http://www.cardiodb.org/APPRAISE] provides access to these models and predictions. CONCLUSIONS: Our Bayesian framework provides a transparent, flexible and robust framework for the analysis and interpretation of rare genetic variants. Models tailored to specific genes outperform genome-wide approaches, and can be sufficiently accurate to inform clinical decision-making

Airborne observations of the tropospheric CO2 distribution and its controlling factors over the South Pacific Basin

Highly precise measurements of CO2 mixing ratios were recorded aboard both the NASA DC-8 and P3-B aircraft during the Pacific Exploratory Mission-Tropics conducted in August-October 1996. Data were obtained at altitudes ranging from 0.1 to 12 km over a large portion of the South Pacific Basin representing the most geographically extensive CO2 data set recorded in this region. These data along with CO2 surface measurements from the National Oceanic and Atmospheric Administration/Climate Monitoring and Diagnostics Laboratory (NOAA/CMDL) and the National Institute of Water and Atmospheric Research (NIWA) were examined to establish vertical and meridional gradients. The CO2 spatial distribution in the southern hemisphere appeared to be largely determined by interhemispheric transport as air masses with depleted CO2 levels characteristic of northern hemispheric air were frequently observed south of the Intertropical Convergence Zone. However, regional processes also played a role in modulating background concentrations. Comparisons of CO2 with other trace gases indicated that CO2 values were influenced by continental sources. Large scale plumes from biomass burning activities produced enhanced CO2 mixing ratios within the lower to midtroposphere over portions of the remote Pacific. An apparent CO2 source was observed in the NOAA/ CMDL surface data between 15° N and 15° S and in the lower altitude flight data between 8° N and 8.5° S with a zone of intensity from 6.5° N to 1° S. Inferred from these data is the presence of a Southern Ocean sink from south of 15° S having two distinct zones seasonally out of phase with one another. Copyright 1999 by the American Geophysical Union

Mesoscopic theory for inhomogeneous mixtures

Mesoscopic density functional theory for inhomogeneous mixtures of sperical particles is developed in terms of mesoscopic volume fractions by a systematic coarse-graining procedure starting form microscopic theory. Approximate expressions for the correlation functions and for the grand potential are obtained for weak ordering on mesoscopic length scales. Stability analysis of the disordered phase is performed in mean-field approximation (MF) and beyond. MF shows existence of either a spinodal or a $\lambda$-surface on the volume-fractions - temperature phase diagram. Separation into homogeneous phases or formation of inhomogeneous distribution of particles occurs on the low-temperature side of the former or the latter surface respectively, depending on both the interaction potentials and the size ratios between particles of different species. Beyond MF the spinodal surface is shifted, and the instability at the $\lambda$-surface is suppressed by fluctuations. We interpret the $\lambda$-surface as a borderline between homogeneous and inhomogeneous (containing clusters or other aggregates) structure of the disordered phase. For two-component systems explicit expressions for the MF spinodal and $\lambda$-surfaces are derived. Examples of interaction potentials of simple form are analyzed in some detail, in order to identify conditions leading to inhomogeneous structures.Comment: 6 figure