Encounter complexes and dimensionality reduction in protein-protein association

An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition

The 10Be contents of SNC meteorites

Several authors have explored the possibility that the Shergottites, Nakhlites, and Chassigny (SNC) came from Mars. The spallogenic gas contents of the SNC meteorites have been used to: constrain the sizes of the SNC's during the last few million years; to establish groupings independent of the geochemical ones; and to estimate the likelihood of certain entries in the catalog of all conceivable passages from Mars to Earth. The particular shielding dependence of Be-10 makes the isotope a good probe of the irradiation conditions experienced by the SNC meteorites. The Be-10 contents of nine members of the group were measured using the technique of accelerator mass spectrometry. The Be-10 contents of Nakhla, Governador Valadares, Chassigny, and probably Lafayette, about 20 dpm/kg, exceed the values expected from irradiation of the surface of a large body. The Be-10 data therfore do not support scenario III of Bogard et al., one in which most of the Be-10 in the SNC meteorites would have formed on the Martian surface; they resemble rather the Be-10 contents found in many ordinary chondrites subjected to 4 Pi exposures. The uncertainties of the Be-10 contents lead to appreciable errors in the Be-10 ages, t(1) = -1/lambda ln(1 Be-10/Be-10). Nonetheless, the Be-10 ages are consistent with the Ne-21 ages calculated assuming conventional, small-body production rates and short terrestrial ages for the finds. It is believed that this concordance strengthens the case for at least 3 different irradiation ages for the SNC meteorites. Given the similar half-thicknesses of the Be-10 and Ne-21 production rates, the ratios of the Be-10 and Ne-21 contents do not appear consistent with common ages for any of the groups. In view of the general agreement between the Be-10 and Ne-21 ages it does not seem useful at this time to construct multiple-stage irradiation histories for the SNC meteorites

Beable trajectories for revealing quantum control mechanisms

The dynamics induced while controlling quantum systems by optimally shaped laser pulses have often been difficult to understand in detail. A method is presented for quantifying the importance of specific sequences of quantum transitions involved in the control process. The method is based on a ``beable'' formulation of quantum mechanics due to John Bell that rigorously maps the quantum evolution onto an ensemble of stochastic trajectories over a classical state space. Detailed mechanism identification is illustrated with a model 7-level system. A general procedure is presented to extract mechanism information directly from closed-loop control experiments. Application to simulated experimental data for the model system proves robust with up to 25% noise.Comment: Latex, 20 pages, 13 figure

Teratogenic risk and contraceptive counselling in psychiatric practice: analysis of anticonvulsant therapy

<p>Background: Anticonvulsants have been used to manage psychiatric conditions for over 50 years. It is recognised that some, particularly valproate, carbamazepine and lamotrigine, are human teratogens, while others including topiramate require further investigation. We aimed to appraise the documentation of this risk by psychiatrists and review discussion around contraceptive issues.</p> <p>Methods: A retrospective review of prescribing patterns of four anticonvulsants (valproate, carbamazepine, lamotrigine and topiramate) in women of child bearing age was undertaken. Documented evidence of discussion surrounding teratogenicity and contraceptive issues was sought.</p> <p>Results: Valproate was most commonly prescribed (n=67). Evidence of teratogenic risk counselling at medication initiation was sub-optimal – 40% of individuals prescribed carbamazepine and 22% of valproate. Documentation surrounding contraceptive issues was also low- 17% of individuals prescribed carbamazepine and 13% of valproate.</p> <p>Conclusion: We found both low rates of teratogenic risk counselling and low rates of contraception advice in our cohort. Given the high rates of unplanned pregnancies combined with the relatively high risk of major congenital malformations, it is essential that a detailed appraisal of the risks and benefits associated with anticonvulsant medication occurs and is documented within patients’ psychiatric notes.</p&gt

Hydrogen Bond Dynamics Near A Micellar Surface: Origin of the Universal Slow Relaxation at Complex Aqueous Interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than a hundred picosecond. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5kcal/mole.Comment: 12 pages. Phys. Rev. Lett. (Accepted) (2002

Electronic Structure of Lanthanum Hydrides with Switchable Optical Properties

Recent dramatic changes in the optical properties of LaH_{2+x} and YH_{2+x} films discovered by Huiberts et al. suggest their electronic structure is described best by a local model. Electron correlation is important in H^- -centers and in explaining the transparent insulating behavior of LaH_3. The metal-insulator transition at $x\sim 0.8$ takes place in a band of highly localized states centered on the $H$-vacancies in the LaH_3 structure.Comment: plain tex, 3 figure

Aromaticity in a Surface Deposited Cluster: Pd4_4 on TiO2_2 (110)

We report the presence of \sigma-aromaticity in a surface deposited cluster, Pd$_4$ on TiO$_2$ (110). In the gas phase, Pd$_4$ adopts a tetrahedral structure. However, surface binding promotes a flat, \sigma-aromatic cluster. This is the first time aromaticity is found in surface deposited clusters. Systems of this type emerge as a promising class of catalyst, and so realization of aromaticity in them may help to rationalize their reactivity and catalytic properties, as a function of cluster size and composition.Comment: 4 pages, 3 figure

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

Angular Dependences of Third Harmonic Generation from Microdroplets

We present experimental and theoretical results for the angular dependence of third harmonic generation (THG) of water droplets in the micrometer range (size parameter $62<ka<248$). The THG signal in $p$- and $s$-polarization obtained with ultrashort laser pulses is compared with a recently developed nonlinear extension of classical Mie theory including multipoles of order $l\leq250$. Both theory and experiment yield over a wide range of size parameters remarkably stable intensity maxima close to the forward and backward direction at ``magic angles''. In contrast to linear Mie scattering, both are of comparable intensity.Comment: 4 pages, RevTeX, 3 figures available on request from [email protected], submitted to PR