Diastereoselective synthesis of (+/-)-(3-aminocyclopentane)alkylphosphinic acids, conformationally restricted analogues of GABA

A divergent synthesis of both diastereoisomers of (+/-)-(3-aminocyclopentane)alkylphosphinic acid is described. Both diastereoisomers are obtained in 5 steps from the key (+/-)-(3-hydroxycyclopent-1-ene)alkylphosphinate esters which are prepared via a palladium catalysed C-P bond forming reaction.     

Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences

The present work is concerned with a fast and accurate sequence comparison method: the count of the number of words of length k letters shared by two sequences, also known as the D2 statistic. We link recent theoretical advances in the characterization of D2 asymptotic distributions with applications to biological sequences. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

A comparison of lobe and cartesian gaussian basis sets for molecular calculations

Lobe gaussian and cartesian gaussian basis sets, of approximately minimal basis Slater accuracy, have been compared for molecular calculations. The basis sets were constructed so that they only differed in the representation of the angular dependence of the p function. Calculation of total energy and several one-electron properties for a series of nine molecules shows that, for molecular calculations, the lobe and cartesian gaussian representations are equivalent.     

Use of automatic relevance determination in QSAR studies using Bayesian neural networks

We describe the use of Bayesian regularized artificial neural networks (BRANNs) coupled with automatic relevance determination (ARD) in the development of quantitative structure-activity relationship (QSAR) models. These BRANN-ARD networks have the potential to solve a number of problems which arise in QSAR modeling such as the following: choice of model; robustness of model; choice of validation set; size of validation effort; and optimization of network architecture. The ARD method ensures that irrelevant or highly correlated indices used in the modeling are neglected as well as showing which are the most important variables in modeling the activity data. The application of the methods to QSAR of compounds active at the benzodiazepine and muscarinic receptors as well as some toxicological data of the effect of substituted benzenes on Tetetrahymena pyriformis is illustrated.     

EDQNM and DNS — Comparitive calculations

EDQNM and DNS calculations of homogenous axisymmetric turbulence in the absence of a mean flow are compared. Special care is taken in making sure that exactly equivalent initial conditions are used in the two methods. Three calculations with different degrees of anisotropy have been carried out.     

Membrane surface dynamics of DNA-threaded nanopores revealed by simultaneous single-molecule optical and ensemble electrical recording

We describe a method for simultaneous single-molecule optical and electrical characterization of membrane-based sensors that contain ion-channel nanopores. The technique is used to study the specific and nonspecific interactions of streptavidin-capped DNA polymers with lipid bilayers composed of diphytanoyl phosphatidylcholine and diphytanoyl phosphatidylglycerol. Biotinylated DNA that is bound to fluorescently labeled streptavidin is electrophoretically driven into, or away from, the lumen of alpha hemolysin (alphaHL) ion channels by an external electric field. Confocal microscopy simultaneously captures single-molecule fluorescence dynamics from the membrane interface at different applied potentials. Fluorescence correlation analysis is used to determine the surface number density and diffusion constant of membrane-associated complexes. The dual optical and electrical approach can detect membrane-associated species at a surface coverage below 10(-5) monolayers of streptavidin, a sensitivity that surpasses most other in vitro surface analysis techniques. By comparing the change in transmembrane current to the number of fluorescent molecules leaving the bilayer when the electrical potential is reversed, we demonstrate the general utility of the approach within the context of nanopore-based sensing and discuss a mechanism by which DNA-streptavidin complexes can be nonspecifically retained at the membrane interface.     

Comparison of anisotropic atomic motions in biological macromolecules

A compact and convenient graphical technique for assessing agreement between spatial atomic distributions in large molecules determined from alternate sources is presented. The procedure is available as downloadable software. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)