The influence of cytosine methylation on the chemoselectivity of benzo[a]pyrene diol epoxide‐oligonucleotide adducts determined using nanoLC/MS/MS

Benzo[a]pyrene is a major carcinogen implicated in human lung cancer. Almost 60% of human lung cancers have a mutation in the p53 tumor suppressor gene at several specific codons. An on‐line nanoLC/MS/MS method using a monolithic nanocolumn was applied to investigate the chemoselectivity of the carcinogenic diol epoxide metabolite, ( ± )‐(7R,8S,9S,10R)‐benzo[a]pyrene 7,8‐diol 9,10‐epoxide [( ± )‐anti‐benzo[a]pyrene diol epoxide (BPDE)], which was reacted in vitro with a synthesized 14‐mer double stranded oligonucleotide (5′‐ACCCG₅CG₇TCCG₁₁CG₁₃C‐3′/5′‐GCGCGGGCGCGGGT‐3′) derived from the p53 gene. This sequence contained codons 157 and 158, which are considered mutational ‘hot spots’ and have also been reported as chemical ‘hot spots’ for the formation of BPDE‐DNA adducts. In evaluating the effect of cytosine methylation on BPDE‐DNA adduct binding, it was found that codon 156, containing the nucleobase G₅ instead of the mutational hot spot codons 157 (G₇) and 158 (G₁₁), was the preferential chemoselective binding site for BPDE. In all permethylated cases studied, the relative ratio for adduction was found to be G₅? G₁₁ > G₁₃ > G₇. Permethylation of CpG dinucleotide sites on either the nontranscribed or complementary strand did not change the order of sequence preference but did enhance the relative adduction level of the G₁₁ CpG site (codon 158) approximately two‐fold versus the unmethylated oligomer. Permethylation of all CpG dinucleotide sites on the duplex changed the order of relative adduction to G₅? G₇ > G₁₁ > G₁₃. The three‐ to four‐fold increase in adduction at the mutational hot spot codon 157 (G₇) relative to the unmethylated or single‐stranded permethylated cases suggests a possible relationship between the state of methylation and adduct formation for a particular mutation site in the p53 gene. Using this method, only 125 ng (30 pmol) of adducted oligonucleotide was analyzed with minimal sample cleanup and high chromatographic resolution of positional isomers in a single chromatographic run. Copyright © 2009 John Wiley & Sons, Ltd.     

Pulsed-electric-field crossflow ultrafiltration of bovine serum albumin

A conventional crossflow ultrafiltration (CUF) apparatus was modified by the inclusion of electrodes which permitted a pulsed electric field to be produced across the ultrafiltration membrane (PEF-UF process). Using this apparatus, a discontinuous electrophoretic velocity was imposed upon the proteins being concentrated, opposing their convective movement toward the CUF membrane. This resulted in a lower concentration of rejected solute protein in the fluid boundary layer adjacent to the high-pressure side of the membrane and, hence, in a lower solute-related filtration resistance than in the case of conventional ultrafiltration (zero electric field). Studies of the PEF-UF process with bovine serum albumin (BSA) in the range of 0.5–5% w/v demonstrated a 25–40% decrease in the solute-related resistance to the permeate flux compared to the case of a zero electric field. Accordingly, higher permeate fluxes and, therefore, higher rates of concentration of the protein solution were obtained than for conventional crossflow ultrafiltration. When the electric field was reimposed following a period of operation under conventional CUF conditions, the permeate flux could be restored to nearly the same higher value observed initially for the PEF-UF process.     

Helium emission spectra—II. Pressures to 0.91 torr

Electron impact excitation is employed to study the pressure variation of the steady state luminescence from 27 levels of helium. Apparent cross sections are determined for these levels over the pressure range 0.025–0.91 torr, a much broader pressure range for observing collisional excitation transfer processes than has been previously investigated. Model calculations are carried out in which the data is fit to a set of coupled steady state equations. Primary and secondary electron excitation, radiative transfer, and bimolecular and termolecular collisional processes are accounted for in the analysis. We find that n¹P→n¹D collisional excitation transfer is much more important as a populating mechanism for n¹D levels than has been previously believed. The cross section for 4¹P→4¹D collisional transfer is estimated to be (1.3±0.3)×10^?14 cm². A termolecular process, believed to involve formation of He₂⁺, becomes an important loss mechanism for the 3¹P and 4¹P levels at pressures above 0.5 torr. Rate constants for this process are estimated to be (6.6±1.0)×10^?27 cm⁶/sec and (1.9±0.4)×10^?26 cm⁶/sec for 3¹P and 4¹P, respectively. The magnitude of the 3³D and 4³D apparent cross sections require a large 4³F population, a result which leads us to conclude that the 4F level is singlet-triplet mixed. There is evidence that collision induced transitions between all sublevels do not occur with equal probability. The most internally consistent results are arrived at by assuming ΔJ=0 to be a favored collisional transfer process.     

Identification of ligand binding sites on proteins using a multi-scale approach

Identification of a ligand binding site on a protein is pivotal to drug discovery. To date, no reliable and computationally feasible general approach to this problem has been published. Here we present an automated efficient method for determining binding sites on proteins for potential ligands without any a priori knowledge. Our method is based upon the multiscale concept where we deal with a hierarchy of models generated using a k-means clustering algorithm for the potential ligand. This is done in a simple approach whereby a potential ligand is represented by a growing number of feature points. At each increasing level of detail, a pruning of potential binding site is performed. A nonbonding energy function is used to score the interactions between molecules at each step. The technique was successfully employed to seven protein-ligand complexes. In the current paper we show that the algorithm considerably reduces the computational effort required to solve this problem. This approach offers real opportunities for exploiting the large number of structures that will evolve from structural genomics.     

A parallel multi-configuration self-consistent field algorithm

A scalable multi-configuration self-consistent field (MCSCF) algorithm is described. The method for optimizing the orbital and configurational parameters is based upon the two-step Newton–Raphson approach with an augmented orbital Hessian matrix. A single copy of the two-electron integrals in the molecular orbital basis is distributed over the memory of all processors. Storage of the augmented Hessian is avoided by re-computing its elements as needed. A replicated data approach is used to parallelize the configuration interaction step. Scalability to 1024 processors is demonstrated.     

Steady-State Work by an Asymmetrically Inelastic Gravitator in a Gas: A Second Law Paradox

A new member of a growing class of unresolved second law paradoxes is examined.^(1–7) In a sealed blackbody cavity, a spherical gravitator is suspended in a low density gas. Infalling gas suprathermally strikes the gravitator which is spherically asymmetric between its hemispheres with respect to surface trapping probability for the gas. In principle, this system can be made to perform steady-state work solely at the expense of heat from the heat bath, this in apparent violation of the second law of thermodynamics. Detailed three-dimensional test particle simulations of this system support this prediction. Standard resolutions to the paradox are discussed and found to be untenable. Experiments corroborating a central physical process of the paradox are discussed briefly. The paradox is discussed in the context of the Maxwell demon.     

The structure of 5-p-N,N-dimethylaminophenyl-10,11-dihydro-5H-dibenzo[b,f]silepin

The structure of 5-p-N-N-dimethylaminophenyl-10,11-dihydro-5H-dibenzo-[b,f]silepin has been determined from three-dimensional X-ray data collected by counter methods. The compound crystallizes in the monoclinic space group P2₁/ca  14.121(4), b  14.379(3), c  9.126(2) Å and β = 99.57(2)°. The observed and calculated densities (Z  4) are 1.19 and 1.20 g cm^?3, respectively. Anisotropic refinement of nonhydrogen atoms with hydrogen atoms at fixed calculated positions gave a conventional R-factor of 4.6% for 2023 reflections with F$\text{2}\text{0}$ > 3σ(F²₀). The central seven-membered ring of the tricyclic system exhibits a folded boat conformation; the dihedral angle between the benzo groups is 137.2°. The benzo groups are twisted approximately 21° relative to one another and skewed such that the two carbons bonded to silicon are 0.33 Å closer to one another than the two benzo ring carbons one atom removed from the silicon. The nitrogen atom is displaced 0.04 Å from the plane of the adjacent carbon atoms.