Assembly of the hexameric Escherichia coli arginine repressor investigated by nano-electrospray ionization time-of-flight mass spectrometry

The arginine repressor (ArgR) from Escherichia coli regulates genes for L-arginine metabolism and is a required recombination factor for colE1 plasmid replication. Both functions require binding of L-arginine to the protein. In this work, nano-electrospray ionization time-of-flight mass spectrometry (nano-ESI-TOFMS) is used to study conformational and oligomeric states of intact ArgR and its isolated structural domains. In agreement with X-ray diffraction studies, it is shown that ArgR oligomerizes to form hexamers in both the presence and absence of L-arginine, and the basic unit of oligomerization appears to be the trimer. Higher-order assembly into dodecamers is also detected. The isolated C-terminal domain is found to associate into trimers and hexamers whereas the N-terminal domain is detected in its monomeric form. The observed species distributions suggest a role for the N-terminal domain in hexamer stabilization.     

Formation of stable Meisenheimer adduct ion pairs in apolar solvents: implications for stereoselective reactions

[reaction: see text] A detailed study concerning the formation of Meisenheimer adducts in biphasic solvent systems is described. The process relies on utilizing a significantly lipophilic quaternary ammonium salt to transfer a nucleophile (e.g., hydroxide ion) between an aqueous and organic layer containing the electron-deficient aromatic substrate. Provided that the organic layer is sufficiently apolar, the resultant Meisenheimer adduct is considerably stable, likely the result of a strong ion-pairing interaction between the large polarizable anionic complex and the diffusively charged tetraalkylammonium cation. Using the diethylamide of 3,5-dinitrobenzoic acid as a model compound, the influence of ion-pairing reagents and solvents on adduct formation was investigated. Dramatically increased equilibrium formation of the Meisenheimer adduct is observed in the biphasic medium (e.g., benzene/2 M NaOH) relative to the same adduct generated in single-phase systems. Spectroscopic studies on this adduct are consistent with those conducted in single-phase polar or dipolar aprotic solvents. The methodology is extended to performing highly enantioselective biphasic kinetic resolutions of several racemic electron-deficient amides.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Development and validation of a SUPG finite element scheme for the compressible Navier–Stokes equations using a modified inviscid flux discretization

This paper considers the streamline‐upwind Petrov–Galerkin (SUPG) method applied to the unsteady compressible Navier–Stokes equations in conservation‐variable form. The spatial discretization, including a modified approach for interpolating the inviscid flux terms in the SUPG finite element formulation, and the second‐order accurate time discretization are presented. The numerical method is discussed in detail. The performance of the algorithm is then investigated by considering inviscid flow past a circular cylinder. Validation of the finite element formulation via comparisons with experimental data for high‐Mach number perfect gas laminar flows is presented, with a specific focus on comparisons with experimentally measured skin friction and convective heat transfer on a 15° compression ramp. Copyright © 2007 John Wiley & Sons, Ltd.     

Stream function solution of Navier-Stokes problems with inter-element penalties

In this note, we apply a finite element stream function formulation with inter-element penalties to the Navier-Stokes equations. The approach is an extension of a technique previously introduced for Stokes, flow. The solution is obtained by iterative linearization using successive approximation, and results for a standard numerical test case are given.     

A framework for user equilibrium dynamic traffic assignment

Several analytic approaches have been developed to describe or predict traffic flows on networks with time-varying (dynamic) travel demands, flows and travel times. A key component of these models lies in modelling the flows and/or travel times on the individual links, but as this is made more realistic or accurate it tends to make the overall model less computationally tractable. To help overcome this, and for other reasons, we develop a bi-level user equilibrium (UE) framework that separates the assignment or loading of flows on the time–space network from the modelling of flows and trip times within individual links. We show that this model or framework satisfies appropriate definitions of UE satisfies a first-in-first-out (FIFO) property of road traffic, and has other desirable properties. The model can be solved by iterating between (a) a linear network-loading model that takes the lengths of time–space links as fixed (within narrow ranges), and (b) a set of link flow sub-models which update the link trip times to construct a new time–space network. This allows links to be processed sequentially or in parallel and avoids having to enumerate paths and compute path flows or travel times. We test and demonstrate the model and algorithms using example networks and find that the algorithm converges quickly and the solutions behave as expected. We show how to extend the model to handle elastic demands, multiple destinations and multiple traffic types, and traffic spillback within links and from link to link.