Validation of membrane protein topology models by oxidative labeling and mass spectrometry

Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ·OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008, 70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ·OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms.

Functional characterization and membrane topology of Escherichia coli WecA, a sugar-phosphate transferase initiating the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide

WecA is an integral membrane protein that initiates the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide (LPS) by catalyzing the transfer of N-acetylglucosamine (GlcNAc)-1-phosphate onto undecaprenyl phosphate (Und-P) to form Und-P-P-GlcNAc. WecA belongs to a large family of eukaryotic and prokaryotic prenyl sugar transferases. Conserved aspartic acids in putative cytoplasmic loops 2 (Asp90 and Asp91) and 3 (Asp156 and Asp159) were targeted for replacement mutagenesis with either glutamic acid or asparagine. We examined the ability of each mutant protein to complement O-antigen LPS synthesis in a wecA-deficient strain and also determined the steady-state kinetic parameters of the mutant proteins in an in vitro transfer assay. Apparent K(m) and V(max) values for UDP-GlcNAc, Mg(2+), and Mn(2+) suggest that Asp156 is required for catalysis, while Asp91 appears to interact preferentially with Mg(2+), possibly playing a role in orienting the substrates. Topological analysis using the substituted cysteine accessibility method demonstrated the cytosolic location of Asp90, Asp91, and Asp156 and provided a more refined overall topological map of WecA. Also, we show that cells expressing a WecA derivative C terminally fused with the green fluorescent protein exhibited a punctate distribution of fluorescence on the bacterial surface, suggesting that WecA localizes to discrete regions in the bacterial plasma membrane.

Network Topology, Higher Orders of Stability and Efficiency

Stable networks of order r where r is a natural number refer to those networks that are immune to coalitional deviation of size r or less. In this paper, we introduce stability of a finite order and examine its relation with efficient networks under anonymous and component additive value functions and the component-wise egalitarian allocation rule. In particular, we examine shapes of networks or network architectures that would resolve the conflict between stability and efficiency in the sense that if stable networks assume those shapes they would be efficient and if efficient networks assume those shapes, they would be stable with minimal further restrictions on value functions.

The CACTOS Vision of Context-Aware Cloud Topology Optimization and Simulation

Recent advances in hardware development coupled with the rapid adoption and broad applicability of cloud computing have introduced widespread heterogeneity in data centers, significantly complicating the management of cloud applications and data center resources. This paper presents the CACTOS approach to cloud infrastructure automation and optimization, which addresses heterogeneity through a combination of in-depth analysis of application behavior with insights from commercial cloud providers. The aim of the approach is threefold: to model applications and data center resources, to simulate applications and resources for planning and operation, and to optimize application deployment and resource use in an autonomic manner. The approach is based on case studies from the areas of business analytics, enterprise applications, and scientific computing.

Topology of megagauss magnetic fields and of heat-carrying electrons produced in a high-power laser-solid interaction

The intricate spatial and energy distribution of magnetic fields, self-generated during high power laser irradiation (at Iλ2∼1013-1014W.cm-2.μm2) of a solid target, and of the heat-carrying electron currents, is studied in inertial confinement fusion (ICF) relevant conditions. This is done by comparing proton radiography measurements of the fields to an improved magnetohydrodynamic description that fully takes into account the nonlocality of the heat transport. We show that, in these conditions, magnetic fields are rapidly advected radially along the target surface and compressed over long time scales into the dense parts of the target. As a consequence, the electrons are weakly magnetized in most parts of the plasma flow, and we observe a reemergence of nonlocality which is a crucial effect for a correct description of the energetics of ICF experiments.

Implementing a structural continuity constraint and a halting method for the topology optimization of energy absorbers

This study investigates topology optimization of energy absorbing structures in which material damage is accounted for in the optimization process. The optimization objective is to design the lightest structures that are able to absorb the required mechanical energy. A structural continuity constraint check is introduced that is able to detect when no feasible load path remains in the finite element model, usually as a result of large scale fracture. This assures that designs do not fail when loaded under the conditions prescribed in the design requirements. This continuity constraint check is automated and requires no intervention from the analyst once the optimization process is initiated. Consequently, the optimization algorithm proceeds towards evolving an energy absorbing structure with the minimum structural mass that is not susceptible to global structural failure. A method is also introduced to determine when the optimization process should halt. The method identifies when the optimization method has plateaued and is no longer likely to provide improved designs if continued for further iterations. This provides the designer with a rational method to determine the necessary time to run the optimization and avoid wasting computational resources on unnecessary iterations. A case study is presented to demonstrate the use of this method.

Electron collisions with Fe-peak elements: Forbidden transitions between the low lying valence states 3d6, 3d54s, and 3d54p of Fe III:

Effective collision strengths are presented for the Fe-peak element Fe III at electron temperatures (Te in degrees Kelvin) in the range 2 × 103 to 1 × 106. Forbidden transitions results are given between the 3d6, 3d54s, and the 3d54p manifolds applicable to the modeling of laboratory and astrophysical plasmas.

Analysis and Synthesis of pHEMT Class-E Amplifiers with Shunt Inductor including ON-State Active-Device Resistance Effects

In this theoretical paper, the analysis of the effect that ON-state active-device resistance has on the performance of a Class-E tuned power amplifier using a shunt inductor topology is presented. The work is focused on the relatively unexplored area of design facilitation of Class-E tuned amplifiers where intrinsically low-output-capacitance monolithic microwave integrated circuit switching devices such as pseudomorphic high electron mobility transistors are used. In the paper, the switching voltage and current waveforms in the presence of ON-resistance are analyzed in order to provide insight into circuit properties such as RF output power, drain efficiency, and power-output capability. For a given amplifier specification, a design procedure is illustrated whereby it is possible to compute optimal circuit component values which account for prescribed switch resistance loss. Furthermore, insight into how ON-resistance affects transistor selection in terms of peak switch voltage and current requirements is described. Finally, a design example is given in order to validate the theoretical analysis against numerical simulation.

Inverse Class E amplifier and oscillator phase noise characteristics

This paper gives the first experimental characterisation of the phase noise response of the recently introduced Inverse Class E topology when operated as an amplifier and then as an oscillator. The results indicate that in amplifier and oscillator modes of operation conversion efficiencies of 64%, and 42% respectively are available, and that the excess PM noise added as a consequence of saturated Class E operation results in about a 10 dB increase in PM over that expected from a small-signal Class A amplifier operating at much lower efficiency. Inverse Class E phase transfer dependence on device drain bias and flicker noise are presented in order to show, respectively, that the Inverse Class E amplifier and oscillator follow the trends predicted by conventional phase noise theory. © 2007 EuMA.

Transmission line matching effects on the performance of shunt-C/series-tuned and series-L/parallel-tuned Class-E amplifiers

The impact that the transmission-line load-network has on the performance of the recently introduced series-L/parallel-tuned Class-E amplifier and the classic shunt-C/series-tuned configuration when compared to optimally derived lumped load networks is discussed. In addition an improved load topology which facilitates harmonic suppression of up to 5 order as required for maximum Class-E efficiency as well as load resistance transformation and a design procedure involving the use of Kuroda's identity and Richard's transformation enable a distributed synthesis process which dispenses with the need for iterative tuning as previously required in order to achieve optimum Class-E operation. © 2005 IEEE.

Periodically loaded 1-D metallodielectric electromagnetic bandgap structures for miniaturisation and bandwidth enhancement

Periodic loading of 1-D metallodielectric electromagnetic bandgap (MEBG) structures has been rigorously investigated. Miniaturised and broadband MEBG structures have been produced by means of periodically loading a dipole array. A study has been carried out with regard to the loading mechanism, the number of stubs, the topology of the structure and the order of loading. Simulations have been carried out using a method of moments based software. First order uniform loading stubs have yielded a significant size reduction of the MEBG array and the bandwidth has doubled. Good agreement between simulations and measurements has been achieved. The current distribution on the proposed structure has been studied, yielding valuable insight. An interdigital topology has resulted in further miniaturisation and bandwidth enhancement. Fractal-type arrays have been produced after applying second order loading. A maximum miniaturisation of 2.5:1 has been achieved.