Resolving the energy paradox of chaperone/usher-mediated fibre assembly

Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles of Gram-negative pathogens in a process that has been suggested to be driven by folding energy. Structures of mutant chaperone-subunit complexes revealed a final folding transition (condensation of the subunit hydrophobic core) on the release of organelle subunit from the chaperone-subunit pre-assembly complex and incorporation into the final fibre structure. However, in view of the large interface between chaperone and subunit in the pre-assembly complex and the reported stability of this complex, it is difficult to understand how final folding could release sufficient energy to drive assembly. In the present paper, we show the X-ray structure for a native chaperone-fibre complex that, together with thermodynamic data, shows that the final folding step is indeed an essential component of the assembly process. We show that completion of the hydrophobic core and incorporation into the fibre results in an exceptionally stable module, whereas the chaperone-subunit preassembly complex is greatly destabilized by the high-energy conformation of the bound subunit. This difference in stabilities creates a free energy potential that drives fibre formation.

Techniques for analysis of proteins by SDS-polyacrylamide gel electrophoresis and Western blotting

The separation of mixtures of proteins by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) is a technique that is widely used—and, indeed, this technique underlies many of the assays and analyses that are described in this book. While SDS-PAGE is routine in many labs, a number of issues require consideration before embarking on it for the first time. We felt, therefore, that in the interest of completeness of this volume, a brief chapter describing the basics of SDS-PAGE would be helpful. Also included in this chapter are protocols for the staining of SDS-PAGE gels to visualize separated proteins, and for the electrotransfer of proteins to a membrane support (Western blotting) to enable immunoblotting, for example. This chapter is intended to complement the chapters in this book that require these techniques to be performed. Therefore, detailed examples of why and when these techniques could be used will not be discussed here.

Rovibrational energy levels of hydrogen peroxide, studied by MULTIMODE with a reaction path Hamiltonian

Recently. Carter and Handy [J. Chem. Phys. 113 (2000) 987] have introduced the theory of the reaction path Hamiltonian (RPH) [J. Chem. Phys. 72 (1980) 99] into the variational scheme MULTIMODE, for the calculation of the J = 0 vibrational levels of polyatomic molecules, which have a single large-amplitude motion. In this theory the reaction path coordinate s becomes the fourth dimension of the moment-of-inertia tensor, and must be treated separately from the remaining 3N - 7 normal coordinates in the MULTIMODE program. In the modified program, complete integration is performed over s, and the M-mode MULTIMODE coupling approximation for the evaluation of the matrix elements applies only to the 3N - 7 normal coordinates. In this paper the new algorithm is extended to the calculation of rotational-vibration energy levels (i.e. J > 0) with the RPH, following from our analogous implementation for rigid molecules [Theoret. Chem. Acc. 100 (1998) 191]. The full theory is given, and all extra terms have been included to give the exact kinetic energy operator. In order to validate the new code, we report studies on hydrogen peroxide (H2O2), where the reaction path is equivalent to torsional motion. H2O2 has previously been studied variationally using a valence coordinate Hamiltonian; complete agreement for calculated rovibrational levels is obtained between the previous results and those from the new code, using the identical potential surface. MULTIMODE is now able to calculate rovibrational levels for polyatomic molecules which have one large-amplitude motion. (C) 2003 Elsevier B.V. All rights reserved.

A variational method for the calculation of spin-rovibronic energy levels of any triatomic molecule in an electronic triplet state

The triatomic spin-rovibronic variational code RVIB3 has been extended to include the effect of two uncoupled electrons, for both (3)Sigma(-) and (3)Pi (Renner-Teller) electronic states. The spin-orbital-rotational kinetic energy is included in the usual way, via terms (J+L+S). The phenomenological terms AL.S and lambda 2/3(3S(z)(2)) are introduced to reproduce the 3 spin-orbit and spin-spin splittings, respectively. Calculations are performed to evaluate the spin-rovibronic energy levels of CCO (X) over tilde (3) Sigma(-) and CCO (A) over tilde (3) Pi for which the Born-Oppenheimer potentials are derived from high-accuracy ab initio calculations.

2,2-Dialkyl-2H-benzimidazoles, the high energy tautomers of the corresponding 1,2-dialkyl-1H-benzimidazoles. Syntheses and their complexes with Cu(I) and Ag(I)

Reaction of Cu(1,2-phenylenediamine)(2)(ClO4)(2) with neat RR'=O (R = methyl and/or ethyl) (lives Cu(2,2-dialkyl-2H-benzimidazole)ClO4. demetallation of which by the action of aqueous ammonia yields Pure 2,2-dialkyl-2H-benzimidazoles. These are characterised by NMR. hi the X-ray crystal Structure, Ag(2,2-methyl-2H-benzimi-dazolc)NO3 is Found to be a spiral 1D coordination polymer where the 2H-benzimidazole acts as an N,N bridge between two Ag(I) centus. Although 2H-benzimidazoles are very unstable in the free state, they are quite stable in their Cu(I)(1) and Ag(I) complexes. The 1,2-tautomerisation in imidazole and benzimidazole have been Studied by means of transition state calculations at B3LYP/6-3 11 +G(2d,p)* level.

Building operational energy consumption of Chongqing and its exergy assessment

Building energy consumption(BEC) accounting and assessment is fundamental work for building energy efficiency(BEE) development. In existing Chinese statistical yearbook, there is no specific item for BEC accounting and relevant data are separated and mixed with other industry consumption. Approximate BEC data can be acquired from existing energy statistical yearbook. For BEC assessment, caloric values of different energy carriers are adopted in energy accounting and assessment field. This methodology obtained much useful conclusion for energy efficiency development. While the traditional methodology concerns only on the energy quantity, energy classification issue is omitted. Exergy methodology is put forward to assess BEC. With the new methodology, energy quantity and quality issues are both concerned in BEC assessment. To illustrate the BEC accounting and exergy assessment, a case of Chongqing in 2004 is shown. Based on the exergy analysis, BEC of Chongqing in 2004 accounts for 17.3% of the total energy consumption. This result is quite common to that of traditional methodology. As far as energy supply efficiency is concerned, the difference is highlighted by 0.417 of the exergy methodology to 0.645 of the traditional methodology.

Modelling energy consumption of relay-enabled MAC protocols in ad hoc networks

To enhance the throughput of ad hoc networks, dual-hop relay-enabled transmission schemes have recently been proposed. Since in ad hoc networks throughput is normally related to their energy consumption, it is important to examine the impact of using relay-enabled transmissions on energy consumption. In this paper, we present an analytical energy consumption model for dual-hop relay-enabled medium access control (MAC) protocols. Based on the recently reported relay-enabled distributed coordination function (rDCF), we have shown the efficacy of the proposed analytical model. This is a generalized model and can be used to predict energy consumption in saturated relay-enabled ad hoc networks via energy decomposition. This is helpful in designing MAC protocols for cooperative communications and it is shown that using a relay results not only in a better throughput but also better energy efficiency.

Modeling energy consumption of dual-hop relay based MAC protocols in ad hoc networks

Given that the next and current generation networks will coexist for a considerable period of time, it is important to improve the performance of existing networks. One such improvement recently proposed is to enhance the throughput of ad hoc networks by using dual-hop relay-based transmission schemes. Since in ad hoc networks throughput is normally related to their energy consumption, it is important to examine the impact of using relay-based transmissions on energy consumption. In this paper, we present an analytical energy consumption model for dual-hop relay-based medium access control (MAC) protocols. Based on the recently reported relay-enabled Distributed Coordination Function (rDCF), we have shown the efficacy of the proposed analytical model. This is a generalized model and can be used to predict energy consumption in saturated relay-based ad hoc networks. This model can predict energy consumption in ideal environment and with transmission errors. It is shown that using a relay results in not only better throughput but also better energy efficiency. Copyright (C) 2009 Rizwan Ahmad et al.

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase.

A data framework for measuring the energy consumption of the non-domestic building stock

The transition to a low-carbon economy urgently demands better information on the drivers of energy consumption. UK government policy has prioritized energy efficiency in the built stock as a means of carbon reduction, but the sector is historically information poor, particularly the non-domestic building stock. This paper presents the results of a pilot study that investigated whether and how property and energy consumption data might be combined for non-domestic energy analysis. These data were combined in a ‘Non-Domestic Energy Efficiency Database’ to describe the location and physical attributes of each property and its energy consumption. The aim was to support the generation of a range of energy-efficiency statistics for the industrial, commercial and institutional sectors of the non-domestic building stock, and to provide robust evidence for national energy-efficiency and carbon-reduction policy development and monitoring. The work has brought together non-domestic energy data, property data and mapping in a ‘data framework’ for the first time. The results show what is possible when these data are integrated and the associated difficulties. A data framework offers the potential to inform energy-efficiency policy formation and to support its monitoring at a level of detail not previously possible.