Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Conservation and sustainable use of wild species as sources of new ornamentals

While only about 1-200 species are used intensively in commercial floriculture (e.g. carnations, chrysanthemums, gerbera, narcissus, orchids, tulips, lilies, roses, pansies and violas, saintpaulias, etc.) and 4-500 as house plants, several thousand species of herbs, shrubs and trees are traded commercially by nurseries and garden centres as ornamentals or amenity species. Most of these have been introduced from the wild with little selection or breeding. In Europe alone, 12 000 species are found in cultivation in general garden collections (i.e. excluding specialist collections and botanic gardens). In addition, specialist collections (often very large) of many other species and/or cultivars of groups such as orchids, bromeliads, cacti and succulents, primulas, rhododendrons, conifers and cycads are maintained in several centres such as botanic gardens and specialist nurseries, as are 'national collections' of cultivated species and cultivars in some countries. Specialist growers, both professional and amateur, also maintain collections of plants for cultivation, including, increasingly, native plants. The trade in ornamental and amenity horticulture cannot be fully estimated but runs into many billions of dollars annually and there is considerable potential for further development and the introduction of many new species into the trade. Despite this, most of the collections are ad hoc and no co-ordinated efforts have been made to ensure that adequate germplasm samples of these species are maintained for conservation purposes and few of them are represented at all adequately in seed banks. Few countries have paid much attention to germplasm needs of ornamentals and the Ornamental Plant Germplasm Center in conjunction with the USDA National Plant Germplasm System at The Ohio State University is an exception. Generally there is a serious gap in national and international germplasm strategies, which have tended to focus primarily on food plants and some forage and industrial crops. Adequate arrangements need to be put in place to ensure the long- and medium-term conservation of representative samples of the genetic diversity of ornamental species. The problems of achieving this will be discussed. In addition, a policy for the conservation of old cultivars or 'heritage' varieties of ornamentals needs to be formulated. The considerable potential for introduction of new ornamental species needs to be assessed. Consideration needs to be given to setting up a co-ordinating structure with overall responsibility for the conservation of germplasm of ornamental and amenity plants.

Metal complexes of a tetraazacyclophane: solution and molecular modelling studies

An alternative synthetic approach to yield the compound 2,3,5,6,8,9,11,14-octahydrobenzo[1][ 1,4,7,10]tetraazacyclotetradecine (bz[14]N-4) is presented. The protonation constants of bz[14]N-4 and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, Pb2+ were determined in H2O at 25degreesC with ionic strength 0.10 mol dm(-3) in KNO3 and they were compared with structurally related macrocycles cyclam (1,4,8,11-tetraazacyclotetradecane) and cyclen (1,4,7,10-tetraazacyclododecane). These studies indicate that only 1 : 1 ( M : L) species are formed in solution, and the ligand exhibits a high affinity for larger ions such as Cd2+ and Pb2+. The X-ray study of [bz[14]N4H3](3+) shows that an inclusion compound with a chloride counter-anion is formed through NH...Cl hydrogen bonds. Spectroscopic data in solution ( electronic and NMR spectra) showed that the macrocycle adopts a planar arrangement upon metal complexation. Molecular mechanics calculations reveal that in spite of the presence of the benzene ring in the macrocyclic framework this ligand can encapsulate metal ions with different stereo-electronic sizes in square planar arrangements. Our results indicate that the presence of the benzene ring in the backbone of the bz[14]N-4 confers a coordination behaviour intermediate between that of cyclam and cyclen.

Methylene spacer-regulated structural variation in cobalt(II/III) complexes with bridging acetate and Salen- or Salpn-type Schiff-base ligands

Two linear, trinuclear mixed-valence complexes, [Co-II{(mu-L-1)(mu-OAc)Co-III (OAc)}(2)] (1) and [Co-II(mu-L-2) (mu-OAc)Co-III(OAc)}(2)] (2) and two mononuclear Con' complexes [Co-III{L-3)(OAc)] (3), and [Co-III {L-4}(OAc)] (4) were prepared and the molecular structures of 1, 2 and 4 elucidated on the basis of X-ray crystallography [OAc = Acetate ion, H2L1 = H(2)Salen 1,6-bis(2-hydroxyphenyl)-2,5-diazahexa-1,5-diene, H2L2 H2Me2-Salen = 2,7-bis(2-hydroxyphenyl)-2,6-diazaocta-2,6-diene, H2L3 = H(2)Salpn = 1,7-bis(2-hydroxyphenyl)-2,6-diazahepta1,6-diene, H2L4 = H(2)Me(2)Salpn = 2,8-bis(2-hydroxyphenyl)3,7-diazanona-2,7-dienel. In complexes I and 2, the acetate groups show both monodentate and bridging bidentate coordination modes, whereas chelating bidentate acetate is present in 4. The terminal (CoN2O4)-N-III centres in 1 and 2 exhibit uniform facial arrangements of both non-bridged N2O and bridging O-3 donor sets and the Co-II centre is coordinated to six (four phenoxo and two acetato) oxygen atoms of the bridging ligands. The effective magnetic moment at room temperature corresponds to the presence of high-spin Coll in both 1 and 2. The complexes 1 and 2 are thus Co-III(S = 0)Co-II(S = 3/2)-Co-II(S = 0) trimers. Complexes 3 and 4 are monomeric and diamagnetic containing low-spin Co-III(S = 0) with chelating tetradentate Schiff base and bidentate acetate. Calculations based on DFT rationalise the formation of trinuclear or monomiclear complexes. (C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).

Proteomic profiling of neuromas reveals alterations in protein composition and local protein synthesis in hyper-excitable nerves

Neuropathic pain may arise following peripheral nerve injury though the molecular mechanisms associated with this are unclear. We used proteomic profiling to examine changes in protein expression associated with the formation of hyper-excitable neuromas derived from rodent saphenous nerves. A two-dimensional difference gel electrophoresis ( 2D-DIGE) profiling strategy was employed to examine protein expression changes between developing neuromas and normal nerves in whole tissue lysates. We found around 200 proteins which displayed a > 1.75-fold change in expression between neuroma and normal nerve and identified 55 of these proteins using mass spectrometry. We also used immunoblotting to examine the expression of low-abundance ion channels Nav1.3, Nav1.8 and calcium channel alpha 2 delta-1 subunit in this model, since they have previously been implicated in neuronal hyperexcitability associated with neuropathic pain. Finally, S(35)methionine in vitro labelling of neuroma and control samples was used to demonstrate local protein synthesis of neuron-specific genes. A number of cytoskeletal proteins, enzymes and proteins associated with oxidative stress were up-regulated in neuromas, whilst overall levels of voltage-gated ion channel proteins were unaffected. We conclude that altered mRNA levels reported in the somata of damaged DRG neurons do not necessarily reflect levels of altered proteins in hyper-excitable damaged nerve endings. An altered repertoire of protein expression, local protein synthesis and topological re-arrangements of ion channels may all play important roles in neuroma hyper-excitability.

Halo-derivatised calix[4]tubes

Halo functionalisation of calix[4] tubes has been investigated through both derivatisation of individual calix[4]arenes and calix[4] tubes, using classical synthetic methods, to allow preparation of a series of novel derivatives. The solution and solid state properties are in accordance with the constituent calix[4] arenes adopting flattened cone arrangements which on complexation with potassium simplify to a regular cone. Electrospray and H-1 NMR studies, combined with molecular modelling have been used to ascertain the metal binding of this new series of cryptand like ionophores, demonstrating their retained selectivity for binding potassium over other Group 1 metals and the dependence on counter anion in the weak binding of silver.

Making sense of supply chain management: acomparative study of aerospace and construction

Current recipes for learning across business sectors too often fail to recognize the embedded and contextual nature of management practice. The existing literature gives little emphasis to the symbiotic relationship between supply chain management and the broader dynamics of context. The aerospace and construction sectors are selected for comparison on the basis that they are so different. The UK aerospace sector has undergone extensive consolidation as a result of the imperatives of global competitive pressures. In contrast, the construction industry has experienced decades of fragmentation and remains highly localized. An increasing proportion of output in the aerospace sector occurs within a small number of large, globally orientated firms. In contrast, construction output is dominated by a plethora of small firms with high levels of subcontracting and a widespread reliance on self-employment. These differences have fundamental implications for the way that supply chain management is understood and implemented in the two sectors. Semi-structured interviews with practitioners from both sectors support the contention that supply chain management is more established in aerospace than construction. The introduction of prime contracting and the increasing use of framework agreements within the construction sector potentially provide a much more supportive climate for supply chain management than has traditionally prevailed. However, progress depends upon an improved continuity of workload under such arrangements.

Understanding construction consortia: Theory, practice and opinions

Firms form consortia in order to win contracts. Once a project has been awarded to a consortium each member then concentrates on his or her own contract with the client. Therefore, consortia are marketing devices, which present the impression of teamworking, but the production process is just as fragmented as under conventional procurement methods. In this way, the consortium forms a barrier between the client and the actual construction production process. Firms form consortia, not as a simple development of normal ways of working, but because the circumstances for specific projects make it a necessary vehicle. These circumstances include projects that are too large or too complex to undertake alone or projects that require on-going services which cannot be provided by the individual firms inhouse. It is not a preferred way of working, because participants carry extra risk in the form of liability for the actions of their partners in the consortium. The behaviour of members of consortia is determined by their relative power, based on several factors, including financial commitment and ease of replacement. The level of supply chain visibility to the public sector client and to the industry is reduced by the existence of a consortium because the consortium forms an additional obstacle between the client and the firms undertaking the actual construction work. Supply chain visibility matters to the client who otherwise loses control over the process of construction or service provision, while remaining accountable for cost overruns. To overcome this separation there is a convincing argument in favour of adopting the approach put forward in the Project Partnering Contract 2000 (PPC2000) Agreement. Members of consortia do not necessarily go on to work in the same consortia again because members need to respond flexibly to opportunities as and when they arise. Decision-making processes within consortia tend to be on an ad hoc basis. Construction risk is taken by the contractor and the construction supply chain but the reputational risk is carried by all the firms associated with a consortium. There is a wide variation in the manner that consortia are formed, determined by the individual circumstances of each project; its requirements, size and complexity, and the attitude of individual project leaders. However, there are a number of close working relationships based on generic models of consortia-like arrangements for the purpose of building production, such as the Housing Corporation Guidance Notes and the PPC2000.

The impact of procurement method on costs of procurement

Collaborative working methods offer the hope of reduced waste, lower tendering costs and improved outputs. The costs of tendering may be influenced by the introduction of different working methods. Transaction cost economics appears to offer an analytical framework for studying the costs of tendering, but it is more to do with providing explanations at the institutional/industry level, not at the level of individual projects. Surveys and interviews were carried out with small samples in UK. The data show that that while tendering costs are not necessarily higher in collaborative working arrangements, there is no correlation between costs of tendering and the way the work is organized. Practitioners perceive that the benefits of working in collaborative procurement routes far outweigh the costs. Tendering practices can be improved to avoid waste, and the suggested improvements include restricting selective tendering lists to 23 bidders, letting bidders know who they are competing with, reimbursing tendering costs for aborted projects and ensuring that timely and comprehensive information is provided to bidders.

Developing a system for assessing the costs associated with different procurement routes in the construction industry

In developing techniques for monitoring the costs associated with different procurement routes, the central task is disentangling the various project costs incurred by organizations taking part in construction projects. While all firms are familiar with the need to analyse their own costs, it is unusual to apply the same kind of analysis to projects. The purpose of this research is to examine the claims that new, ways of working such as strategic alliancing and partnering bring positive business benefits. This requires that costs associated with marketing, estimating, pricing, negotiation of terms, monitoring of performance and enforcement of contract are collected for a cross-section of projects under differing arrangements, and from those in the supply, chain from clients to consultants, contractors, subcontractors and suppliers. Collaboration with industrial partners forms the basis for developing a research instrument, bused on time sheets, which will be relevant for all those taking part in the work. The signs are that costs associated with,with tendering are highly variable, 1-15%, depending upon what precisely, is taken into account. The research to date reveals that there are mechanisms for measuring the costs of transactions and these will generate useful data for subsequent analysis.

Reaching for the skies: Time and turbulence in digital technologies and practices

This research examines dynamics associated with new representational technologies in complex organizations through a study of the use of a Single Model Environment, prototyping and simulation tools in the mega-project to construct Terminal 5 at Heathrow Airport, London. The ambition of the client, BAA. was to change industrial practices reducing project costs and time to delivery through new contractual arrangements and new digitally-enabled collaborative ways of working. The research highlights changes over time and addresses two areas of 'turbulence' in the use of: 1) technologies, where there is a dynamic tension between desires to constantly improve, change and update digital technologies and the need to standardise practices, maintaining and defending the overall integrity of the system; and 2) representations, where dynamics result from the responsibilities and liabilities associated with sharing of digital representations and a lack of trust in the validity of data from other firms. These dynamics are tracked across three stages of this well-managed and innovative project and indicate the generic need to treat digital infrastructure as an ongoing strategic issue.

Molecular interactions between the penetration enhancer 1,8-cineole and human skin

Penetration enhancers are chemicals that temporarily and reversibly diminish the barrier function of the outermost layer of skin, the stratum corneum, to facilitate drug delivery to and through the tissue. In the current study, the complex mechanisms by which 1,8-cineole, a potent terpene penetration enhancer, disrupts the stratum corneum barrier is investigated using post-mortem skin samples. In order to validate the use of excised tissue for these and related studies, a fibre optical probe coupled to an FT-Raman spectrometer compared spectroscopic information for human skin recorded from in vivo and in vitro sampling arrangements. Spectra from full-thickness (epidermis and dermis) post-mortem skin samples presented to the spectrometer with minimal sample preparation (cold acetone rinse) were compared with the in vivo system (the forearms of human volunteers). No significant differences in the Raman spectra between the in vivo and in vitro samples were observed, endorsing the use of post-mortem or surgical samples for this investigational work. Treating post-mortem samples with the penetration enhancer revealed some unexpected findings: while evidence for enhancer-induced disruption of the barrier lipid packing in the stratum corneum was detected in some samples, spectra from other samples revealed an increase in lipid order on treatment with the permeation promoter. These findings are consistent with phase-separation of the enhancer within the barrier lipid domains as opposed to homogeneous disruption of the lipid lamellae. Copyright (C) 2006 John Wiley & Sons, Ltd.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Green noise or green value? Measuring the effects of environmental certification on office values

This study investigates the price effects of environmental certification on commercial real estate assets. It is argued that there are likely to be three main drivers of price differences between certified and noncertified buildings. These are additional occupier benefits, lower holding costs for investors and a lower risk premium. Drawing upon the CoStar database of U.S. commercial real estate assets, hedonic regression analysis is used to measure the effect of certification on both rent and price. The results suggest that, compared to buildings in the same submarkets, eco-certified buildings have both a rental and sale price premium.