Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Rapid climate change: an overview for economists

The possibility of future rapid climatic changes is a pressing concern amongst climate scientists. For example, an abrupt collapse of the ocean's Thermohaline Circulation (THC) would rapidly cool the northern hemisphere and reduce the net global primary productivity of vegetation, according to computer models. It is unclear how to incorporate such low-probability, high-impact events into the development of economics policies. This paper reviews the salient aspects of rapid climate change relevant to economists and policy makers. The main scientific certainties and uncertainties are clearly delineated, with the aim of guiding economics goals and ensuring that they retain fidelity to their scientific underpinnings.

Edaphic influences on plant community adaptation in the Chiquibul forest of Belize

Edaphic variables figure significantly in plant community adaptations in tropical ecosystems but are often difficult to resolve because of the confounding influence of climate. Within the Chiquibul forest of Belize, large areas of Ultisols and Inceptisols occur juxtaposed within a larger zone of similar climate, permitting unambiguous assessment of edaphic contributions to forest composition. Wet chemical analyses, X-ray diffraction and X-ray fluorescence spectroscopy were employed to derive chemical (pH, exchangeable cations, CEC, total and organic C, total trace elements) and physical (texture, mineralogy) properties of four granite-derived Ustults from the Mountain Pine Ridge plateau and four limestone-derived Ustepts from the San Pastor region. The soils of these two regions support two distinct forests, each possessing a species composition reflecting the many contrasting physicochemical properties of the underlying soil. Within the Mountain Pine Ridge forest, species abundance and diversity is constrained by nutrient deficiencies and water-holding limitations imposed by the coarse textured, highly weathered Ultisols. As a consequence, the forest is highly adapted to seasonal drought, frequent fires and the significant input of atmospherically derived nutrients. The nutrient-rich Inceptisols of the San Pastor region, conversely, support an abundant and diverse evergreen forest, dominated by Sabal mauritiiformis, Cryosophila stauracantha and Manilkara spp. Moreover, the deep, fine textured soils in the depressions of the karstic San Pastor landscape collect and retain during the wet season much available water, thereby serving as refugia during particularly long periods of severe drought. To the extent that the soils of the Chiquibul region promote and maintain forest diversity, they also confer redundancy and resilience to these same forests and, to the broader ecosystem, of which they are a central part. (C) 2005 Elsevier B.V. All rights reserved.

The bond scheme

Under the bond scheme, a pre-determined series of payments would compensate farmers for lost revenues resulting from policy change. Unlike the Single Payment Scheme, payments would be fully decoupled: recipients would not have to retain farmland, or remain in agriculture. If vested in a paper asset, the guaranteed, unencumbered, income stream would be similar to that from a government bond. Recipients could exchange this for a capital sum reflecting the net present value of future payments, and reinvest in other business ventures, either on- or offfarm.With a finite, declining flow of payments, budget expenditure would reduce, releasing funds for other uses.

On the time for fold surfaces to order during the crystallization of polyethylene from the melt and its dependence on molecular parameters

New experiments underpin the interpretation of the basic division in crystallization behaviour of polyethylene in terms of whether or not there is time for the fold surface to order before the next molecular layer is added at the growth front. For typical growth rates, in Regime 11, polyethylene lamellae form with disordered {001} fold surfaces then transform, with lamellar thickening and twisting, towards the more-ordered condition found for slower crystallization in Regime 1, in which lamellae form with and retain {201} fold surfaces. Several linear and linear-low-density polyethylenes have been used to show that, for the same polymer crystallized alone or in a blend, the growth rate at which the change in initial lamellar condition occurs is reasonably constant thereby supporting the concept of a specific time for surfaces to attain the ordered {201}) state. This specific time, in the range from milliseconds to seconds, increases with molecular length, and in linear-low-density polymer, for higher branch contents. (c) 2006 Elsevier Ltd. All rights reserved.

Infant feeding choices: experience, self-identity and lifestyle

In England 78% of mothers initiate breastfeeding and in the UK less than 1% exclusively breastfeed until 6 months, despite WHO recommendations to do so. This study investigated women’s infant feeding choices using in-depth interviews with 12 mothers of infants aged 7-18 weeks. Using content analysis, four themes emerged: (1) Information, Knowledge and Decision Making, (2) Physical Capability, (3) Family and Social Influences, (4) Lifestyle, Independence and Self-Identity. Whilst women were aware of the ‘Breast is Best’ message, some expressed distrust in this information if they had not been breastfed themselves. Women felt their own infant feeding choice was influenced by the perceived norm amongst family and friends. Women described how breastfeeding hindered their ability to retain their self-identities beyond motherhood as it limited their independence. Several second-time mothers felt they lacked support from health professionals when breastfeeding their second baby, even if they had previously encountered breastfeeding difficulties. The study indicates that experience of breastfeeding, and belief in the health benefits associated with it are important factors for initiation of breastfeeding, whilst decreased independence and self-identity may influence duration of breastfeeding. Intervention and support schemes should tackle all mothers, not just first-time mothers.

Stomatal guard cells are totipotent

It has been successfully demonstrated, using epidermis explants of sugar beet (Beta vulgaris L.), that stomatal guard cells retain full totipotent capacity. Despite having one of the highest degrees of morphological adaptation and a unique physiological specialization, it is possible to induce a re-expression of full (embryogenic) genetic potential in these cells in situ by reversing their highly differentiated nature to produce regenerated plants via a callus stage. The importance of these findings both to stomatal research and to our understanding of cytodifferentiation in plants is discussed.

Do construction companies need to match employees' expectations?

Commitment of employees is relatively low in construction. This problem is exasperated by companies inability to attract, motivate, and retain talent that is then often channelled into other more attractive industrial sectors where the prospects, conditions and rewards are perceived to be much higher. The purpose of this study is thus primarily to develop a generic model to maximise employees' engagement, improve their motivation and increase the retention levels. To achieve this aim, the investigation looks into how perceived employment obligations and expectations impact commitment and through that organisational performance. The study is based on the postulations of Luhmann's theory of social systems with communication viewed as a constitutive element of a social system. Consequently expectations of a particular party in an employment relationship are represented in a communicative space requiring the other party's understanding in order to align expectations of both sides in the relationship. Explicitly, alignment of by an employee perceived manager's expectations determines his/ her commitment to fulfil obligations towards the manager. The result of this first stage of research is a conceptual model developed following the substantial supporting evidence in the literature and it forms the framework for mitigation of low commitment, motivation and retention of employees. The model particularly focuses on factors affecting employees' perceived expectations like reneging, incongruence and the process of communication. In the future the model will be validated using empirical data from a combination of observational and enquiry-based research. Once completed, the model will provide a framework for informing Human Resource Management policies with the aim to improve commitment of employees, increase the levels of retention and consequently improve the performance of construction organisations.

Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes

Background: We report an analysis of a protein network of functionally linked proteins, identified from a phylogenetic statistical analysis of complete eukaryotic genomes. Phylogenetic methods identify pairs of proteins that co-evolve on a phylogenetic tree, and have been shown to have a high probability of correctly identifying known functional links. Results: The eukaryotic correlated evolution network we derive displays the familiar power law scaling of connectivity. We introduce the use of explicit phylogenetic methods to reconstruct the ancestral presence or absence of proteins at the interior nodes of a phylogeny of eukaryote species. We find that the connectivity distribution of proteins at the point they arise on the tree and join the network follows a power law, as does the connectivity distribution of proteins at the time they are lost from the network. Proteins resident in the network acquire connections over time, but we find no evidence that 'preferential attachment' - the phenomenon of newly acquired connections in the network being more likely to be made to proteins with large numbers of connections - influences the network structure. We derive a 'variable rate of attachment' model in which proteins vary in their propensity to form network interactions independently of how many connections they have or of the total number of connections in the network, and show how this model can produce apparent power-law scaling without preferential attachment. Conclusion: A few simple rules can explain the topological structure and evolutionary changes to protein-interaction networks: most change is concentrated in satellite proteins of low connectivity and small phenotypic effect, and proteins differ in their propensity to form attachments. Given these rules of assembly, power law scaled networks naturally emerge from simple principles of selection, yielding protein interaction networks that retain a high-degree of robustness on short time scales and evolvability on longer evolutionary time scales.

Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol

IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexafluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.

Regulation of SHP-1 tyrosine phosphatase in human platelets by serine phosphorylation at its C terminus

SHP-1 is a Src homology 2 (SH2) domain-containing tyrosine phosphatase that plays an essential role in negative regulation of immune cell activity. We describe here a new model for regulation of SHP-1 involving phosphorylation of its C-terminal Ser(591) by associated protein kinase Calpha. In human platelets, SHP-1 was found to constitutively associate with its substrate Vav1 and, through its SH2 domains, with protein kinase Calpha. Upon activation of either PAR1 or PAR4 thrombin receptors, the association between the three proteins was retained, and Vav1 became phosphorylated on tyrosine and SHP-1 became phosphorylated on Ser(591). Phosphorylation of SHP-1 was mediated by protein kinase C and negatively regulated the activity of SHP-1 as demonstrated by a decrease in the in vitro ability of SHP-1 to dephosphorylate Vav1 on tyrosine. Protein kinase Calpha therefore critically and negatively regulates SHP-1 function, forming part of a mechanism to retain SHP-1 in a basal active state through interaction with its SH2 domains, and phosphorylating its C-terminal Ser(591) upon cellular activation leading to inhibition of SHP-1 activity and an increase in the tyrosine phosphorylation status of its substrates.

Patterns of peristome reduction and ornamentation in African Entodontaceae

The Entodontaceae is characterised by erect capsules with inset and substantially reduced peristomes. Differences in peristome morphology and ornamentation delimit both genera and species within the family. The Entodontaceae, as presently recognised, consists of four genera, Entodon, Erythrodontium, Mesonodon and Pylaisiobryum, which show a variety of peristome ornamentation patterns, and exhibit differing levels of peristome reduction. This variation encompasses an unusual combination of structurally reduced peristomes, which retain massive exostome ornamentation, and residual peristome function. As part of a taxonomic revision of the family in Africa, generic patterns of peristome reduction and ornamentation are described. Inter- and intra-specific variation patterns of both the exostome and endostome have been investigated using detailed SEM studies of material from Africa and beyond. Structural reduction of the peristome is associated with high levels of intra-specific variation in peristome ornamentation patterns. Common trends in these patterns of variation are identified within the family. Putative hybrid sporophytes have been identified in Entodon, and the taxonomic implications of these observations are considered for a family where species delimitation has in the past often depended on minor variation in peristome structure or ornamentation patterns. (author abst.)

Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol

IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexa-fluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.

High-affinity small molecule-phospholipid complex formation: Binding of siramesine to phosphatidic acid

Siramesine (SRM) is a sigma-2 receptor agonist which has been recently shown to inhibit growth of cancer cells. Fluorescence spectroscopy experiments revealed two distinct binding sites for this drug in phospholipid membranes. More specifically, acidic phospholipids retain siramesine on the bilayer surface due to a high-affinity interaction, reaching saturation at an apparent 1:1 drug-acidic phospholipid stoichiometry, where after the drug penetrates into the hydrocarbon core of the membrane. This behavior was confirmed using Langmuir films. Of the anionic phospholipids, the highest affinity, comparable to the affinities for the binding of small molecule ligands to proteins, was measured for phosphatidic acid (PA, mole fraction Of X-PA = 0.2 in phosphatidylcholine vesicles), yielding a molecular partition coefficient of 240 +/- 80 x 10(6). An MD simulation on the siramesine:PA interaction was in agreement with the above data. Taking into account the key role of PA as a signaling molecule promoting cell growth our results suggest a new paradigm for the development of anticancer drugs, viz. design of small molecules specifically scavenging phospholipids involved in the signaling cascades controlling cell behavior.