Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D2O and compare with experimental observations.Netherlands Organization for Scientific Research (VIDI grant)National Science Foundation (U.S.) ((NSF) CHE-0911107

The pursuit of happiness: the social and scientific origins of Hans Selye’s natural philosophy of life

© The Author(s) 2012. Open access article.In 1956, Hans Selye tentatively suggested that the scientific study of stress could ‘help us to formulate a precise program of conduct’ and ‘teach us the wisdom to live a rich and meaningful life’. Nearly two decades later, Selye expanded this limited vision of social order into a full-blown philosophy of life. In Stress without Distress, first published in 1974, he proposed an ethical code of conduct designed to mitigate personal and social problems. Basing his arguments on contemporary understandings of the biological processes involved in stress reactions, Selye referred to this code as ‘altruistic egotism’. This article explores the origins and evolution of Selye’s ‘natural philosophy of life’, analysing the links between his theories and adjacent intellectual developments in biology, psychosomatic and psychosocial medicine, cybernetics and socio-biology, and situating his work in the broader cultural framework of modern western societies.Wellcome Trus

Awards, Archives, and Affects: Tropes in the World Press Photo Contest 2009 - 2011

__Abstract__ Photography contests have assumed an increasingly significant public role in the context of the global surge of mass-mediated war reporting. This study focuses on the recurrence of visual tropes in press photographs awarded in the annual contest World Press Photo (WPP) in the years 2009–11. By tropes, we mean conventions (e.g. a mourning woman, a civilian facing soldiers, a distressed witness to an atrocity) that remain unchanged despite their travels across the visual sphere, gaining professional and public recognition and having a strong affective impact. We contend that photography contests such as the WPP influence and organize a process of generic understanding of war, disaster and atrocity that is based on a number of persistent tropes, such as the mourner, the protester or the survivor amidst chaos and ruins. We further show that these tropes are gendered along traditional conceptions of femininity and masculinity, appealing strongly to both judges and wider audiences. The evidence for our claim comes from an analysis of the photographs that won awards, observation of the judging sessions, semi-structured interviews with three jury chairmen, and public commentary on the juries’ choices (blogs, newspapers and websites)

A proteomic approach to investigating gene cluster expression and secondary metabolite functionality in Aspergillus fumigatus.

A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (p<0.05) of proliferating cell nuclear antigen (PCNA), NADH-quinone oxidoreductase and the gliotoxin oxidoreductase GliT, along with significantly attenuated abundance (p<0.05) of a heat shock protein, an oxidative stress protein and an autolysis-associated chitinase, when gliotoxin and H2O2 were present, compared to H2O2 alone. Moreover, gliotoxin exposure significantly reduced the abundance of selected proteins (p<0.05) involved in de novo purine biosynthesis. Significantly elevated abundance (p<0.05) of a key enzyme, xanthine-guanine phosphoribosyl transferase Xpt1, utilised in purine salvage, was observed in the presence of H2O2 and gliotoxin. This work provides new insights into the A. fumigatus proteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism

Ergothioneine Biosynthesis and Functionality in the Opportunistic Fungal Pathogen, Aspergillus fumigatus.

Ergothioneine (EGT; 2-mercaptohistidine trimethylbetaine) is a trimethylated and sulphurised histidine derivative which exhibits antioxidant properties. Here we report that deletion of Aspergillus fumigatus egtA (AFUA_2G15650), which encodes a trimodular enzyme, abrogated EGT biosynthesis in this opportunistic pathogen. EGT biosynthetic deficiency in A. fumigatus significantly reduced resistance to elevated H2O2 and menadione, respectively, impaired gliotoxin production and resulted in attenuated conidiation. Quantitative proteomic analysis revealed substantial proteomic remodelling in ΔegtA compared to wild-type under both basal and ROS conditions, whereby the abundance of 290 proteins was altered. Specifically, the reciprocal differential abundance of cystathionine γ-synthase and β-lyase, respectively, influenced cystathionine availability to effect EGT biosynthesis. A combined deficiency in EGT biosynthesis and the oxidative stress response regulator Yap1, which led to extreme oxidative stress susceptibility, decreased resistance to heavy metals and production of the extracellular siderophore triacetylfusarinine C and increased accumulation of the intracellular siderophore ferricrocin. EGT dissipated H2O2 in vitro, and elevated intracellular GSH levels accompanied abrogation of EGT biosynthesis. EGT deficiency only decreased resistance to high H2O2 levels which suggests functionality as an auxiliary antioxidant, required for growth at elevated oxidative stress conditions. Combined, these data reveal new interactions between cellular redox homeostasis, secondary metabolism and metal ion homeostasis

Assessment of the realisation of the right to adequate food in the Blue Crane Route (Eastern Cape, South Africa)

To assess whether the right to adequate food (RtF) is realised by children and primary caregivers and what actions are required to fully realise this right.A cross-sectional, descriptive study was undertaken using a mixed-methods approach.Rural and urban primary caregivers of children (one to five years old) were recruited if they had resided in the Blue Crane Route (Eastern Cape) for at least six months. Purposefully selected key informants (KIs) involved in nutrition and food security, health or governance participated in in-depth interviews.Primary caregivers responded to interviewer-administered questionnaires (IAQ) (N = 161), which investigated various indicators supporting the realisation of the RtF. Statistical analysis of quantitative data examined relationships between urban and rural participants. Significance was considered at p < 0.05. In-depth interviews with key informants (KIs) examined the perceptions of 11 prominent community leaders. Qualitative data were coded deductively and common themes identified

Internal representations of smell in the Drosophila brain

Recent advances in sensory neuroscience using Drosophila olfaction as a model system have revealed brain maps representing the external world. Once we understand how the brain's built-in capability generates the internal olfactory maps, we can then elaborate how the brain computes and makes decision to elicit complex behaviors. Here, we review current progress in mapping Drosophila olfactory circuits and discuss their relationships with innate olfactory behaviors

Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

Item does not contain fulltextIsotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides