The effects of guanidine hydrochloride on the ’random coil‘ conformations and NMR chemical shifts of the peptide series GGXGG

The effects of the commonly used denaturant guanidine hydrochloride(GuHCl) on the random coil conformations and NMR chemical shifts of theproteogenic amino acids have been characterized using the peptide seriesAc-Gly-Gly-X-Gly-Gly-NH₂. The angle-sensitive couplingconstants, ROESY cross peak intensities and proline cis–trans isomerratios of a representative subset of these peptides are unaffected by GuHCl,which suggests that the denaturant does not significantly perturb intrinsicbackbone conformational preferences. A set of³J_HNH values is presented which agreewell with predictions of recently developed models of the random coil. Wehave also measured the chemical shifts of all 20 proteogenic amino acids inthese peptides over a range of GuHCl concentrations. The shifts exhibit alinear dependence on denaturant concentration and we report here correctionfactors for the calculation of random coil ¹H chemicalshifts at any arbitrary denaturant concentration. Studies of arepresentative subset of peptides indicate that ¹³C and¹⁵N chemical shifts are also perturbed by the denaturant.These results should facilitate the application of chemical shift-basedanalytical techniques to the study of polypeptides in solution with GuHCl.The effects of the denaturant on the quality of NMR spectra and on chemicalshift referencing are also addressed.     

‘Random coil’ 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG

Summary Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D ¹H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chain assignments in previous studies to be resolved. An additional benefit of the temperature data is that they can be used to obtain ‘random coil’ amide proton chemical shifts at any temperature between 278 and 318 K by interpolation. Changes of chemical shift as a function of trifluoroethanol concentration have also been determined at a variety of temperatures for a subset of peptides. Significant changes are found in backbone and side-chain amide proton chemical shifts in these ‘random coil’ peptides with increasing amounts of trifluoroethanol, suggesting that caution is required when interpreting chemical shift changes as a measure of helix formation in peptides in the presence of this solvent. Comparison of the proton chemical shifts obtained here for H-Gly-Gly-X-Gly-Gly-OH with those for H-Gly-Gly-X-Ala-OH [Bundi, A. and Wüthrich, K. (1979) Biopolymers, 18, 285–297] and for Ac-Gly-Gly-X-Ala-Gly-Gly-NH₂ [Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81] generally shows good agreement for CH protons, but reveals significant variability for NH protons. Amide proton chemical shifts appear to be highly sensitive to local sequence variations and probably also to solution conditions. Caution must therefore be exercised in any structural interpretation based on amide proton chemical shifts.     

Sequence specific 1H, 13C and 15N resonance assignments of hahellin in 8 M urea

The sequence specific ¹H, ¹³C and ¹⁵N resonance assignments of hahellin in 8 M urea-denatured state have been accomplished by NMR spectroscopy. Secondary chemical shift analysis reveals the native-like propensities for β-rich conformation in the denatured state.     

Prediction of proton chemical shifts in RNA – Their use in structure refinement and validation

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct., 76, 81–92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341–346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the ¹H chemical shifts revealing their physical origin. For example, a down-field shift of either H2 or H3 or both indicates a high-syn/syn -angle. In an A-helix it is essentially the 5-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed ¹H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings.     

Cuticular hydrocarbon divergence in the jewel wasp Nasonia: evolutionary shifts in chemical communication channels?

The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyse their chemical divergence and investigate their role as species‐specific sexual signalling cues. Males and females of all four Nasonia species showed unique, nonoverlapping CHC profiles unambiguously separating them. Surprisingly, male and female phylogenies based on the chemical distances between their CHC profiles differed dramatically, where only male CHC divergence parallels the molecular phylogeny of Nasonia. In particular, N. giraulti female CHC profiles were the most divergent from all other species and very different from its most closely related sibling species N. oneida. Furthermore, although our behavioural assays indicate that female CHC profiles can generally be perceived as sexual cues attracting males in Nasonia, this function has apparently been lost in the highly divergent female N. giraulti CHC profiles. Curiously, N. giraulti males are still attracted to heterospecific, but not to conspecific female CHC profiles. We suggest that this striking discrepancy has been caused by an extensive evolutionary shift in female N. giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to.     

Aromatic interactions in model peptide β-hairpins: ring current effects on proton chemical shifts

Crystal structures of eight peptide β-hairpins in the sequence Boc-Leu-Phe-Val-Xxx-Yyy-Leu-Phe-Val-OMe revealed that the Phe(2) and Phe(7) aromatic rings are in close spacial proximity, with the centroid-centroid distance (R(cen)) of 4.4-5.4 ? between the two phenyl rings. Proton NMR spectra in chloroform and methanol solution reveal a significant upfield shift of the Phe(7) C(δ,δ') H(2) protons (6.65-7.04 ppm). Specific assignments of the aromatic protons have been carried out in the peptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (6). The anticipated ring current shifts have been estimated from the aromatic ring geometrics observed in crystals for all eight peptides. Only one of the C(δ,δ') H proton lies in the shielding zone with rapid ring flipping, resulting in averaging between the two extreme chemical shifts. An approximate estimate of the population of conformations, which resemble crystal state orientation, may be obtained. Key nuclear Overhauser effects (NOEs) between facing Phe side chains provide support for close similarity between the solid state and solution conformation. Temperature dependence of aromatic ring proton chemical shift and line widths for peptide 6 (Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe) and the control peptide Boc-Leu-Val-Val-(D)Pro-Gly-Leu-Phe-Val-OMe establish an enhanced barrier to ring flipping when the two Phe rings are in proximity. Modeling studies suggest that small, conformational adjustment about C(α)-C(β) (χ(1) ) and C(β)-C(γ) (χ(2) ) bonds of both the Phe residues may be required in order to permit unhindered, uncorrelated flipping of both the Phe rings. The maintenance of the specific aromatic ring orientation in organic solvents provides evidence for significant stabilizing interaction.     

Derivation of 13C chemical shift surfaces for the anomeric carbons of oligosaccharides and glycopeptides using ab initio methodology

The dependence between the anomeric carbon chemical shift and the glycosidic bond , dihedral angles in oligosaccharide and glycopeptide model compounds was studied by Gauge-Including Atomic Orbital (GIAO) ab initio calculations. Complete chemical shift surfaces versus and for d-Glcp-d-Glcp disaccharides with (11), (12), (13), and (14) linkages in both - and -configurations were computed using a 3-21G basis set, and scaled to reference results from calculations at the 6-311G^** level of theory. Similar surfaces were obtained for GlcNAcThr and GlcNAcSer model glycopeptides in - and -configurations, using in this case different conformations for the peptide moiety. The results obtained for both families of model compounds are discussed. We also present the determination of empirical formulas of the form ¹³C=f(,) obtained by fitting the raw ab initio data to trigonometric series expansions suitable for use in molecular mechanics and dynamics simulations. Our investigations are consistent with experimental observations and earlier calculations performed on smaller glycosidic bond models, and show the applicability of chemical shift surfaces in the study of the conformational behavior of oligosaccharides and glycopeptides.     

Ontogenetic shifts in a prey’s chemical defences influence feeding responses of a snake predator

Foraging theory suggests that predator responses to potential prey should be influenced by prey chemical defences, but the effects of ontogenetic variation in such defences on prey vulnerability to predators remain unclear. Cane toads (Rhinella marina) are toxic to anurophagous snakes, including the keelback (Tropidonophis mairii, a natricine colubrid that occurs within the toads' invasive range in Australia). Toxin levels and diversity change through toad ontogeny, decreasing from the egg stage to metamorphosis, then increasing in postmetamorphic toads. If the toxin content of a prey item influences predator responses, we predict that keelbacks should exhibit selective predation on toads close to metamorphosis. The results of our laboratory trials on adult (field-collected, and thus toad-experienced) and hatchling (laboratory-incubated, and thus toad-naive) keelbacks supported this prediction. The snakes selectively consumed later-stage rather than earlier-stage tadpoles, and earlier-stage rather than later-stage metamorphs. Our data are thus consistent with the hypothesis that ontogenetic changes in toxin content can affect individuals' vulnerability to predation.     

Structural information from NMR secondary chemical shifts of peptide α C−H protons in proteins

The secondary chemical shift experienced by the¹H-NMR resonances of the α C?H protons in proteins can be correlated with their backbone torsional angles ψ, which dictate the orientation of the α C?H proton to the adjacent carbonyl group. It is shown that α C?H protons present in β-sheet regions experience downfield secondary shifts , whereas those in α-helix regions experience upfield secondary shifts. The predictive use of this correlation in assignment studies is illustrated for the calcium-binding protein paravalbumin, for which a crystal structure is available, and troponin C, for which no crystallographic data are available.     

Latitudinal shifts in the distribution of exploited fishes in Korean waters during the last 30 years: a consequence of climate change

Sea surface temperatures in Korean waters have increased by approximately 1 °C during the past 40 years, implying possible range shifts of marine fishes and invertebrates. We analyzed spatially explicit, commercial catch data for 12 major fish species collected from 1984 to 2010 in Korean waters to evaluate and project their range shifts based on climate-driven hydrographic changes simulated by a general circulation model under a climate change scenario. There were significant relationships between the mean latitude of the catch distribution and water temperature for seven of the 12 species examined. Our circulation model projected that temperature stratification in the Korea Strait will disappear by 2030, and our empirical relationships predicted that the ranges of five of the fish species examined will shift poleward by 19–71 km from the 2000s to the 2030s. Compared with studies of demersal fishes in the western North Atlantic and the North Sea, our estimated speeds of shift in mean latitude of fishes were, on average, slower by factors of 2.3 and 5.7, respectively. This suggests that the pattern of range shift of marine species can vary regionally, depending on oceanographic and geomorphologic conditions. International cooperative research among fisheries scientists from countries throughout the region, especially Japan and China, is required to more reliably and comprehensively assess and project the range shifts of fish species. This will provide a scientific basis for the development of fishery policies and their adaptation to climate change in the western North Pacific.     

Quantum chemical studies on the inhibition potentials of some Penicillin compounds for the corrosion of mild steel in 0.1 M HCl

Inhibitive and adsorption properties of Penicillin G, Amoxicillin and Penicillin V potassium were studied using gravimetric, gasometric and quantum chemical methods. The results obtained indicate that these compounds are good adsorption inhibitors for the corrosion of mild steel in HCl solution. The adsorption of the inhibitors on mild steel surface is spontaneous, exothermic and supports the mechanism of physical adsorption. From DFT results, the sites for nucleophilic attacks in the inhibitors are the carboxylic acid functional group while the sites for electrophilic attacks are in the phenyl ring. There was a strong correlation between theoretical and experimental inhibition efficiencies.     

After 8 years of annual pollen trapping across the tree line in western Norway: are the data still anomalous?

The modern pollen production of local sub-alpine and alpine vegetation has been monitored over 8 years by using pollen traps situated along an elevational transect crossing the Pinus sylvestris and Betula pubescens elevational limits and continuing into the mid- and high-alpine vegetation in western Norway. The aim of the study is to monitor annual variation in the pollen production and hence the representation of common taxa found at or near the tree-line. The results can be used to derive critical pollen values that can be used to infer the presence of these taxa in the past, and to reconstruct past changes in tree line positions. Nine modified Tauber pollen traps were critically positioned in the vegetation from 663 to 1,347 m a.s.l. Three sub-aquatic traps were located in a small lake at 800 m a.s.l. just above the present-day B. pubescens tree-line. The traps have been sampled from 2004 to 2012. The results display large variations in pollen percentages and pollen accumulation rates from year to year, as well as great differences between the traps placed in the vegetation and in the lake, suggesting that further pollen trapping is needed to get a solid long-term average. The vegetation traps follow the vegetation distribution better and, as expected, give a more local signal than the lake traps.     

Combined use of 13C chemical shift and 1Hα−13Cα heteronuclear NOE data in monitoring a protein NMR structure refinement

Summary A large portion of the ¹³C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28°C has been determined at natural isotope abundance. Sequence-specific ¹³C assignments are reported for 100% of the assignable C, 96% of the C, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C chemical shifts for regions of regular -sheet structure. These assignments also provide the basis for interpreting ¹H–¹³C heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high internal mobility, indicated by these ¹H–¹³C HNOE measurements, correlate with locations of residues involved in the putative mEGF-receptor binding site. Using four families of mEGF structures obtained over the last few years, we demonstrate that standard deviations between experimental and back-calculated C values can be used to monitor the refinement of this protein's structure, particularly for -sheet regions. Improved agreement between calculated and observed values of C is correlated with other measures of structure quality, including lowered values of residual constraint violations and more negative values of conformational energy. These results support the view that experimental conformation-dependent chemical shifts, C, can provide a reliable source of information for monitoring the process of protein structure refinement and are potentially useful restraints for driving the refinement.Abbreviations HSQC heteronuclear single-quantum coherence spectroscopy - PFG pulsed-field gradient - TOCSY ¹H-¹H total correlation spectroscopy - EGF epidermal growth factor - mEGF murine EGF - hEGF human EGF - hTGF human type- transforming growth factor - DIPSI spm-locking pulse sequence - NOE nuclear Overhauser effect - HNOE heteronuclear Overhauser effect     

Caspase-8 and its inhibitors in RCCs in vivo: the prominent role of ARC

Activation of the initiator-caspase, caspase-8 is under tight control of multiple antiapoptotic regulators including ARC, cFlip_S, cFlip_L and PED/PEA-15. Since there is little data regarding the expression of caspase-8 and its antiapoptotic regulators in human tumours in vivo, we analysed their expression in renal cell carcinomas (RCCs) to identify which of these genes might be crucial for the well known impaired apoptosis and—as a result—resistance towards chemotherapy and ionizing radiation of RCCs. Caspase-8, cFlip_S, cFlip_L and PED/PEA-15 mRNA expression was significantly increased only in early stages of RCCs compared to non-neoplastic renal tissue. In contrast, ARC mRNA expression was significantly increased in RCCs of all stages without differences between the tumour stages and grades. Importantly, the relative mRNA expression ratio between ARC and caspase-8 was significantly increased during carcinogenesis and tumour progression. In contrast, the relative mRNA expression ratio between cFlip_S, cFlip_L or PED/PEA-15 and caspase-8 remained constant during all tumour stages. In conclusion, our analysis revealed that ARC is the only caspase-8 inhibiting regulator being constantly overexpressed in RCCs. Furthermore, the balance between antiapoptotic ARC and proapoptotic caspase-8 is the only one to be disturbed during carcinogenesis and tumour progression of RCCs. This inhibition of Caspase-8 might therefore be one example for the multiple antiapoptotic functions of ARC in RCCs possibly contributing to the marked resistance of RCCs towards radio- and chemotherapy and reflects a shift of gene expression towards a more antiapoptotic context in RCCs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Random fluctuations in readings of measurement devices: cosmophysic effects?

Fluctuations of "computer time" provided by the PC quartz generator were studied. It was shown that variations in the yearly course of the quartz generator frequency occur with periodicities of 13-15 days and 28-30 days. Regular fluctuations with periods of 0.5 and 1.0 min are typical of the short-term spectral component. Impulses of sharp and intense deceleration of "computer time" are often observed against the background of these regular fluctuations. The conclusion is made that fluctuations of "computer time" are of cosmophysical origin.     

Microarrays: lost in a storm of data?

Microarray expression profiling is instrumental to our understanding of the function of the genome. Resolution of functionally relevant expression patterns will require the analysis of large data sets compiled from multiple investigators. For this and other reasons, I argue that it is crucial for array data to be publicly shared in a format as close to the 'raw data' as possible. Issues such as protection of intellectual property, ensuring quality of the data, and the format and timing for sharing array data are also discussed.     

Learning without Borders: A Review of the Implementation of Medical Error Reporting in Médecins Sans Frontières

Objective

To analyse the results from the first 3 years of implementation of a medical error reporting system in Médecins Sans Frontières-Operational Centre Amsterdam (MSF) programs.

Methodology

A medical error reporting policy was developed with input from frontline workers and introduced to the organisation in June 2010. The definition of medical error used was “the failure of a planned action to be completed as intended or the use of a wrong plan to achieve an aim.” All confirmed error reports were entered into a database without the use of personal identifiers.

Results

179 errors were reported from 38 projects in 18 countries over the period of June 2010 to May 2013. The rate of reporting was 31, 42, and 106 incidents/year for reporting year 1, 2 and 3 respectively. The majority of errors were categorized as dispensing errors (62 cases or 34.6%), errors or delays in diagnosis (24 cases or 13.4%) and inappropriate treatment (19 cases or 10.6%). The impact of the error was categorized as no harm (58, 32.4%), harm (70, 39.1%), death (42, 23.5%) and unknown in 9 (5.0%) reports. Disclosure to the patient took place in 34 cases (19.0%), did not take place in 46 (25.7%), was not applicable for 5 (2.8%) cases and not reported for 94 (52.5%). Remedial actions introduced at headquarters level included guideline revisions and changes to medical supply procedures. At field level improvements included increased training and supervision, adjustments in staffing levels, and adaptations to the organization of the pharmacy.

Conclusion

It was feasible to implement a voluntary reporting system for medical errors despite the complex contexts in which MSF intervenes. The reporting policy led to system changes that improved patient safety and accountability to patients. Challenges remain in achieving widespread acceptance of the policy as evidenced by the low reporting and disclosure rates.