NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason-Pfizer Monkey Virus

The high-resolution structure of the N-terminal domain (NTD) of the retroviral capsid protein (CA) of Mason-Pfizer monkey virus (M-PMV), a member of the betaretrovirus family, has been determined by NMR. The M-PMV NTD CA structure is similar to the other retroviral capsid structures and is characterized by a six α-helix bundle and an N-terminal β-hairpin, stabilized by an interaction of highly conserved residues, Pro1 and Asp57. Since the role of the β-hairpin has been shown to be critical for formation of infectious viral core, we also investigated the functional role of M-PMV β-hairpin in two mutants (i.e., ΔP1NTDCA and D57ANTDCA) where the salt bridge stabilizing the wild-type structure was disrupted. NMR data obtained for these mutants were compared with those obtained for the wild type. The main structural changes were observed within the β-hairpin structure; within helices 2, 3, and 5; and in the loop connecting helices 2 and 3. This observation is supported by biochemical data showing different cleavage patterns of the wild-type and the mutated capsid-nucleocapsid fusion protein (CANC) by M-PMV protease. Despite these structural changes, the mutants with disrupted salt bridge are still able to assemble into immature, spherical particles. This confirms that the mutual interaction and topology within the β-hairpin and helix 3 might correlate with the changes in interaction between immature and mature lattices.     

Improving the analysis of NMR spectra tracking pH‐induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift

pH‐induced chemical shift perturbations (CSPs) can be used to study pH‐dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH‐dependent structural transitions in bovine β‐lactoglobulin (βLG) by analyzing its NMR pH‐titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in βLG. The results show that around 20% of the amide nuclei CSPs in βLG originate exclusively from “through‐space” electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH‐dependent structural transitions in βLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH‐dependent conformational change. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Lipid Dependent Cardio- Haemodynamic Tolerability of Liposomes in Rats

Abstract

Rationale and Objectives:

The use of contrast-carrying liposomes in diagnostic applications (1) or of haemoglobin liposomes in blood replacement therapy (2) requires infusion of large lipid doses. Saturated lipids like HSPC are often used in these formulations to render the liposomes more stable (3). Previous studies have indicated that intravenous injection of such liposome preparations can result in significant haemodynamic changes in rats (14). The purpose of this study was to systematically evaluate cardio- and haemodynamic effects of liposomes prepared from saturated and unsaturated phosphatidylcholine alone or in combination with other lipid components.

Methods;

Liposomes made from SPC, HSPC, DSPC, DSPC/CH, DSPC/DSPG, DSPC/CH/DSPG were infused in anaesthetized rats (total lipid dose: 300 mg lipid/kg BW) and cardio-heamodynamic parameters were measured.

Results:

DSPC-liposomes significantly reduced blood pressure (BP) and total peripheral resistance (TPR) by -53.7 % and -45.7 % of prevalue, respectively. Similar results were obtained for HSPC-liposomes. Marked ECG-changes were recorded for both formulations. SPC-liposomes caused a transient and moderate reduction of BP and TPR (-17.0 % and -22.3 %, respectively). Short-lasting ECG changes were also observed. The addition of cholesterol or DSPG to DSPC liposomes reduced cardiac and haemodynamic side effects in rats.

Conclusion;

The lipid composition of liposomes is of major importance for the incidence of cardiovascular side effects in rats. Liposomes composed of pure saturated phosphatidylcholine cause significant changes which can be diminished by the addition of other lipid components like cholesterol.     

Seasonal variation patterns of the fish community in the littoral waters of northern Lake Ontario,the Pickering-Darlington area

The ecotone fish community of the littoral waters is a mixture of onshore migratory pelagian species and littoral species. It is characterized by high numeric and diversity variations produced under the effect of migrations, thermal perturbations and the local habitat variations. The sixty analyzed sampling units belong to five years of records, three seasons and three types of littoral habitats. The Kendall tau test identifies the seasonal variation as a significant criterion for sample classification. From the ecological view point it corresponds to phases of the thermal stratification. The start of the thermal stratification identifies the season of a highest pelagian onshore migration. The maximum thermal stratification shows the community structure at the end of a massive pelagian return. The late fall circulation describes the community structure prevailed by the local populations. The quantitative patterns were evaluated for each season based on a 95% confidence interval of the mean and on normalized weighed averages. A comparison of subsequent community structures allowed a species classification by the magnitude of their numeric variations. Regarding the analyses of the diversity variations, a new strategy was introduced based on independently derived indices of the community diversity. The strategy identifies two features: the seasonal models of the diversity variation and the abnormal cases. The models depict the trends/features of the diversity variations. The abnormal cases evaluate the local/temporal side effects.     

Fault bars in bird feathers: mechanisms,and ecological and evolutionary causes and consequences

Fault bars are narrow malformations in feathers oriented almost perpendicular to the rachis where the feather vein and even the rachis may break. Breaks in the barbs and barbules result in small pieces of the feather vein being lost, while breaks in the rachis result in loss of the distal portion of the feather. Here, we provide a comprehensive review of 74 papers on fault bar formation in hopes of providing a clearer approach to their study. First, we review the evidence that the propensity to develop fault bars is modified by natural selection. Given that fault bars persist in the face of survival costs, we conclude that they must be an unfortunate consequence of some alternative adaptation that outweighs the fitness costs of fault bars. Second, we summarize evidence that the development of fault bars is triggered by psychological stress such as that of handling or predation attempts, and that they persist because the sudden contractions of the muscles in the feather follicle that control fright moults also causes the development of fault bars in growing feathers. Third, we review external and physiological (e.g. corticosterone) agents that may affect the likelihood that an acute stress will result in a growing feather exhibiting a fault bar. These modifying factors have often been treated as fundamental causes in the earlier literature on fault bars. Fourth, we then use this classification to propose a tentative model where fault bars of different severity (from light to severe) are the outcome of the interaction between the propensity to produce fault bars (which differs between species, individuals and feather follicles within individuals) and the intensity of the perturbation. This model helps to explain contradictory results in the literature, to identify gaps in our knowledge, and to suggest further studies. Lastly, we discuss ways in which better understanding of fault bars can inform us about other aspects of avian evolutionary ecology, such as the physiology of moult, the integration of moult into avian life cycles, and the strategies used to minimize stress during moult. Moreover, the study of fault bars may be relevant to understanding the aerodynamics of flight and the early evolution of flight.     

Measurement of the influence of titanium hip prosthesis on therapeutic electron beam dose distributions in a novel pelvic phantom

PurposeTo investigate the degree of 18 and 22 MeV electron beam dose perturbations caused by unilateral hip titanium (Ti) prosthesis.MethodsMeasurements were acquired using Gafchromic EBT2 film in a novel pelvic phantom made out of Nylon-12 slices in which a Ti-prosthesis is embedded. Dose perturbations were measured and compared using depth doses for 8 × 8, 10 × 10 and 11 × 11 cm² applicator-defined field sizes at 95 cm source-surface-distance (SSD). Comparisons were also made between film data at 100 cm SSD for a 10 × 10 cm² field and dose calculations made on CMS XiO treatment planning system utilizing the pencil beam algorithm. The extent of dose deviations caused by the Ti prosthesis based on film data was quantified through the dose enhancement factor (DEF), defined as the ratio of the dose influenced by the prosthesis and the unchanged beam.ResultsAt the interface between Nylon-12 and the Ti implant on the prosthesis entrance side, the dose increased to values of 21 ± 1% and 23 ± 1% for 18 and 22 MeV electron beams, respectively. DEFs increased with increasing electron energy and field size, and were found to fall off quickly with distance from the nylon-prosthesis interface. A comparison of film and XiO depth dose data for 18 and 22 MeV gave relative errors of 20% and 25%, respectively.ConclusionThis study outlines the lack of accuracy of the XiO TPS for electron planning in highly heterogeneous media. So a dosimetric error of 20–25% could influence clinical outcome.     

Perturbation of the intermolecular contact regions (molecular surface) of hemoglobin S by intramolecular low-O2-affinity-inducing central cavity cross-bridges

The general assumption among researchers on hemoglobin is that the intramolecular central cavity cross-bridging of Hb does not result in any generalized perturbations at the protein surface. A corollary of this is that central cavity cross-bridges are unlikely to influence the polymerization of deoxy HbS, since polymerization is a protein surface phenomenon involving the participation of multiple protein surface amino acid residues. In an attempt to evaluate this experimentally, we have introduced two low-O₂-affinity-inducing central cavity cross-bridges into HbS, -sebacyl [between the two Lys-82() residues] and -fumaryl [between the two Lys-99() residues], and investigated their influence on the polymerization of the deoxy protein. The O₂ affinities of the cross-bridged HbS exhibited sensitivity toward the buffer ions and pH in a cross-link-specific fashion. The modulation of the O₂ affinity of these cross-bridged HbS in the presence of allosteric effectors, DPG and L-35, is also very distinct, reflecting the differences in the conformational features these two cross-bridges induce within the central cavity at the respective effector-binding domains. In addition, the -fumaryl cross bridge inhibited the polymerization, reflecting the perturbation of the microenvironment of one or more intermolecular contact residues, protein surface residues, as a consequence of the central cavity cross-bridge. On the other hand, the -sebacyl cross-bridge exerted a slight potentiating effect on the polymerization of HbS. This reflects the fact that the perturbations at the protein surface are limited and favor polymerization. The results presented demonstrate that the structural changes induced by the central cavity cross-bridges are very specific and not simply restricted to the sites of modification, but are propagated to distant sites/domains, both within and outside the central cavity. It is conceivable that other surface regions that are not involved in the polymerization could also experience similar structural/conformational consequences. These results should be taken into consideration in designing intramolecularly cross-bridged asymmetric hybrid HbS for mapping the contribution of the intermolecular contact residues in the cis and trans dimers of deoxy HbS during polymerization.     

Conformational interconversions in peptide β-turns: Discrimination between enantiomeric conformations by chiral perturbation

The crystal structure of the model tripeptide Boc-Aib-Gly-Leu-OMe ( 1 ) reveals two independent molecules in the asymmetric unit that adopt “enantiomeric” type I and type I′ β-turn conformations with the Aib and Gly residues occupying the corner (i + 1 and i + 2) positions. ¹³C cross polarization and magic angle sample spinning spectra in the solid state also support the coexistence of two conformational species. ¹³C-nmr in CDCl₃ establishes the presence of a single species or rapid exchange between conformations. 400 MHz ¹H-nmr provides evidence for conformational exchange involving a major and minor species, with β-turn conformations supported by the low solvent exposure of Leu(3) NH and the observation of N_iH ↔ N_i+1H nuclear Overhauser effects. CD bands in the region 190–230 nm are positive, supporting a major population of type I′ β-turns. The isomeric peptide, Boc-Gly-Leu-Aib-OMe ( 2 ), adopts an “open” type II′ β-turn conformation in crystals. Solid state and solution nmr support population of a single conformational species. Chiral perturbation introduced outside the folded region of peptides may provide a means of modulating screw sense in achiral sequences. © 1998 John Wiley & Sons, Inc. Biopoly 45: 191–202, 1998     

Solid-state spectral perturbations in square-planar complexes

A brief overview of color changes of square-planar complexes upon crystallization is presented along with selected spectra and theoretical spectral modeling results. In general, brilliant colored crystals of several square-planar complexes develop from colorless solution. The systems include Magnus’ green salt, tetracyanometallates, and bis(dimethylglyoximato)nickel(II). It is generally accepted that the transition responsible for a spectral red shift and increase in intensity is from an uppermost filled orbital with a large metal d_z² component to a low-lying empty metal-based p_z orbital. Since these orbitals are largely oriented out of plane, they interact most strongly when the planes are aggregated. Experimental data from selected single-crystal polarized specular reflectance spectra and ZINDO calculations on several systems are reviewed.