Roles of non‐native hydrogen‐bonding interaction in helix‐coil transition of a single polypeptide as revealed by comparison between Gō‐like and non‐Gō models

To explore the role of non‐native interactions in the helix‐coil transition, a detailed comparison between a Gō‐like model and a non‐Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō‐like model, and the non‐native ones with sequence interval more than 4 is also included into the non‐Gō model. Some significant differences between the results from those two models have been found. The non‐native hydrogen bonds were found most populated at temperature around the helix‐coil transition. The rearrangement of non‐native hydrogen bonds into native ones in the formation of α‐helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non‐Gō model for a non‐short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non‐native hydrogen bonds have complicated the temperature‐dependence of Zimm‐Bragg nucleation constant. The increase of relative probability of non‐native hydrogen bonding for long polypeptide chains leads to non‐monotonous chain length effect on the transition temperature. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Trait plasticity alters the range of possible coexistence conditions in a competition–colonisation trade‐off

Most of the classical theory on species coexistence has been based on species‐level competitive trade‐offs. However, it is becoming apparent that plant species display high levels of trait plasticity. The implications of this plasticity are almost completely unknown for most coexistence theory. Here, we model a competition–colonisation trade‐off and incorporate trait plasticity to evaluate its effects on coexistence. Our simulations show that the classic competition–colonisation trade‐off is highly sensitive to environmental circumstances, and coexistence only occurs in narrow ranges of conditions. The inclusion of plasticity, which allows shifts in competitive hierarchies across the landscape, leads to coexistence across a much broader range of competitive and environmental conditions including disturbance levels, the magnitude of competitive differences between species, and landscape spatial patterning. Plasticity also increases the number of species that persist in simulations of multispecies assemblages. Plasticity may generally increase the robustness of coexistence mechanisms and be an important component of scaling coexistence theory to higher diversity communities.     

The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

Upon ATP binding, myosin motor protein is found in two alternative conformations, prerecovery state M* and postrecovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in prerecovery state to “down” position in postrecovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force‐generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487, and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. Proteins 2012; © 2012 Wiley Periodicals, Inc.     

Kinetic Modelling of in Vitro Lipid Peroxidation Experiments - 'Low Level' Validation of a Model of in Vivo Lipid Peroxidation

Kinetic modelling overcomes some of the drawbacks of purely intuitive thinking in integrating information accumulated on chemical reactions involved in oxidative stress. However, it is important to assess if current knowledge about the reactions that mediate lipid peroxidation already allows satisfactory modelling of this process in near-to-physiological conditions. In this paper, a set of increasingly complex in vitro experiments on antioxidants (a-tocopherol and ascorbate) and lipid peroxidation in heterogeneous systems is simulated. Quantitative to semiquantitative agreement is found between experimental and simulation results. In addition, this theoretical analysis provided useful insights, suggested new hypotheses and experiments and pointed out relevant aspects needing further research. The results encourage and serve as partial validation for the formulation of relatively detailed mathematical models of in vivo lipid peroxidation. Some important aspects of the formulation and analysis of such models are discussed.     

Development of an epiphyte indicator of nutrient enrichment: A critical evaluation of observational and experimental studies

An extensive review of the literature describing epiphytes on submerged aquatic vegetation (SAV), especially seagrasses, was conducted in order to evaluate the evidence for response of epiphyte metrics to increased nutrients. Evidence from field observational studies, together with laboratory and field mesocosm experiments, was assembled from the literature and evaluated for a hypothesized positive response to nutrient addition. There was general consistency in the results to confirm that elevated nutrients tended to increase the load of epiphytes on the surface of SAV, in the absence of other limiting factors. In spite of multiple sources of uncontrolled variation, positive relationships of epiphyte load to nutrient concentration or load (either nitrogen or phosphorus) often were observed along strong anthropogenic or natural nutrient gradients in coastal regions. Such response patterns may only be evident for parts of the year. Results from both mesocosm and field experiments also generally support the increase of epiphytes with increased nutrients, although outcomes from field experiments tended to be more variable. Relatively few studies with nutrient addition in mesocosms have been done with tropical or subtropical species, and more such controlled experiments would be helpful. Experimental duration influenced results, with more positive responses of epiphytes to nutrients at shorter durations in mesocosm experiments versus more positive responses at longer durations in field experiments. In the field, response of epiphyte biomass to nutrient additions was independent of climate zone. Mesograzer activity was a critical covariate for epiphyte response under experimental nutrient elevation, but the epiphyte response was highly dependent on factors such as grazer identity and density, as well as nutrient and ambient light levels. The balance of evidence suggests that epiphytes on SAV will be a useful indicator of persistent nutrient enhancement in many situations. Careful selection of appropriate temporal and spatial constraints for data collection, and concurrent evaluation of confounding factors will help increase the signal to noise ratio for this indicator.     

Towards the Understanding of the Folding of Methylene Units in the Glutamine Residue

The conformational preferences of the methylenic sequence in the side chain of the glutamine residue were investigated by ab initio and semi-empirical quantum mechanical calculations and examination of both the Brookhaven Protein Databank and Cambridge Structural Data Base. The results were analysed on the basis of our previous findings about the folding of methylene groups in aliphatic segments. Both energy calculations and the crystallographic structure of small peptides indicate that methylene units of the glutamine residue tend to fold in a gauche conformation. In contrast, such groups usually adopt an all-trans conformation in proteins due basically to the entropic and solvent contributions. These results have been demonstrated by computing the entropic correction to the free energy and evaluating the solvent effects through SCRF calculations     

Weighting indicators of tourism sustainability: A critical note

Indicator weighting is an important issue in the measurement of tourism sustainability. Its importance derives from the fact that weights can have a significant effect on the rankings of analysed regions and subsequent policymaking. This is because relative indicator weights may significantly differ depending on the chosen weighting procedure. Relevant studies have however not paid particular attention to this issue so far, which is a gap this note aims to fill. An illustrative comparison of indicator weights from available studies further indicates potentially serious problems with some commonly used weighting procedures.     

Stratified or Multicentre Analysis with Extended Mantel–Haenszel Statistics

Since its introduction in 1959 the ability of the classical Mantel-Haenszel (M–H) procedure for combining the odds ratios of a set of I 2 × 2 tables has led to its use also in stratified or multicentre type clinical trials. A familiar application is the M–H logrank test in survival analysis. An extension of the M–H procedure covering the case of 2 × K contingency tables (MANTEL , 1963) with ordered levels retains the essential property of pooling the results of I homogeneous tables (i.e. in absence of qualitative interactions). The assignment of some score for the K columns of a table is essential for the use of the method (in comparing 2 treatments). Some possibilities of score assignment are discussed: for clinical outcome variables such as the degree of severity of a disease, pain and so on, the score is at hand in a natural way. A less well-known type of scoring consists in ranking the observations of a continuous variable, leading to cell sizes of 1 or 0. In this case, however, if equidistant ranking was used, the E–M–H procedure appears as an extension of Wilcoxon's rank sum test and represents a powerful non-parametric approach in stratified or multicentre type designs with non normally distributed outcome variables. The results of some Monte-Carlo simulations for 2 possible equidistant ranking procedures are presented, which indicate only a moderate gain in power as compared to Wilcoxon's rank sum test under the common situation of centre effects not exceeding treatment effects. Use of the E–M–H pro?edure is also recommended as a simple method to overcome the potential bias due to unequally distributed prognostic factors among treatment groups.     

Feasibility of setting up generic alert levels for maximum skin dose in fluoroscopically guided procedures

PurposeThe feasibility of setting-up generic, hospital-independent dose alert levels to initiate vigilance on possible skin injuries in interventional procedures was studied for three high-dose procedures (chemoembolization (TACE) of the liver, neuro-embolization (NE) and percutaneous coronary intervention (PCI)) in 9 European countries.MethodsGafchromic® films and thermoluminescent dosimeters (TLD) were used to determine the Maximum Skin Dose (MSD). Correlation of the online dose indicators (fluoroscopy time, kerma- or dose-area product (KAP or DAP) and cumulative air kerma at interventional reference point (K_a,r)) with MSD was evaluated and used to establish the alert levels corresponding to a MSD of 2 Gy and 5 Gy. The uncertainties of alert levels in terms of DAP and K_a,r, and uncertainty of MSD were calculated.ResultsAbout 20–30% of all MSD values exceeded 2 Gy while only 2–6% exceeded 5 Gy. The correlations suggest that both DAP and K_a,r can be used as a dose indicator for alert levels (Pearson correlation coefficient p mostly >0.8), while fluoroscopy time is not suitable (p mostly <0.6). Generic alert levels based on DAP (Gy cm²) were suggested for MSD of both 2 Gy and 5 Gy (for 5 Gy: TACE 750, PCI 250 and NE 400). The suggested levels are close to the lowest values published in several other studies. The uncertainty of the MSD was estimated to be around 10–15% and of hospital-specific skin dose alert levels about 20–30% (with coverage factor k = 1).ConclusionsThe generic alert levels are feasible for some cases but should be used with caution, only as the first approximation, while hospital-specific alert levels are preferred as the final approach.