Molecular Mechanics Calculations of Proteins. Comparison of Different Energy Minimization Strategies

Abstract

A general strategy for performing energy minimization of proteins using the SYBYL molecular modelling program has been developed. The influence of several variables including energy minimization procedure, solvation, dielectric function and dielectric constant have been investigated in order to develop a general method, which is capable of producing high quality protein structures. Avian pancreatic polypeptide (APP) and bovine pancreatic phospholipase A2 (BP PLA2) were selected for the calculations, because high quality X-ray structures exist and because all classes of secondary structure are represented in the structures. The energy minimized structures were evaluated relative to the corresponding X-ray structures. The overall similarity was checked by calculating RMS distances for all atom positions. Backbone conformation was checked by Ramachandran plots and secondary structure elements evaluated by the length on hydrogen bonds. The dimensions of active site in BP PLA2 is very dependent on electrostatic interactions, due to the presence of the positively charged calcium ion. Thus, the distances between calcium and the calcium-coordinating groups were used as a quality index for this protein. Energy minimized structures of the trimeric PLA2 from Indian cobra (N.n.n. PLA2) were used for assessing the impact of protein-protein interactions. Based on the above mentioned criteria, it could be concluded that using the following conditions: Dielectric constant ? = 4 or 20; a distance dependent dielectric function and stepwise energy minimization, it is possible to reproduce X-ray structures very accurately without including explicit solvent molecules.     

A Structural View on the Functional Importance of the Sugar Moiety and Steroid Hydroxyls of Cardiotonic Steroids in Binding to Na,K-ATPase

The Na,K-ATPase is specifically inhibited by cardiotonic steroids (CTSs) like digoxin and is of significant therapeutic value in the treatment of congestive heart failure and arrhythmia. Recently, new interest has arisen in developing Na,K-ATPase inhibitors as anticancer agents. In the present study, we compare the potency and rate of inhibition as well as the reactivation of enzyme activity following inhibition by various cardiac glycosides and their aglycones at different pH values using shark Na,K-ATPase stabilized in the E2MgP_i or in the E2BeF_x conformations. The effects of the number and nature of various sugar residues as well as changes in the positions of hydroxyl groups on the β-side of the steroid core of cardiotonic steroids were investigated by comparing various cardiac glycoside compounds like ouabain, digoxin, digitoxin, and gitoxin with their aglycones. The results confirm our previous hypothesis that CTS binds primarily to the E2-P ground state through an extracellular access channel and that binding of extracellular Na⁺ ions to K⁺ binding sites relieved the CTS inhibition. This reactivation depended on the presence or absence of the sugar moiety on the CTS, and a single sugar is enough to impede reactivation. Finally, increasing the number of hydroxyl groups of the steroid was sterically unfavorable and was found to decrease the inhibitory potency and to confer high pH sensitivity, depending on their position on the steroid β-face. The results are discussed with reference to the recent crystal structures of Na,K-ATPase in the unbound and ouabain-bound states.     

Climate‐induced changes in the distribution of freshwater fish: observed and predicted trends

1. Climate change could be one of the main threats faced by aquatic ecosystems and freshwater biodiversity. Improved understanding, monitoring and forecasting of its effects are thus crucial for researchers, policy makers and biodiversity managers. 2. Here, we provide a review and some meta‐analyses of the literature reporting both observed and predicted climate‐induced effects on the distribution of freshwater fish. After reviewing three decades of research, we summarise how methods in assessing the effects of climate change have evolved, and whether current knowledge is geographically or taxonomically biased. We conducted multispecies qualitative and quantitative analyses to find out whether the observed responses of freshwater fish to recent changes in climate are consistent with those predicted under future climate scenarios. 3. We highlight the fact that, in recent years, freshwater fish distributions have already been affected by contemporary climate change in ways consistent with anticipated responses under future climate change scenarios: the range of most cold‐water species could be reduced or shift to higher altitude or latitude, whereas that of cool‐ and warm‐water species could expand or contract. 4. Most evidence about the effects of climate change is underpinned by the large number of studies devoted to cold‐water fish species (mainly salmonids). Our knowledge is still incomplete, however, particularly due to taxonomic and geographic biases. 5. Observed and expected responses are well correlated among families, suggesting that model predictions are supported by empirical evidence. The observed effects are of greater magnitude and show higher variability than the predicted effects, however, indicating that other drivers of changes may be interacting with climate and seriously affecting freshwater fish. 6. Finally, we suggest avenues of research required to address current gaps in what we know about the climate‐induced effects on freshwater fish distribution, including (i) the need for more long‐term data analyses, (ii) the assessment of climate‐induced effects at higher levels of organisation (e.g. assemblages), (iii) methodological improvements (e.g. accounting for uncertainty among projections and species’ dispersal abilities, combining both distributional and empirical approaches and including multiple non‐climatic stressors) and (iv) systematic confrontation of observed versus predicted effects across multi‐species assemblages and at several levels of biological organisation (i.e. populations and assemblages).     

Real-time metabolomic analysis of lactic acid bacteria as monitored by in vitro NMR and chemometrics

Introduction

Lactic acid bacteria (LAB) play an important role in the food industry as starter cultures to manufacture fermented food, and as probiotics. In recent years, there has been an increasing interest in using LAB cultures for biopreservation of food products. It is therefore of great interest to study the detailed metabolism of these bacteria.

Objectives

This study aimed at developing an efficient analytical protocol for real-time in vitro NMR measurements of LAB fermentations, from sample preparation, over data acquisition and preprocessing, to the extraction of the kinetic metabolic profiles.

Method

The developed analytical protocol is applied to an experimental design with two LAB strains (Lactobacillus rhamnosus DSM 20021 and Lactobacillus plantarum subsp. plantarum DSM 20174), two initial pH levels (pH_i 6.5 and 5.5), two levels of glucose concentration (2.5 and 0.25 g/l), and two batch fermentation replicates.

Results

The design factors proved to be strongly significant and led to interesting biological information. The protocol allowed for detailed real-time kinetic analysis of 11 major metabolites involved in the glycolysis, pyruvate catabolism, amino acid catabolism and cell energy metabolism. New biological knowledge was obtained about the different patterns of glutamine and aspartic acid consumption by the two strains. It was observed that L. plantarum consumes more glutamine at low pH (pH 5.5) whereas the opposite applies to L. rhamnosus. Regarding aspartic acid, both of the strains consume it higher at low pH, and overall L. plantarum consumes it more. L. rhamnosus did not consume aspartic acid at pH 6.5.

Conclusion

The developed analytical protocol for real-time in vitro NMR measurements of bacterial metabolism allows a relatively easy investigation of different fermentation factors such as new strains, new substrates, cohabitations, temperature, and pH and has a great potential in biopreservation studies to discover new efficient bioprotective cultures.

     

Biological oxidation of metallic copper by Acidithiobacillus ferrooxidans

This is a report on the kinetic aspects and the analytical study of the bioproducts of the oxidation of zero-valence copper by immobilized Acidithiobacillus ferrooxidans. Two different mechanisms of oxidation were considered: direct and indirect. A custom-built bioreactor was used to grow A. ferrooxidans in an iron-free media, which was required for the study of the direct mechanism. X-ray microdiffraction analysis of the copper after biooxidation in the sulfate-free medium revealed the presence of the copper sulfate, piypite, K(2)Cu(2)O(SO(4))(2), which indicates biooxidation of Cu metal has occurred. It was shown that the direct oxidation exists, but it is relatively slow, as compared to the indirect mechanism.