The Development and Assessment of Computational Approaches to the Thermodynamics and Kinetics of Binding

Molecular recognition refers to the interaction between two or more molecules through complementary noncovalent bonding, for example, via hydrogen bonding, electrostatic interactions, van der Waals forces or hydrophobic forces. Molecular recognition plays an important role in biology and mediates interactions between receptors and ligands, antigens and antibodies, nucleic acids and proteins, proteins and proteins, enzymes and substrates, and nucleic acids with each other. Many cellular processes are governed by a group of proteins acting in a coordinated manner; such complicated mechanisms are closely regulated: changes in the populations of particular complexes or changes in concentrations of the products of protein mediated reactions can switch cells from one state to another (from replication to apoptosis, for example). These small variations in molecular populations are caused by very delicate differences in the thermodynamics or kinetics of reactions. This implies that in order to understand not only biological systems in terms of their molecular components, but also to be able to predict and model system response to stimuli (whether it is a natural substrate or a drug), characterisation of the thermodynamic and kinetic components of the binding process is of paramount importance. This combined computational-experimental project was focused on the development of new computational approaches able to predict the enthalpic component of ligand binding, using quantum mechanics. A concept of ‘theoceptors’ was developed, which are theoretical receptors constructed by computing the optimal geometry of ligands binding in the receptor. This project was supported by AstraZeneca, and it included an industrial placement in the Structural and Biophysical Sciences area, where the experimental data was generated to characterise the thermodynamics and kinetics of binding of a range of ligands to two biological targets, using two experimental techniques, isothermal titration calorimetry and surface plasmon resonance. The findings contribute greatly to the process currently underway of expanding our understanding of the relevance of both of these aspects of biochemistry to drug discovery

Carbon Tetrachloride as Thermoporometry Liquid-probe to Study the Cross linking of Styrene Copolymer Networks

Mesh Size Distributions (MSDs) of swollen cross linked styrene copolymer networks have been measured by thermoporometry using CCl4 as a probe liquid. All numerical relationships required for the calculation of the MSD were established for both the liquid-to-solid and the solid-to-solid thermal transitions of CCl4 and successfully validated on test samples. It was found that the polymer network, for both thermally and photo-cross linked materials, was completely built in about four hours of exposure. A clear correlation was established between the average mesh size of the swollen polymer network on the one hand and the benzoyl peroxide groups content and swelling ratio on the other hand

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims: Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods: We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results: Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86yr−1 for Fagus sylvatica and 0.88yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30% higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions: We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reportin

Plasma proteome of brain-dead organ donors predicts heart transplant outcome

Publisher Copyright: © 2021 The AuthorsBackground: The pathophysiological changes related to brain death may affect the quality of the transplanted organs and expose the recipients to risks. We probed systemic changes reflected in donor plasma proteome and investigated their relationship to heart transplant outcomes. Methods: Plasma samples from brain-dead multi-organ donors were analyzed by label-free protein quantification using high-definition mass spectrometry. Unsupervised and supervised statistical models were used to determine proteome differences between brain-dead donors and healthy controls. Proteome variation and the corresponding biological pathways were analyzed and correlated with transplant outcomes. Results: Statistical models revealed that donors had a unique but heterogeneous plasma proteome with 237 of 463 proteins being changed compared to controls. Pathway analysis showed that coagulation, gluconeogenesis, and glycolysis pathways were upregulated in donors, while complement, LXR/RXR activation, and production of nitric oxide and reactive oxygen species in macrophages pathways were downregulated. In point-biserial correlation analysis, lysine-specific demethylase 3A was moderately correlated with any grade and severe PGD. In univariate and multivariate Cox regression analyses myosin Va and proteasome activator complex subunit 2 were significantly associated with the development of acute rejections with hemodynamic compromise within 30 days. Finally, we found that elevated levels of lysine-specific demethylase 3A and moesin were identified as predictors for graft-related 1-year mortality in univariate analysis. Conclusions: We show that brain death significantly changed plasma proteome signature Donor plasma protein changes related to endothelial cell and cardiomyocyte function, inflammation, and vascular growth and arteriogenesis could predict transplant outcome suggesting a role in donor evaluation.Peer reviewe

Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs.

We have applied the two most commonly used methods for automatic matched pair identification, obtained the optimum settings, and discovered that the two methods are synergistic. A turbocharging approach to matched pair analysis is advocated in which a first round (a conservative categorical approach that uses an analogy with coin flips, heads corresponding to an increase in a measured property, tails to a decrease, and a biased coin to a structural change that reliably causes a change in that property) provides the settings for a second round (which uses the magnitude of the change in properties). Increased chemical specificity allows reliable knowledge to be extracted from smaller sets of pairs, and an assay-specific upper limit can be placed on the number of pairs required before adequate sampling of variability has been achieved

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86 yr−1 for Fagus sylvatica and 0.88 yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11 yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30 % higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reporting

Acceptability of Dry-Cured Belly (Pancetta) from Entire Males, Immunocastrates or Surgical Castrates: Study with Slovenian Consumers

Abandoning of male piglets castration in the European Union is a challenge for the pork production sector in particular for high-quality dry-cured traditional products. The information on consumer acceptability of dry-cured products from alternatives is limited, so the objective was to test the consumer acceptability of unsmoked traditional dry-cured belly (Kraška panceta) processed from three sex categories, i.e., surgical castrates (SC), entire males (EM) and immunocastrates (IC). Consumers (n = 331) were asked to taste dry-cured bellies from EM, IC and SC and to score the taste appreciation on a 9 cm unstructured scale. After tasting the pancetta of three sex categories, the consumers attributed the lowest acceptability scores to SC, whereas IC and EM received similar scores. Only about a quarter of consumers attributed the lowest score to EM, mainly when boar taint compounds were present. The results of this study indicate that a certain share of consumers was sensitive to taste deficiencies and that the leanness of this product is very important for consumersinfo:eu-repo/semantics/publishedVersio

Investigating tree foliar preference by the earthworms Aporrectodea longa and Allolobophora chlorotica in reclaimed and loam soil

Afforestation can improve the delivery of ecosystem services from reclaimed landfill sites. Tree health is a key determinant of ecosystem service delivery, and is directly impacted by soil quality; which is driven by biological processes in the soil, reliant on leaf litter inputs to function. Different tree species have different litter quality, affecting the degree to which they support biological processes in soils and the development of abundant and diverse soil faunal communities. In recognition of their key role in improving soil structure and fertility - key attributes of soil quality, earthworms have often been the subject of research as a part of land reclamation, and these organisms have displayed preferences for specific types of leaf litter. This work utilised a choice chamber design to measure the foliar material palatability of two tree species used in land restoration (Alnus cordata and Acer platanoides) as a food source for two common European earthworm species (Aporrectodea longa and Allolobophora chlorotica), and the effect of a reclaimed soil quality on earthworm growth, survival and feeding preferences. The research revealed that both earthworm species initially preferred the foliar material of A. cordata over A. platanoides, with the leaves of the latter requiring higher degradation to become palatable to earthworms. The consumption of fresh leaves showed these are a suitable food source for earthworms in choice chamber experiments, which historically have instead relied on senescent leaf litter. Finally, high survival rates of both A. longa and A. chlorotica in the reclaimed soil treatment, in addition to consumption of leaf material of two tree species now widely used on reclaimed landfill sites, demonstrated that these earthworm species are suitable candidates for inoculation to reclaimed land