34 research outputs found

    Interactions of water and calcium ions with food components, studied by NMR

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    NMR studies of water oxygen-17 relaxation in aqueous sucrose and lysozyme solutions have been carried out to investigate the interactions of water with sucrose and lysozyme. The effect of sucrose and lysozyme concentration on water oxygen-17 relaxation has been studied in detail. The dependence of relaxation on frequency and pH has also been analysed. The existing model, describing the relaxation of water oxygen-17 in aqueous protein solutions suggested by Halle in 1981, is tested to see whether it gives a true representation. It is found that at low concentrations of sucrose and lysozyme, the experimental data give good agreement with the model. However, at saturated sucrose concentration the agreement is not so good. An extra contribution to the transverse relaxation rate is seen. A possible explanation for the extra contribution to the transverse relaxation rate at high sucrose content is discussed. The effect of ionic charge on oxygen-17 relaxation in lysozyme solutions is also investigated. It is observed that both the ionic charge of lysozyme as well as lysozyme aggregation strongly affect the relaxation of water oxygen-17. A method for analysing the experimental data for water oxygen-17 relaxation in aqueous sucrose and lysozyme solutions using Halle's model is presented and employed to calculate the various parameters of the model. The relaxation and chemical shift of calcium-43 in simple calcium salts, calcium acetate and calcium ascorbate have been studied as a function of concentration and pH. The complexation of calcium to sucrose and to lysozyme has also been investigated. In almost all cases, a significant calcium-43 chemical shift has been detected. The direct measurement of complexation and binding of calcium by relaxation time and chemical shift measurements has been of particular interest

    Isolation of rotational isomers and developments derived therefrom

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    Isolation of rotational isomer models of ethane-type molecules is described. We could experimentally prove that, if rotational isomers whose molecular shape was chiral, the molecule could be optically active, even though it did not carry an asymmetric carbon atom. As an extension, other types of stereochemically fundamental and optically active molecules were isolated and their absolute stereochemistry was determined. One example is the model of meso-tartaric acid, for which optical inactivity had been attributed to internal compensation but is now explained as follows. On dissolution of meso-tartaric acid in a solvent, the molecule gives two kinds of conformers, one of which is a Ci molecule and the other is a C1 molecule. Although the latter is intrinsically optically active, the optical activity is cancelled by its enantiomer. The theory of internal compensation is recommended to be abandoned. As an extension to another area, some reactions of conformers are also discussed

    3D-Structural Homology Detection via Unassigned Residual Dipolar Couplings

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    Recognition of a protein\u27s fold provides valuable information about its function. While many sequence-based homology prediction methods exist, an important challenge remains: two highly dissimilar sequences can have similar folds --- how can we detect this rapidly, in the context of structural genomics? High-throughput NMR experiments, coupled with novel algorithms for data analysis, can address this challenge. We report an automated procedure for detecting 3D-structural homologies from sparse, unassigned protein NMR data. Our method identifies the 3D-structural models in a protein structural database whose geometries best fit the unassigned experimental NMR data. It does not use sequence information and is thus not limited by sequence homology. The method can also be used to confirm or refute structural predictions made by other techniques such as protein threading or sequence homology. The algorithm runs in O(pnk3) time, where p is the number of proteins in the database, n is the number of residues in the target protein, and k is the resolution of a rotation search. The method requires only uniform 15N-labelling of the protein and processes unassigned 1H-15N residual dipolar couplings, which can be acquired in a couple of hours. Our experiments on NMR data from 5 different proteins demonstrate that the method identifies closely related protein folds, despite low-sequence homology between the target protein and the computed model

    The aqueous environment as an active participant in the protein folding process

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    Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. This work focuses on the following sample proteins: Engrailed homeodomain (RCSB: 1 enh), Chicken villin subdomain hp-35, n68h (RCSB: 1yrf), Chicken villin sub-domain hp-35, k65(nle), n68h, k70(nle) (RCSB: 2f4k), Thermostable subdomain from chicken villin headpiece (RCSB: 1vii), de novo designed single chain three-helix bundle (a3d) (RCSB: 2a3d), albumin-binding domain (RCSB: 1prb) and lambda repressor-operator complex (RCSB: 1lmb). (C) 2018 The Authors. Published by Elsevier Inc

    Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

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    Equation of motion coupled-cluster singles and doubles (EOM-CCSD) is one of the most accurate computational methods for the description of one-electron vertical transitions. However, its O(N6) scaling, where N is the number of basis functions, often makes the study of molecules larger than 10–15 heavy atoms prohibitive. In this work we investigate how accurately less expensive methods can approximate the EOM-CCSD results. We focus on our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid scheme, where the system is partitioned into regions which are treated with different levels of theory. For our set of benchmark calculations, the comparison of conventional configuration interaction singles (CIS), time-dependent Hartree–Fock (TDHF), and time-dependent density functional theory (TDDFT) methods and ONIOM (with different low level methods) showed that the best accuracy-computational time combination is obtained with ONIOM(EOM:TDDFT), which has a rms of the error with respect to the conventional EOM-CCSD of 0.06 eV, compared with 0.47 eV of the conventional TDDFT

    Op soek na ’n gebalanseerde beeld van H.F. Verwoerd

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    Towards a balanced view of H.F. Verwoerd. Doctor H.F. Verwoerd is possibly the most controversial political figure in South African history. In life he was revered by his followers, but even critics acknowledged his stature. Today he is mostly depicted as a brutal symbol of racial suppression. This article first gives insight into various, contradictory views expressed in the press on Verwoerd during his life, immediately after his death and in recent years. This is discussed in view of some media-theoretical perspectives. It is followed by an overview of views expressed on Verwoerd in literature, including recent works by eminent historian Hermann Giliomee. Against this background of diverse and sometimes one-sided views, J.J. (Ponti) Venter’s analysis of Verwoerdian thought, as published in a 1999 issue of Koers – Bulletin for Christian Scholarship, is presented as an example of a balanced intellectual contribution to an ongoing debate. It is argued that Venter’s contribution was important as it provides incisive criticism of Verwoerd not found elsewhere. Venter’s article, which was based on texts of speeches, however lacks some context. This is provided by other publications and press coverage. It is suggested that no assessment of an important historical figure is ever definitive, least so by consulting only the press. As is the case with Verwoerd, contemporaneous press coverage needs to be supplemented by solid research on the subject. In particular the sober analysis of public intellectuals such as J.J. Venter is needed and should be included in assesments of Verwoerd

    The aqueous environment as an active participant in the protein folding process

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    © 2018 The Authors Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. This work focuses on the following sample proteins: Engrailed homeodomain (RCSB: 1enh), Chicken villin subdomain hp-35, n68h (RCSB: 1yrf), Chicken villin subdomain hp-35, k65(nle), n68h, k70(nle) (RCSB: 2f4k), Thermostable subdomain from chicken villin headpiece (RCSB: 1vii), de novo designed single chain three-helix bundle (a3d) (RCSB: 2a3d), albumin-binding domain (RCSB: 1prb) and lambda repressor-operator complex (RCSB: 1lmb)
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