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6 (A) The structure of the octahedral complex between Co 3+ -atom and EDTA. (B) Typical coordination of the central ion at various ratios between its radius and the radii of the surrounding electron donors. (Adapted from Pauling, L., 1970. General Chemistry. W.H. Freeman & Co., New York (Chapter 19).)
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This chapter describes the electrostatic interactions and its features induced by the protein globule and its aqueous environment. It discusses how to estimate the interaction of charges taking into account the interface between the protein and water. The value of permittivity Ɛ is determined by the atomic structure of the medium. If the medium con...
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... the field in A should be strengthened, because it goes from +q to A through a space with a lower (on average) permittivity than that of pure water. But in fact… Answer: Oddly, the field in A is reduced! Since the vacuum bubble is not polarized, and water is polarized, waters turn their "minuses" towards +q, and their "pluses" away from +q (see Fig. 6.1). As a result, a positive induced charge arises at that surface of the bubble which faces +q, and a negative induced charge arises on the opposite surface of the bubble facing the point A (the sum of these induced charges is zero, according to a theorem in electrostatics given, eg, in Landau et al., 1984). The induced "minus," which is ...
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... is the behaviour of the field of the charge positioned in water near the surface of a protein ( Fig. 6.1). Here, polarization of the protein (with ε % 3) can be neglected, to the first approximation, as compared with that of water (with ε % ...
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... resulting distribution of numerical values of ε eff "in and around the protein" for the field produced by the charge È and the induced polarized charges looks as shown in Fig. 6.2A if È is in water near the protein surface, and as in Fig. 6.2B if it is deep in the protein. Let me remind you that ε eff is the effective value of permittivity for the point r to be used in the formula φ(r) ¼ q 1 /[ε eff jr-r 1 j] to calculate the potential of the charge È located at r 1 ...
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... resulting distribution of numerical values of ε eff "in and around the protein" for the field produced by the charge È and the induced polarized charges looks as shown in Fig. 6.2A if È is in water near the protein surface, and as in Fig. 6.2B if it is deep in the protein. Let me remind you that ε eff is the effective value of permittivity for the point r to be used in the formula φ(r) ¼ q 1 /[ε eff jr-r 1 j] to calculate the potential of the charge È located at r 1 ...
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... both cases, with electrons shifted or molecules turned, polarization of the medium partially screens the immersed charges (È and ⊝, see Fig. 6.3A) and thereby diminishes the electric field in the medium compared with what it would have been in a ...
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... located between charges increases rather than decreases their interaction, and thus this central dipole does not increase the value of permittivity. The permittivity is increased not by the central but by other dipoles. Thus, we can conclude that the charges are quite well shielded by solute molecules coming from other sides and from the flanks (Fig. 6.3B): these molecules become polarized (in the case of water, they simply turn), so that their "+"s shift towards the charge ⊝, and their "À"s towards the charge ...
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... we see again (see also Fig. 6.2A and B) that the electrostatic interaction between the charges occurs mainly via the medium of a higher permittivity and nearly ignores the medium of weak ...
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... basis of these experiments is as follows. There are proteins (enzymes) that exhibit a particularly high activity at a certain value of pH (Nelson and Cox, 2012); they are said to have a pH-optimum. This pH-optimum can be shifted (Fig. 6.4) using a charged residue introduced to the protein by mutating its gene, and the electric field induced at the active site by the charge of the mutated residue can be estimated by the shift of the ...
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... for remote (and shaded by the protein body) ones. The fact that ε eff can reach a value of 100 appeared to be not a little surprising to those believing that ε eff must lie between 3 (as inside the protein) and, at the most, 80 (as in water). However, for us, these values are not surprising, since they are in good agreement with what follows from Fig. ...
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... So far, I have discussed only the interaction of separate charges. However, electrostatics also covers the interactions of dipoles (eg, the dipoles H (+) -O (À) and H (+) -N (À) involved in hydrogen bonding) as well as quadruples; the latter are present, for example, in aromatic rings (Fig. ...
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... coordinate bonding, the metal ion binds to several donors of electrons. Then a small (radius $0.7 A ˚ ) di-or trivalent ion is surrounded by large-atom donors (radius $1.5 A ˚ ). Mostly, there are six of these coordinating donor atoms located at the apices of a regular octahedron (Pauling, 1970) (Fig. ...
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... by several atoms of one molecule are called chelate (claw-shaped). The role of these bonds in proteins, specifically at their active sites, will be considered later on. Also, we will see later, that chelate complexes coating ions completely can be members of the hydrophobic protein core. At the moment I would like to draw your attention again to Fig. 6.6 presenting the widely used reagent EDTA (ethylenediaminetetraacetic acid) that participates in a chelate bond to the metal. For EDTA, this bond is particularly strong because the negatively charged COO À groups of EDTA are bound to the positively charged metal ...
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This chapter overviews the computational techniques and theoretical models used for exploring structure and dynamics of complex biomolecular systems at the atomistic level of detail. Particular focus is put on the application of statistical mechanics methods combined with the classical molecular mechanics approach to the description of phase transitions in polypetides and proteins. The molecular mechanics approach permits simulating a large variety of biomacromolecular systems (both in vacuum and in ubiquitous environments) and their transformations at different thermal and biologically relevant conditions as well as at various external stresses. This chapter presents several illustrative examples of such computational research related to protein folding, unbinding of protein-ligand complex, and DNA unzipping.
The associative phase separation of biomacromolecules can produce both liquid-like coacervates or solid-like precipitates. In this study, we found that sodium chloride (NaCl) can programme the phase transition of β-conglycinin/lysozyme (β-CG/LYS) complexes. NaCl reduced the ζ-potential of both β-CG and LYS. Their complex coacervate was formed at pHs 6 and 7 with 5–80 mM NaCl and at pH 8 with 40–80 mM NaCl. Unlike the high critical salt concentration and entropy gain driving force of polyelectrolyte-based complex coacervation, 100 mM NaCl almost completely inhibited β-CG/LYS complexation, and the exothermic enthalpy change was the main driving force for β-CG/LYS complex formation. Confocal laser scanning microscopy with fluorescein isothiocyanate-labeled proteins demonstrated dynamic protein exchange in coacervate droplets, similar to that in polyelectrolyte-based complex coacervates.
Two series of highly charged linear aliphatic polymers—sodium polystyrene-4-sulfonate and random copolymer of N-methyl-N-vinylacetamide and N-methyl-N-vinylamine hydrochloride—were studied in water solution without added salts and in solutions containing up to 5 M NaCl. Intrinsic viscosity in salt-free solutions was estimated by a method proposed earlier [Pavlov et al. Russ. J. Appl. Chem. 2006, 79, 1407–1412]. Molecular characteristics were obtained in 0.2 M NaCl. The polyelectrolytes were studied in more than 10-fold range of molar mass. Qualitatively, the conformational status of the polyelectrolyte chains in different ionic strength was defined with the Kuhn–Mark–Houwink–Sakurada plots normalized by the value of linear chain density. In salt-free solution both polyelectrolytes could be attributed to extra rigid chains with the statistical segment length of 650 nm for sodium polystyrene-4-sulfonate and 100 nm for copolymer chains. Such statistical segment lengths are provided by short-range electrostatic intrachain interactions and are comparable with the Debye screening length. At extremely high NaCl concentration polyelectrolyte chains became discriminated by their degree of hydrophobicity. Chains of hydrophobic nature are compacted up to preglobular state, whereas the chains of the hydrophilic nature stay in the conformation of swelling coils at the highest concentration of NaCl.
