Ligand-dependent reactivity of the CysB5[23] b sulfhydryl group of the major haemoglobin of chicken

Chicken haemoglobin contains eight reactive sulfhydryl groups per (tetramer) molecule, as determined by Boyer titration with p-chloromercury(II)benzoic acid. However, only four of these sulfhydryls are reactive towards 5,5@-dithiobis(2-nitrobenzoic acid) (DTNB). They are at the F9[93] and B5[23] positions of each of the two b subunits in the molecule. The time course of the DTNB reaction is biphasic. With oxyhaemoglobin, k the apparent second-order rate constant of the fast phase, increases app, monotonically with pH, the simple proÐle resembling the titration curve of a diprotic acid; the pH-dependence of k for the app slow phase is bowl-shaped. With carbonmonoxyhaemoglobin and aquomethaemoglobin, k for the fast phase is bowl-shaped app whilst k for the slow phase increases monotonically with pH. Quantitative analyses of the simple proÐles show that the app reactivity of the sulfhydryl group to which they may be attributed is subject to the inÑuence of two ionizable groups on the molecule, with mean pK values of 6.4^0.1 and ca. 8.4^0.3. These values are assigned to HisHC3[146]b and CysF9[93]b, a pKa respectively. Quantitative analyses of the bowl-shaped proÐles show that the reactivity of the sulfhydryl group to which they may be attributed is subject to the inÑuence of two ionizable groups on the protein, with mean pK of 6.85^0.05 and 8.3^0.2. as These values are assigned to HisG19[117]b and CysB5[23]b, respectively. It is highly signiÐcant that the CysB5[23]b sulfhydryl groups of carbonmonoxy- and aquomet-haemoglobin react ca. 100 times faster than that of oxyhaemoglobin. By contrast, the di†erence in the reactivities of the CysF9[93]b sulfhydryls of the three haemoglobin derivatives is no more than four-fold. This indicates that, in chicken haemoglobin, changes in the haem ligand give rise to structural changes in the neighbourhood of the CysB5[23]b sulfhydryl which are far more signiÐcant than those in the neighbourhood of the CysF9[93]b sulfhydryl

Unsaturated Ligands Seed an Order to Disorder Transition in Mixed Ligand Shells of CdSe/CdS Quantum Dots.

A phase transition within the ligand shell of core/shell quantum dots is studied in the prototypical system of colloidal CdSe/CdS quantum dots with a ligand shell composed of bound oleate (OA) and octadecylphosphonate (ODPA). The ligand shell composition is tuned using a ligand exchange procedure and quantified through proton NMR spectroscopy. Temperature-dependent photoluminescence spectroscopy reveals a signature of a phase transition within the organic ligand shell. Surprisingly, the ligand order to disorder phase transition triggers an abrupt increase in the photoluminescence quantum yield (PLQY) and full-width at half-maximum (FWHM) with increasing temperature. The temperature and width of the phase transition show a clear dependence on ligand shell composition, such that QDs with higher ODPA fractions have sharper phase transitions that occur at higher temperatures. In order to gain a molecular understanding of the changes in ligand ordering, Fourier transform infrared and vibrational sum frequency generation spectroscopies are performed. These measurements confirm that an order/disorder transition in the ligand shell tracks with the photoluminescence changes that accompany the ligand phase transition. The phase transition is simulated through a lattice model that suggests that the ligand shell is well-mixed and does not have completely segregated domains of OA and ODPA. Furthermore, we show that the unsaturated chains of OA seed disorder within the ligand shell

Influence of ligand shape and steric hindrance on the composition of the nanocrystal ligand shell

Organic ligands play a key role in the synthesis of colloidal semiconductor nanocrystals or quantum dots. Generally they consist of a functional group and an aliphatic chain, with carboxylic acids, thiols and phosphonic acids as typical examples. The functional group ensures the binding to the nanocrystal surface, while the stability of the dispersion strongly depends on the interactions between the organic chains of the adjacent ligands. A number of studies already addressed the binding strength and the type of binding between the nanocrystal surface and the ligand yet none discuss the effect of the organic chain on the ligand exchange. By means of NMR spectroscopy, we examine the ligand shell composition of CdSe nanocrystals originally capped with oleic acid (OA), when exposed to a linear carboxylic acid. Regardless of chain length, we see a one-to-one exchange between the carboxylic acids. The composition of the ligand shell closely matches that of the ligand mixture in solution, indicating that the ligand shell can be seen as an ideal mixture of both ligands. As a consequence, a mixed ligand shell can easily be prepared by adding a ligand mixture with desired composition to the nanocrystal dispersion. On the other hand, when the CdSe nanocrystals are exposed to a branched carboxylic acid with two long aliphatic chains, like 2-hexyldecanoic acid, the ligand shell mainly consists of OA moieties. We interpret these results using an exchange process where the incoming ligand not only displaces oleic acid but also occupies additional space in the ligand shell to accommodate both aliphatic chains. Hence, given a one-for-one exchange reaction, steric hindrance in a fully packed ligand shell will prevent complete ligand exchange. These results can be very useful in view of producing nanocrystals with lower ligand densities by means of synthesis with these branched carboxylic acids

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selectivity and affinity of one of these riboswitches, extensive all-atom molecular dynamics simulations in explicit solvent ({approx}1 µs total simulation length) of the aptamer domain of the guanine sensing riboswitch are performed. The conformational dynamics is studied when the system is bound to its cognate ligand guanine as well as bound to the non-cognate ligand adenine and in its free form. The simulations indicate that residue U51 in the aptamer domain functions as a general docking platform for purine bases, whereas the interactions between C74 and the ligand are crucial for ligand selectivity. These findings either suggest a two-step ligand recognition process, including a general purine binding step and a subsequent selection of the cognate ligand, or hint at different initial interactions of cognate and noncognate ligands with residues of the ligand binding pocket. To explore possible pathways of complex dissociation, various nonequilibrium simulations are performed which account for the first steps of ligand unbinding. The results delineate the minimal set of conformational changes needed for ligand release, suggest two possible pathways for the dissociation reaction, and underline the importance of long-range tertiary contacts for locking the ligand in the complex

Amine, Amido, and Imido Complexes of Tantalum Supported by a Pyridine-Linked Bis(phenolate) Pincer Ligand: Ta−N π-Bonding Influences Pincer Ligand Geometry

A series of tantalum imido and amido complexes supported by a pyridine-linked bis(phenolate) ligand has been synthesized. Characterization of these complexes via X-ray crystallography reveals both C_s and C_2 binding modes of the bis(phenolate)pyridine ligand, with complexes containing two or fewer strong π-donor interactions from ancillary ligands giving C_s symmetry, whereas three strong π-donor interactions (e.g., three amido ligands or one amido ligand and one imido ligand) give C_2-symmetric binding of the bis(phenolate)pyridine ligand. DFT calculations and molecular orbital analyses of the complexes have revealed that the preference for C_s-symmetric ligand binding is a result of tantalum−phenolate π-bonding, whereas in cases where tantalum−phenolate π-bonding is overridden by stronger Ta−N π-bonding, C_2-symmetric ligand binding is preferred, likely because conformationally this is the lowest-energy arrangement. This electronically driven change in geometry indicates that, unlike analogous metallocene systems, the bis(phenolate)pyridine pincer ligand is not a strong enough π-donor to exert dominant control over the electronic and geometric properties of the complex

Increased accuracy of ligand sensing by receptor internalization

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.Comment: 9 pages, 4 figures, accepted for publication in Physical Review

Morphology of passivating organic ligands around a nanocrystal

Semiconductor nanocrystals are a promising class of materials for a variety of novel optoelectronic devices, since many of their properties, such as the electronic gap and conductivity, can be controlled. Much of this control is achieved via the organic ligand shell, through control of the size of the nanocrystal and the distance to other objects. We here simulate ligand-coated CdSe nanocrystals using atomistic molecular dynamics, allowing for the resolution of novel structural details about the ligand shell. We show that the ligands on the surface can lie flat to form a highly anisotropic 'wet hair' layer as opposed to the 'spiky ball' appearance typically considered. We discuss how this can give rise to a dot-to-dot packing distance of one ligand length since the thickness of the ligand shell is reduced to approximately one-half of the ligand length for the system sizes considered here; these distances imply that energy and charge transfer rates between dots and nearby objects will be enhanced due to the thinner than expected ligand shell. Our model predicts a non-linear scaling of ligand shell thickness as the ligands transition from 'spiky' to 'wet hair'. We verify this scaling using TEM on a PbS nanoarray, confirming that this theory gives a qualitatively correct picture of the ligand shell thickness of colloidal quantum dots.Comment: 17 Pages, 9 Figure

Seven coordinate molybdenum and tungsten complexes containing Tpm and Tpm derivatives and the impact of ligand substitution on NMR chemical shifts

A series of known and new seven coordinate molybdenum and tungsten complexes of tris(pyrazolyl)methane (Tpm) and substituted Tpm, [TpmM(CO)3X]+, have been synthesized. Depending on the identity of X, (bromo, iodo, hydrido) and the substitution of the Tpm ligand, substantial chemical shift differences are observed for the hydrogen on the central carbon of the Tpm ligand. Factors impacting the chemical shift of the hydrogen on the central carbon of the Tpm ligand, such as the electron donating ability of the Tpm ligand and the electronegativity of the additional ligand on the metal, will be discussed

Dewetting-controlled binding of ligands to hydrophobic pockets

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semi-quantitatively