Multiple-site Model Research Articles

Exploring cavities in Type II porous liquids with xenon

The porous topology of Type II Porous Liquids (PLs), prepared using Noria-OEt as an empty molecular host dissolved in 15-crown-5 solvent, is investigated with 129Xe NMR Spectroscopy. Xenon NMR parameters, such as chemical shifts and T1 relaxation times, measured in PLs solutions prepared at various Noria-OEt concentrations, are related to the intrinsic microporous structure of the material. The experimental data are interpreted on the basis of a multiple-site model for xenon atoms within the multiple PLs cavities. Diffusion NMR experiments show a similar mobility of xenon in PLs compared with the pure solvent.

Mutation frequencies in a birth–death branching process

First, we revisit the stochastic Luria–Delbruck model: a classic two-type branching process which describes cell proliferation and mutation. We prove limit theorems and exact results for the mutation times, clone sizes and number of mutants. Second, we extend the framework to consider mutations at multiple sites along the genome. The number of mutants in the two-type model characterises the mean site frequency spectrum in the multiple-site model. Our predictions are consistent with previously published cancer genomic data.

Transient Protein-Protein Interaction of the SH3-Peptide Complex via Closely Located Multiple Binding Sites

Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes.

Non-linear adsorption modeling of fatty esters and oleic estolide esters via boundary lubrication coefficient of friction measurements

The frictional behaviors of a variety of fatty esters (methyl oleate (MO), methyl palmitate (MP), methyl laurate (ML), and 2-ethylhexyl oleate (EHO)) and oleic estolide esters (methyl oleic estolide ester (ME) and 2-ethylhexyl oleic estolide ester (EHE)) as additives in hexadecane have been examined in a boundary lubrication test regime using steel contacts. Critical additive concentrations were defined and used to perform novel and simple Langmuir analyses that provide an order of adsorption energies: EHE ≥ ME > EHO > MP > MO ≥ ML. Application of Langmuir, Temkin, and Frumkin–Fowler–Guggenheim (FFG) adsorption models via non-linear fitting demonstrates the necessary inclusion of cooperative effects in the applied model. Fits of the steady-state coefficient of friction (COF)-concentration data for EHE, ME, and EHO indicate slight cooperative adsorption. MO, MP, and ML data require larger attractive interaction terms ( α ≤ −2.3) to be adequately fit. Primary adsorption energies calculated via a general adsorption model are necessarily decreased while total adsorption energies correlate well with values obtained via critical concentration analyses. To account for multiple surface-site coverage a multiple-site model was defined. The intuitive assumption of multiple-site coverage of more massive components suggests deceptively increased calculated adsorption energies for typically applied models (e.g. FFG, Langmuir).

Structural study of hexanethiolate on Au(1 1 1) in the ‘striped’ phase

We have studied the structure of the ‘striped’ (flat-lying) phase of hexanethiolate on Au(1 1 1) by using X-ray photoelectron spectroscopy, near edge X-ray absorption fine structure and scanned-energy photoelectron diffraction. Combined results of these techniques indicate that gaseous hexanethiol adsorbs as hexanethiolate in the ‘striped’ phase with the alkyl chain lying down onto the surface and the S head group occupying an atop site. The S–Au distance was determined to be 2.40 ± 0.05 Å. The present experiments clearly exclude both the multiple-site model and the dimer model.

Predicting Multicomponent Transport of Cations in Natural Porous Media

Competitive sorption and transport of cations plays a key role in soil fertility, contaminant displacement, and colloid mobilization in soils and sediments. Understanding the movement of cations in heterogeneous, natural porous media is, therefore, of great importance. Typically, many different cations are present in such systems and they compete with each other for binding sites. Competitive cation binding can lead to quite complex transport phenomena in such multicomponent systems. Our objective was to investigate the competitive binding of three major cations (Ca 2+, Mg 2+, and Na +) in a natural soil material and to predict multicomponent transport from competitive binary and ternary adsorption isotherms. Various single-site and multiple-site models based on competitive Langmuir or cation exchange equations were tested.

VALUING CAMPSITE CHARACTERISTICS: A GENERALIZED TRAVEL-COST MODEL OF DEMAND FOR RECREATIONAL CAMPING

The multiple-site travel cost demand model of Vaughan and Russell is extended to apply to recreational camping. Unlike previous applications, particular attention is paid to the detection and correction of groupwise heteroscedasticity which is likely to arise in multiple-site models. A semi-log demand model estimated in the context of 48 provincial parks in the Province of Onario, Canada, suggests that recreational camping is likely to be an inferior commodity. Also, the consistent significance of the substitute-site variable implies that the demand parameter estimates are likely to be biased in its absence. The model is also used to obtain estimates of the social values of various campsite characteristics in terms of average and marginal consumer surplus. © 1997 John Wiley & Sons, Ltd.

Reactivity of Chromium Oxide in Aqueous Solutions. 2. Acid Dissolution

The influence of the type and the concentration of several mineral acids (HNO 3 , H 2 SO 4 , and HCI) on the dissolution of two different chromium (hydrous) oxides was investigated at 25 and 65 °C. The results were interpreted using a combined approach that takes into account the electrochemical nature of the process, the surface complexation, and multiple-site models for the dissolution of very passive covalent oxides. The attack by protons on oxo bonds is the critical step that strongly enhances the rate of the process at higher acidities. The reactivity of chromium (hydrous) oxides is shown to be related to the degree of cross-linking and not to the water contents.

The nuclear magnetic resonance of 129Xe trapped in clathrates and some other solids

129 Xe NMR spectra were obtained for xenon trapped in the cages of clathrate hydrates and a clathrasil sample. The data, together with shift data for solid xenon, have yielded a linear correlation between the radius of the free space available to the xenon atom and the chemical shift. This observation cannot be rationalized by using simple binary collision theory. In order to account for the observation of anisotropic chemical shifts for xenon trapped in non-spherical environments a simple multiple-site model was developed. Several applications of 129Xe NMR spectroscopy are also presented. These include the identification of new clathrate hydrates, the use of 129Xe NMR to follow changes in site symmetry in a clathrasil and a cyclodextrin inclusion compound, and the observation of trapping sites in crystalline and amorphous solids.

Interactions of inhibitors of the lipoxygenase and cyclooxygenase pathways with a supplementary binding site on soybean lipoxygenase.

The oxygenation of [1-14C]-arachidonic acid by a soluble soybean lipoxygenase (E.C.1.13.11.12) preparation was determined in the presence of various cyclo-oxygenase and lipoxygenase inhibitors. The results showed that several non-inhibitory compounds drastically blunted the inhibitory potency of potent lipoxygenase inhibitors. Studies on the combined effects of a variety of structurally unrelated inhibitors of lipoxygenase, cyclo-oxygenase or both oxygenation pathways provided strong evidence for the existence of a supplementary binding site on soybean lipoxygenase which reduces the effective interactions of inhibitors with the catalytic site. Thus several cyclo-oxygenase inhibitors (which do not inhibit at the lipoxygenase catalytic site), as well as low concentrations of lipoxygenase inhibitors, interact with this putative supplementary site and blunt the inhibitory efficacy of potent lipoxygenase inhibitors. Although the degree of interaction with the catalytic site determines the absolute potency of inhibitors, the additional interaction at the putative supplementary binding site is also obligatory for inhibitory potency. In this new multiple-site model the potent lipoxygenase inhibitors (e.g. acetone phenylhydrazone, phenidone) possess high affinities for both sites, whereas weak inhibitors and certain cyclo-oxygenase inhibitors (e.g. benoxaprofen, phenylbutazone, indomethacin) interact predominantly with the supplementary site on the lipoxygenase but lack affinity for the catalytic site.