Deuterium isotope effects on noncovalent interactions between molecules

The topic of deuterium isotope effects is usually concerned with the effects on chemical reactions that are caused by the substitution of deuterium atoms for protium, or hydrogen, atoms in a molecule. These effects include changes in the rate of cleavage of covalent bonds to deuterium, or to an atom located adjacent to deuterium, in a reactant molecule. Deuterium isotope effects on other, noncovalent, interactions between molecules are known to occur, but they are generally considered to be insignificant, especially in biological experiments where deuterium substituted molecules are used as tracers. Noncovalent interactions between molecules include hydrogen bonding, and ionic and van der Waals interactions. This article reviews evidence for deuterium isotope effects on noncovalent interactions, with an emphasis on binding interactions between molecules of biological interest, but also including examples of nonbiological molecules in order to demonstrate the generality of these effects. The reality of this effect relies on the assumption that the only difference between the isotopomers considered is the presence of deuterium or hydrogen; there are no impurities present. The physical basis of the effect may be due to differences in the polarities and/or sizes of deuterated versus nondeuterated isomers, and the extent of a deuterium isotope effect on a noncovalent interaction depends on the site of deuteration within a biomolecule. The presence of this effect requires careful interpretation of results obtained in experiments with deuterium labeled compounds.     

Pairwise interactions between functional groups improve biological control

Ecologists have long debated whether predators primarily disrupt one another’s prey capture through interspecific interference, or instead complement one another by occupying different feeding niches. Resolution of this debate has been difficult because different experimental designs are typically used to study interference versus complementarity. We adopted a somewhat atypical approach, surveying communities of predatory insects on 73 free-growing Brassica oleracea plants, and then re-constructing each community in field cages to measure its impact on aphid prey. The predator communities naturally varied in species composition, richness, and relative abundance; in our experiment we kept total predator density constant to avoid confounding effects of differing overall abundance. The predator communities’ impacts on aphids differed by >10-fold. Using a generalized linear model, we found that pairings of several predators in the community improved aphid suppression while no pairings disrupted it. Indeed, accounting for the presence of the beneficial pairings provided more power than species richness to explain predators’ impacts on aphids. Altogether, our results suggest generally complementary or neutral, rather than disruptive, multi-predator effects in this community. Our approach may be useful for determining the frequency of complementary species-pairings in many other systems.     

纳米颗粒与生物大分子的相互作用及其生物毒性机制

纳米颗粒已得到广泛的应用,同时其潜在的毒性及生物学效应也引起了广泛的关注。许多文献证实纳米颗粒对生物体具有毒性作用,但在分子水平上对其毒性机制的研究较少。本文对近年来纳米颗粒与生物大分子相互作用的最新研究进行了综述,包括纳米颗粒与蛋白质、脂类、核酸等生物分子间的相互作用。     

Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules

Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is ?5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is ?3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine–water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.     

Intermolecular interactions between protein and other molecules including hydration effects

The structural aspects of protein functions, e.g., molecular recognition such as enzyme-substrate and antibody-antigen interactions, are elucidated in terms of dehydration and atomic interactions. When a protein interacts with some target molecule, water molecules at the interacting regions of both molecules are removed, with loss of the hydration free energy, but gaining atomic interactions between atoms of the contact sites in both molecules. The free energies of association originating from the dehydration and interactions between the atoms can be computed from changes in the accessible surface areas of the atoms involved. The free energy due to interactions between atomic groups at the contact sites is estimated as the sum of those estimated from the changes in the accessible surface area of 7 atomic groups, assuming that the interactions are proportional to the change of the area. The chain enthalpies and entropies evaluated from experimental thermodynamic properties and hydration quantities at the standard temperature for 10 proteins were available to determine the proportional constants for the atomic groups. This method was applied to the evaluation of association constants for the dimerization of proteins and the formation of proteolytic enzyme-inhibitor complexes, and the computed constants were in agreement with the experimental ones. However, the method is not accurate enough to account quantitatively for the change in the thermal stability of mutants of T4 lysozyme. Nevertheless, this method provides a way to elucidate the interactions between molecules in solution.     

Liposomes prepared dynamically by interactions between bile salt and phospholipid molecules

Quasi-elastic light scattering (QELS) studies showed that vesicles can spontaneously form from sodium glycocholate-egg phosphatidylcholine mixed micelles upon dilution with physiological saline buffer (pH 7.5). A water-soluble drug, cytosine arabinoside, did not affect the transition pattern. Transitions were also obtained when dilutions were performed using diluted serum solutions (5% and 10% serum in buffer). However, if intermicellar bile salt monomer concentration (imc) was kept constant in diluent media, the transition was completely suppressed. Approximately 10% of the cytosine arabinoside was trapped inside vesicles which were formed in buffer, although this value decreased to approx. 2.5% when diluted serum was used. These results suggest that the mixed micelle to vesicle transition can be an alternative means to sonication in loading drugs into in vitro vesicles. A good correlation was found between the transmission electron microscopy (TEM) diameter and the mean hydrodynamic diameter obtained by QELS.     

Cooperative interactions between troponin molecules bound to the cardiac thin filament

Striated muscle thin filaments contain many troponin molecules, which contact each other indirectly via tropomyosin and actin. Such allosteric interactions between troponin molecules may be responsible for cooperative Ca2+ binding to the regulatory sites of the cardiac thin filament (Tobacman, L. S., and Sawyer, D. S. (1990) J. Biol. Chem. 265, 931-939). To test whether thin filament-bound troponin molecules interact, we studied the competitive binding of troponin and troponin T-troponin I (an inhibitory complex lacking the Ca2+ binding subunit troponin C) to actin-tropomyosin. The relative affinities of these two forms of troponin for the thin filament depended upon their relative concentrations. Under conditions where total binding was saturated, each form binds with greater apparent affinity to sites that have similar neighbors. A theoretical model for competitive binding of two ligands to interacting sites on a linear lattice was developed and fit to the data. Surprisingly, energetically unfavorable interactions occurred between adjacent troponin and troponin T-troponin I molecules not only in the presence of Ca2+, but also in the presence of [ethylenebis(oxyethylenenitrilo)]tetraacetic acid and/or myosin subfragment 1. Removal of Ca2+ strengthened the affinity of troponin for the thin filament less than 50%. These results suggest that, even in the absence of myosin, long range allosteric interactions occur between troponin molecules. The detailed involvement of tropomyosin and actin in these interactions remains to be established.     

An analysis of the interactions between folic acid and aromatic guest molecules

The formation of complexes between folate and therapeutic drug molecules is well known. In this work, we attempted to elucidate the role of the aromatic rings of folate and drug molecules in interactions between both of these molecules. A detailed molecular simulation study was carried out to explore the associative behavior of folic acid with phenylalanine and tyrosine, which show fluorescence emission following the excitation of these molecules at 257 nm and 274 nm, respectively. Therefore, studies of fluorescence emission from phenylalanine and tyrosine were performed in this work. The results of these studies indicated that folic acid associates with phenylalanine and tyrosine with binding constants ranging from 1.46 × 10⁴ to 2.66 × 10⁴ M^?1. X-ray diffraction studies suggested that folic acid self-assembly is maintained in the presence of associative interactions of the folic acid with guest molecules. These results demonstrate that the aromatic rings in the structures of the folic acid and the therapeutic drug play an important role in the encapsulation of guest molecules through folate self-assembly.     

Surface molecules and cell interactions

Many of the cell surface molecules of lymphocytes or their precursors are expressed in an unpredictable way on a limited set of other cell types. This often seems to involve expression on lymphoid and brain cells. The Thy-1 antigen is in this category, being a major glycoprotein of murine neuronal cells, fibroblasts and thymocytes. Structural studies show that this molecule is homologous with immunoglobulin domains which are the structural sub-units of all immunoglobulin polypeptides. Thy-1 is the size of one immunoglobulin domain and its sequence is most homologous with variable regions of immunoglobulins.It is suggested that Thy-1 is one of a set of surface molecules concerned with triggering interactions between cells and that this is the primitive function of the immunoglobulin domain. Cell interactions could be mediated by domain-like structures and receptors for them in a way which parallels the triggering of immunological effector reactions by the interaction of receptors with immunoglobulin constant regions. If this is so then the structure seen in the immunoglobulin domain would have evolved along with the evolution of cell organisation. The genes specifying the cell interaction molecules could then have provided the genetic material for the evolution of antibody and histocompatibility antigen at the time of vertebrate emergence.     

Oligomeric interactions between phospholamban molecules regulate Ca-ATPase activity in functionally reconstituted membranes

Phospholamban (PLB) is a major target of the beta-adrenergic cascade in the heart, and functions as an endogenous inhibitor of Ca-ATPase transport activity. To identify whether oligomeric interactions between PLB molecules are involved in regulating Ca-ATPase transport activity, we have investigated functional interactions between PLB and the Ca-ATPase in proteoliposomes of purified PLB functionally co-reconstituted with the SERCA2a isoform of the Ca-ATPase isolated from cardiac sarcoplasmic reticulum (SR). The calcium sensitivity of this reconstituted preparation and functional stimulation by cAMP-dependent protein kinase (PKA) are virtually identical to those of the Ca-ATPase in cardiac SR microsomes, ensuring the functional relevance of this reconstituted preparation. Interactions between PLB molecules were measured following covalent modification of the single lysine (i.e., Lys(3)) in PLB isolated from cardiac SR membranes with fluorescein isothiocyanate (FITC) prior to co-reconstitution with the Ca-ATPase. FITC modification of PLB does not interfere with the ability of PLB to inhibit the Ca-ATPase, since FITC-PLB co-reconstituted with the Ca-ATPase exhibits a similar calcium dependence of Ca-ATPase activation to that observed in native SR membranes. Thus, the functional arrangement of PLB with the Ca-ATPase is not modified by FITC modification. Using changes in the anisotropy of FITC-PLB resulting from fluorescence resonance energy transfer (FRET) between proximal PLB molecules to measure the average size and spatial arrangement of FITC chromophores, we find that PLB self-associates to form oligomers whose spatial arrangement with respect to one another is in agreement with earlier suggestions that PLB exists predominantly as a homopentamer. The inability of PKA to activate PLB following covalent modification with FITC permits functional interactions between PLB molecules associated with the Ca-ATPase activation to be identified. A second-order loss of Ca-ATPase activation by PKA is observed as a function of the fractional contribution of FITC-PLB, indicating that PKA-dependent activation of two PLB molecules within a quaternary complex containing the Ca-ATPase is necessary for activation of the Ca-ATPase. We suggest that the requirement for activation of two PLB molecules by PKA represents a physiological mechanism to ensure that activation of the Ca-ATPase following beta-adrenergic stimulation in the heart only occurs above a threshold level of PKA activation.     

Resonant mirror biosensor detection method based on yessotoxin-phosphodiesterase interactions

Yessotoxin (YTX) is a generic name for a group of lipophilic compounds recently discovered and chemically characterized. Association measurements were done in a resonant mirror biosensor. The instrument detects changes in the refractive index and/or thickness occurring within a few hundred nanometers form the sensor surface where a molecule is attached. We used aminosilane surfaces where phosphodiesterase 3',5'-cyclic-nucleotide-specific from bovine brain (PDEs) was immobilized. Over this immobilized ligand different amounts of YTX were added and typical association curve profiles were observed. These association curves fit a pseudo-first-order kinetic equation where the apparent association rate constant (k(on)) can be calculated. The value of this constant increases with YTX concentration. From the representation of k(on) versus YTX concentration we obtained the association rate constant (k(ass)) 248+/-40 M(-1)s(-1) and the dissociation rate constant (k(diss)) 9.36 x 10(-4)+/-1.72 x 10(-4)s(-1). From these values the kinetic equilibrium dissociation constant (K(D)) for YTX-PDEs association can be calculated. The value of this last constant is 3.74 x 10(-6)+/-8.25 x 10(-8)M YTX. The PDE-YTX association was used as a method suitable for determination of the toxin concentration in a shellfish sample. The assay had sufficient sensitivity and can be used on simple shellfish extracts.     

Studies of interactions between uracil-based hybrid molecules and P-glycoprotein--search for multidrug resistance modulators

The hybrid molecules having structural features of anticancer drug, 5-fluorouracil, and MDR modulator, propafenone, have been studied for their interactions with P-glycoprotein (P-gp). Some of the molecules (5, 8, and 9) show considerable interactions with P-gp and could be the potential candidates for their in vivo evaluation as MDR modulators. Further investigations show the dependence of P-gp interacting properties of these compounds on their physico-chemical parameters like logP and total polar surface area.