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PubMed2002

Phosphoramidate-mediated conversion of carbonyl ligands into isocyanide ligands: a new approach to chiral isocyanide ligands.

Metal isocyanides have been used and studied by organometallic chemists for many years and, as a result, they have a rich and interesting chemistry. The nature of metal-free isocyanides and the methods of making isocyanide complexes, however, has resulted in the vast majority of studies to date being performed with structurally simple isocyanides. We report here a new approach to the synthesis of isocyanide ligands that involves the reaction of a metal carbonyl ligand with the anion of a phosphoramidate. As phosphoramidates can be synthesised in one step from amines, our method means that the structural diversity of readily available amines, particularly chiral amines, can now be incorporated into isocyanide ligands.

Journal Article↗
PubMed2004

Gas-phase ligand loss and ligand substitution reactions of platinum(II) complexes of tridentate nitrogen donor ligands.

The source of protons associated with the ligand loss channel of HX((n - 1)+) from [Pt(II)(dien)X](n+) (X = Cl, Br and I for n = 1 and X = NC(5)H(5) for n = 2) in the gas phase was investigated by deuterium-labelling studies. The results of these studies indicate that these protons originate from both the amino groups and the carbon backbone of the dien ligand. In some instances (e.g. X = Br and I), the protons lost from the carbon backbone can be even more abundant than the protons lost from the amino groups. The gas-phase substitution reactions of coordinatively saturated [Pt(II)(L(3))L(a)](2+) complexes (L(3) = tpy or dien) were also examined using ion-molecule reactions. The outcome of the ion-molecule reactions depends on both the ancillary ligand (L(3)) as well as the leaving group (L(a)). [Pt(II)(tpy)L(a)](2+) complexes undergo substitution reactions, with a faster rate when L(a) is a good leaving group, while the [Pt(II)(dien)L(a)](2+) complex undergoes a proton transfer reaction.

Journal Article↗
PubMed1999

Copper(I) Complexes with a NS(2)-Macrocyclic Ligand Bearing a Pendant Naphthyl Group: Structures of {N-[2-(1-Naphthyl)ethyl]-1-aza-4,8-dithiacyclodecane}copper(I)-Ligand, where Ligand = eta(2)-Naphthalene, Acetonitrile, or Triphenylphosphine.

A new macrocyclic ligand with a pendant naphthalene group, N-[2-(1-naphthyl)ethyl]-1-aza-4,8-dithiacyclodecane (L), has been synthesized and characterized. The copper(I)-acetonitrile complex [LCu(CH(3)CN)](PF(6)) (1) was synthesized from L and [Cu(CH(3)CN)(4)](PF(6)). The acetonitrile ligand from 1 was easily removed to give [LCu](PF(6)) (2). Complexes 1 and 2 have been crystallographically characterized. 1: C(21)H(28)N(2)CuF(6)PS(2), triclinic, P&onemacr;, a = 11.1901(10) Å, b = 11.2735(12) Å, c = 12.1350(10) Å, alpha = 98.996(8) degrees, beta = 117.188(6) degrees, gamma = 105.354(7) degrees, Z = 2, R1 = 0.0505 (wR2 = 0.1418). 2.0.5hexane: C(22)H(31)NCuF(6)PS(2), monoclinic, P2(1)/c, a = 15.7318(15) Å, b = 8.9164(10) Å, c = 17.205(5) Å, beta = 102.431(6) degrees, Z = 4, R1 = 0.0587 (wR2 = 0.1545). In addition, a cocrystallized mixture of both complexes was crystallographically characterized. 1&2.hexane: C(46)H(61)N(3)Cu(2)F(12)P(2)S(4), triclinic, P&onemacr;, a = 10.8308(9) Å, b = 12.6320(8) Å, c = 19.9412(13) Å, alpha = 80.445(5) degrees, beta = 76.405(6) degrees, gamma = 78.825(5) degrees, Z = 2, R1 = 0.0661 (wR2 = 0.1871). The solid-state structure of 2 features the pendant naphthalene group bound in an eta(2)-fashion, which is highly unusual for copper complexes. In CDCl(3), 2 exhibits fluxional behavior with the barrier to the process estimated, DeltaG() = 12-13 kcal. Variable temperature NMR spectroscopy gave compelling evidence for solution binding of the naphthalene group in 2, apparently the first example for copper(I). The fluxional process seen for 1 is best described as interconversion of the two enantiomers via a species with an unbound naphthalene group. Consistent with the weak binding of the naphthalene group, it is readily replaced with other ligands, such as triphenylphosphine to form [LCu(PPh(3))](PF(6)) (3). Complex 3 has also been structurally characterized: C(37)H(40)NCuF(6)P(2)S(2), monoclinic, P2(1)/c, a = 11.462(2) Å, b = 15.972(2) Å, c = 19.835(9) Å, beta = 94.50(3) degrees, Z = 4, R1 = 0.0906 (wR2 = 0.1889).

Journal Article↗
PubMed2004

Embracing ligands. Synthesis, characterisation and the correlation between 59Co NMR and ligand field parameters of Co(III) complexes with a new class of nitrogen-thioether multidentate ligand.

The syntheses of the hexadentate ligands 2,2,10,10-tetra(methyleneamine)-4,8-dithiaundecane (PrN4S2amp), 2,2,11,11-tetra(methyleneamine)-4,9-dithiadodecane (BuN4S2amp), and 1,2-bis(4,4-methyleneamine)-2-thiapentyl)benzene (XyN4S2amp) are reported and the complexes [Co(RN4S2amp)]3+ (R = Pr, Bu, Xy) characterised by single crystal X-ray study. The low-temperature (11 K) absorption spectra have been measured in Nafion films. From the observed positions of both spin-allowed 1A1g-->1T1g and 1A1g-->1T2g and spin forbidden 1A1g-->3T1g and 1A1g-->3T2g bands, octahedral ligand-field parameters (10Dq, B and C) have been determined. DFT calculations suggest that significant interaction between the d-d and CT excitations occurs for the complexes. The calculations offer an explanation for the observed deviations from linearity of the relationship between 59Co magnetogyric ratio and beta(DeltaE)(-1)(beta= the nephelauxetic ratio; DeltaE the energy of the 1A1g-->1T1g transition) for a series of amine and mixed amine/thioether donor complexes.

Journal Article↗
PubMed1999

Theoretical analysis of the inter-ligand overhauser effect: a new approach for mapping structural relationships of macromolecular ligands.

A theoretical framework has been developed for the evaluation of inter-ligand Overhauser effects (ILOE), predicted when pairs of ligands are observed in the presence of a macromolecular receptor which can form a ternary complex such that some of the protons on the two ligands are in close proximity with each other (generally less than approximately 5 A). Simulations for a pair of ligands with three spins each have been performed for a variety of geometric and rate parameters. Analogous to previously described calculations of TRNOE behavior, theoretical behavior of each of the nine cross peaks, A(ij), in a NOESY experiment involving ligands which can exist in the free, binary, or ternary complex states can be calculated. However, for exchange which is sufficiently rapid on the relaxation and chemical shift time scales, use of a collapsed matrix, C, corresponding to sums of sets of nine elements, will often be appropriate and generally simplifies the analysis. In order to generate inter-ligand Overhauser effects, it is optimal for the fraction of receptor involved in the ternary complex to be reasonably large; i.e., concentrations of both ligands should be near saturation. Based on a model assuming random binding order of the ligands, the dependence of ILOE resonance intensities on kinetic rate constants roughly parallels the dependence of transferred NOE (TRNOE) intensities. For diffusion controlled binding, i.e., k(on) approximately 10(8) M(-1) s(-1), the method is best suited for equilibrium dissociation constants in the micromolar-millimolar range (k(off) approximately 10(2)-10(5) s(-1)). Toward the slower dissociation rate constant end of this range, TRNOE and ILOE effects are still predicted, but the initial build-up curves become markedly nonlinear. For a kinetic binding scheme which assumes ordered binding of the ligands, the inherent asymmetry of the ligand binding process leads to more complex kinetics and alters the dependence of the ILOE on the kinetic parameters. In this case, the binding of the second ligand effectively reduces the exchange rate of the first ligand, reducing the transfer of NOE and ILOE information. The reduction in TRNOE and ILOE information which is prediced for the ordered ligand binding model is overcome at larger dissociation rate constants for either ligand 1 or ligand 2. In addition to the structural information available from ILOE data, the strong dependence of TRNOE and ILOE curves on ordered ligand binding suggests that such measurements could be useful for the characterization of ligand binding kinetics.

Enzymes↗
PubMedDate not supplied

Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI).

We have developed a novel structure-based chemoinformatics approach to search for Complimentary Ligands Based on Receptor Information (CoLiBRI). CoLiBRI is based on the representation of both receptor binding sites and their respective ligands in a space of universal chemical descriptors. The binding site atoms involved in the interaction with ligands are identified by the means of a computational geometry technique known as Delaunay tessellation as applied to X-ray characterized ligand-receptor complexes. TAE/RECON multiple chemical descriptors are calculated independently for each ligand as well as for its active site atoms. The representation of both ligands and active sites using chemical descriptors allows the application of well-known chemometric techniques in order to correlate chemical similarities between active sites and their respective ligands. We have established a protocol to map patterns of nearest neighbor active site vectors in a multidimensional TAE/RECON space onto those of their complementary ligands and vice versa. This protocol affords the prediction of a virtual complementary ligand vector in the ligand chemical space from the position of a known active site vector. This prediction is followed by chemical similarity calculations between this virtual ligand vector and those calculated for molecules in a chemical database to identify real compounds most similar to the virtual ligand. Consequently, the knowledge of the receptor active site structure affords straightforward and efficient identification of its complementary ligands in large databases of chemical compounds using rapid chemical similarity searches. Conversely, starting from the ligand chemical structure, one may identify possible complementary receptor cavities as well. We have applied the CoLiBRI approach to a data set of 800 X-ray characterized ligand-receptor complexes in the PDBbind database. Using a k nearest neighbor (kNN) pattern recognition approach and variable selection, we have shown that knowledge of the active site structure affords identification of its complimentary ligand among the top 1% of a large chemical database in over 90% of all test active sites when a binding site of the same protein family was present in the training set. In the case where test receptors are highly dissimilar and not present among the receptor families in the training set, the prediction accuracy is decreased; however, CoLiBRI was still able to quickly eliminate 75% of the chemical database as improbable ligands. CoLiBRI affords rapid prefiltering of a large chemical database to eliminate compounds that have little chance of binding to a receptor active site.

Algorithms↗
PubMed1997

Altered ligand binding properties and enhanced stability of a constitutively active estrogen receptor: evidence that an open pocket conformation is required for ligand interaction.

To elucidate the ligand binding properties of the estrogen receptor (ER) and how ligand access to and release from the ligand binding pocket is affected by the conformational state of the receptor, we have measured the rates of estradiol association and dissociation, the equilibrium binding, and the stability of estradiol binding to denaturants, comparing wild-type human ER and a point mutant (Y537S ER) that shows full constitutive activity, i.e., the same full transcriptional activity in the absence or presence of estrogen. Ligand binding kinetics and affinity were measured with the full-length (1-595) ERs and with truncated forms of both receptors containing domains C through F (including the DNA binding, hinge, and ligand binding domains, amino acids 175-595) or domains E and F (the ligand binding domain; amino acids 304-595). With all ERs, the rates of ligand association and dissociation were considerably slower with the Y537S mutant ER than with wild-type ER (6-fold and 3-4-fold, respectively). These marked differences in ligand on and off rates for the wild-type and Y537S receptors result in a predicted (k-1/k+1) and measured Kd that is 2-fold lower for Y537S ER compared to wild-type ER. The binding of estradiol by wild-type ER was disrupted by high concentrations of urea (above 2 M), whereas the Y537S ER was distinctly more resistant to this disruption. These results are consistent with a model in which wild-type ER in the absence of ligand adopts a transcriptionally inactive collapsed pocket conformation, stabilized by specific interactions of Y537 with nearby regions of ER. When estradiol is bound, the wild-type ER adopts a transcriptionally active, closed pocket (ligand occupied) conformation. By contrast, the Y537S mutant ER favors the transcriptionally active closed pocket conformation, whether occupied by ligand or not, the latter state (closed pocket but unoccupied) accounting for its constitutive activity. Our findings suggest that the entry or exit of ligand from the binding pocket requires that ER adopt an open pocket conformation. The reduced rates of ligand association and dissociation in the constitutively active form of the ER, as well as its greater resistance to disruption of ligand binding by urea, support the supposition that the rate at which this open pocket conformation can be accessed from the unoccupied or ligand-occupied Y537S ER is slower than from the unoccupied or occupied forms of wild-type ER. Thus, the binding and release of ligand by ER require that the receptor access an open pocket state, and the ease with which this state can be accessed is affected by mutations that alter receptor conformation.

Binding Sites↗
PubMed1982

Heme ligand replacement reactions of cytochrome P-450. Characterization of the bonding atom of the axial ligand trans to thiolate as oxygen.

Evidence of several types has accumulated that cytochrome P-450 has a thiolate anion as one of the axial ligands to heme (the fifth ligand). On the other hand, there is as yet no general agreement on the nature of the axial ligand trans to thiolate (the sixth ligand), although nitrogen and oxygen have been proposed. To resolve the controversy, the ligand exchange reactions of cytochrome P-450 were investigated by the use of optical spectroscopy. Two isozymes of rabbit liver microsomal cytochrome P-450 were examined: the isozyme induced by phenobarbital (P-450LM2), which has a sixth ligand and is low spin and the isozyme induced by 5,6-benzoflavone (P-450LM4), which is without a sixth ligand and is high spin. A series of artificial ligands was chosen to model the coordination of each of the potential native ligands, including water and certain amino acid residues. When the artificial ligand coordinated through an oxygen atom, the spectrum of pentacoordinate P-450LM4 changed to one closely resembling that of native, hexacoordinate P-450LM2. The spectrum of P-450LM2 was unchanged in the presence of oxygen-coordinating ligands. However, when artificial ligands which coordinate through nitrogen or sulfur were added to either P-450LM2 or P-450LM4, the induced spectra did not resemble the native spectrum and, in fact, were distinctive and characteristic of the particular ligand type. With three of the artificial ligands, 1-butanol, 1-benzylimidazole, and diethylphenylphosphine, the binding was found to be reversible by dilution, ultrafiltration, or gel filtration. The binding of 1-pentanol and 1-benzylimidazole was competitive, as expected for heme ligands, and the number of 1-benzylimidazole binding sites per molecule of P-450LM2 was estimated as 1.1. These results provide strong evidence that the native sixth ligand in P-450LM2 is oxygen rather than nitrogen.

Animals↗
PubMed1996

Selective Azide Oxidation of 1,2-Bis(diphenylphosphino)benzene and Related Ethylenebis(phosphines) to Asymmetric Multifunctional Phosphorus Ligands and Formation of Rhodium(I) Complexes of These Ligands. Structural Characterization of the Prototypical Ligand 1-(((Trimethylsilyl)imino)diphenylphosphorano)-2-(diphenylphosphino)benzene and Its Rhodium(I) Complex: 1-Ph(2)P=N(SiMe(3))C(6)H(4)-2-(Ph(2)P)Rh(CO)Cl.

Selective azide mono-oxidation of o-bis(phosphines) such as o-bis(diphenylphosphino)benzene and other bis(phosphines) with cis-substituents on a rigid backbone such as an ethylene structure occurs as the result of the steric control exerted during the azide oxidation (Staudinger) reaction process. The azides used were the trimethylsilyl, 4-cyanotetrafluorophenyl, benzyl, and diphenoxyphosphonyl azides. The prototypical ligand 1-Ph(2)P=N(SiMe(3))-2-(Ph(2)P)C(6)H(4), 2, has been structurally characterized. Crystal data for 2: crystal dimensions, 0.38 x 0.38 x 0.57 mm; space group, monoclinic, P2(1)/c, (No. 14); a = 11.093(5) Å, b = 14.898(5) Å, c = 18.811(2) Å, beta = 102.76(2) degrees, V = 3031 Å(3), Z = 4. Final R, R(w) and GOF values were 0.068, 0.074, and 1.92 respectively. The P=N-SiMe(3) angle was wide, 152.7(3) degrees, and the P=N bond length short (1.529(5) Å) relative to arylated iminophosphoranes but in keeping with the trends for silylated analogs. The iminophosphorane center can be selectively transformed with other agents in a Wittig type reaction converting the azides to the monooxide, monosulfide, etc. The iminophosphoranophosphines are also good complexing agents and the Rh(I) complex derived from 2, 1-Ph(2)P=N(SiMe(3))-C(6)H(4)-2-(Ph(2)P)Rh(CO)Cl, 15 was structurally characterized. Crystal data for 15: crystal dimensions, 0.32 x 0.44 x 0.66 mm; space group, monoclinic, P2(1)/c (No. 14); a = 13.793(3) Å, b = 12.622(11) Å, c = 20.436(6) Å, beta = 105.93(2) degrees, V = 3421.2 Å(3), Z = 4. Final R, R(w), and GOF values were 0.064, 0.061, and 1.45 respectively. The complex shows typical square planar geometry about Rh, a cis phosphine-CO relationship, and no exceptional steric crowding of the coordination site.

Journal Article↗
PubMed1996

Modulation of protein function by exogenous ligands in protein cavities: CO binding to a myoglobin cavity mutant containing unnatural proximal ligands.

A variety of heterocyclic ligands can be exchanged into the proximal cavity of sperm whale myoglobin mutant H93G, providing a simple method for introduction of the equivalent of unnatural amino acid side chains into a functionally critical location in this protein. These modified proteins bind CO on the distal side. 1H NMR data on H93G(Im)CO, where Im is imidazole, demonstrate that the structure of the distal heme pocket in H93G(Im)CO is very similar to that of wild type; thus, the effects of the proximal ligand's properties on CO binding can be studied with minimal perturbation of distal pocket structure. The exogenous proximal ligands used in this study include imidazole (Im), 4-methylimidazole (4-MeIm), 4-bromoimidazole (4-BrIm), N-methylimidazole (N-MeIm), pyridine (Pyr), and 3-fluoropyridine (3-FPyr). Substitution of the proximal ligand is found to produce substantial changes in the CO on and off rates, the equilibrium binding constant, and the vibrational stretch frequency of CO. Many of the changes are as large as those reported for distal pocket mutants prepared by site-directed mutagenesis. The ability to systematically vary the nature of the proximal ligand is exploited to test the effects of particular properties of the proximal ligand on CO binding. For example, 4-MeIm and 4-BrIm are similar in size and shape but differ significantly in pKa. The same relationship is true for Pyr and 3-FPyr. By comparison of the IR spectra and CO recombination kinetics of these complexes, the effects of proximal ligand pKa on the CO binding are assessed. Likewise, N-MeIm and 4-MeIm are similar in size and pKa but differ in their ability to hydrogen bond to amino acid residues in the proximal cavity. Comparisons of IR spectra and CO binding kinetics in these complexes reveal that proximal ligand conformation and hydrogen bonding affect the kinetics of CO binding. The mechanism of proximal ligand exchange between solution and the proximal cavity in CO complexes was investigated by obtaining the 19F NMR spectrum of H93G(3-FPyr)CO, whose 19F signal can be observed without interference from resonances of the protein. The proximal ligand is found to exchange within a few seconds by saturation transfer. This exchange rate is about 2 orders of magniture faster than what is observed for the isoelectronic metcyano complex [Decatur, S. M., & Boxer, S. G. (1995) Biochemistry 34, 2122-2129]; in both the ferrous CO and ferric cyano complexes, the proximal ligand exchange rate is independent of ligand concentration. These results suggest that the rate-limiting step in proximal ligand exchange is breakage of the iron-ligand bond, followed by rapid diffusion of the ligand through the protein to bulk solution.

Animals↗
PubMed2002

Influencing receptor-ligand binding mechanisms with multivalent ligand architecture.

Multivalent ligands can function as inhibitors or effectors of biological processes. Potent inhibitory activity can arise from the high functional affinities of multivalent ligand-receptor interactions. Effector functions, however, are influenced not only by apparent affinities but also by alternate factors, including the ability of a ligand to cluster receptors. Little is known about the molecular features of a multivalent ligand that determine whether it will function as an inhibitor or effector. We envisioned that, by altering multivalent ligand architecture, ligands with preferences for different binding mechanisms would be generated. To this end, a series of 28 ligands possessing structural diversity was synthesized. This series provides the means to explore the effects of ligand architecture on the inhibition and clustering of a model protein, the lectin concanavalin A (Con A). The structural parameters that were varied include scaffold shape, size, valency, and density of binding elements. We found that ligands with certain architectures are effective inhibitors, but others mediate receptor clustering. Specifically, high molecular weight, polydisperse polyvalent ligands are effective inhibitors of Con A binding, whereas linear oligomeric ligands generated by the ring-opening metathesis polymerization have structural properties that favor clustering. The shape of a multivalent ligand also influences specific aspects of receptor clustering. These include the rate at which the receptor is clustered, the number of receptors in the clusters, and the average interreceptor distance. Our results indicate that the architecture of a multivalent ligand is a key parameter in determining its activity as an inhibitor or effector. Diversity-oriented syntheses of multivalent ligands coupled with effective assays that can be used to compare the contributions of different binding parameters may afford ligands that function by specific mechanisms.

Chemical Precipitation↗
PubMed2006

The Bead blot: a method for identifying ligand-protein and protein-protein interactions using combinatorial libraries of peptide ligands.

Small molecules that bind proteins can be used as ligands for protein purification and for investigating protein-protein and protein-drug interactions. Unfortunately, many methods used to identify new ligands to desired proteins suffer from common shortcomings, including the requirement that the target protein be purified and/or the requirement that the ligands be selected under conditions different from those under which it will be used. We have developed a new method called the Bead blot that can (i) select ligands to unpurified proteins, including trace proteins, present in complex materials (e.g., unfractionated plasma); (ii) select ligands to multiple proteins under a variety of conditions in a single experiment; and (iii) be used with libraries of different types of ligands. In the Bead blot, a library of ligands, synthesized on chromatography resin beads, is incubated with a starting material containing a target protein for which a ligand is sought. The proteins in the material bind to their complementary ligands according to specific affinity interactions. Then the protein-loaded beads are immobilized in a porous matrix, and the proteins are directionally eluted from the beads and captured on a membrane superimposed on the beads. The location of the target protein on the membrane is determined, and because the position of the protein(s) on the membrane reflects the position of the bead(s) in the matrix, the bead that originally bound the protein is identified, with subsequent elucidation of the ligand sequence. Ligands to several targets can be identified in one experiment. Here we demonstrate the broad utility of this method by the selection of ligands that purify plasma protein complexes or that remove pathogens from whole blood with very high affinity constants. We also select ligands to a protein based on competitive elution.

Amino Acid Sequence↗
PubMed2003

Full-length estrogen receptor alpha and its ligand-binding domain adopt different conformations upon binding ligand.

The binding of ligand to a nuclear receptor causes conformational changes that can result in coactivator or corepressor recruitment and subsequent regulation of transcription. Several peptides have previously been identified that bind to the liganded estrogen receptor (ER). One interacting peptide, pepalphaII, was used in the present studies to assess the ability of ligands to induce spatial changes within both the full-length human estrogen receptor alpha (ER-alpha) and a truncated receptor containing the ligand-binding domain (LBD). pepalphaII interacted weakly with the full-length estrogen receptor alpha in the presence of both agonists and antagonists. In contrast, the interaction of pepalphaII with the truncated receptor containing the ligand-binding domain was strongly induced by antagonists and only weakly induced by agonists. Thus, the same ligand can induce different spatial configurations of the full-length and ligand-binding domain of estrogen receptor alpha as measured by pepalphaII affinity. Crystal structures of nuclear hormone receptors solved to date have used ligand-binding domains and therefore may not accurately predict surface interaction domains present in the liganded full-length receptor. Furthermore, the ability of a ligand to induce a strong interaction of pepalphaII with the estrogen receptor alpha ligand-binding domain predicts that the ligand will have greater antagonist activity on the full-length receptor.

Animals↗
PubMed1992

Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association.

A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be extended to more complex situations. The general equation for the isotherm is v/LF = SFKF, where v is the ratio of bound ligands to lattice residues, LF is the free ligand concentration, SF is the fraction of binding sites that are free, and KF is the average association constant of a free site. Solutions are derived for three cases: symmetric ligands, and asymmetric ligands on isotropic or anisotropic lattices. For symmetric ligands there is one NEP, E, which is the ratio of the average binding affinity of a free site if the status of the lattice residue neighboring one end of the site is unspecified (left to chance) to the affinity when this residue is free (holding the other neighbor constant). Thus KF is KE2, where K is the affinity of an isolated site. If a site is n residues long, SF is f ffn-1, where f = 1 - nv is the fraction of residues that are free and ff is the conditional probability that a free residue is bordered on a given side by another free residue. The expression for ff is 1/(1 + x/E), where x is v/f, E is (1 - x + [(1 - x)2 + 4x omega]1/2)/2, and omega is the co-operativity parameter. The binding of asymmetric ligands to an isotropic lattice is described by two NEPs; the last case involves four NEPs and a bound ligand orientation parameter. For each case, the expected length distribution of clusters of bound ligands can be calculated as a function of v. When Scatchard plots with the same intercepts and initial slope are compared, it is found that ligand asymmetry lowers the isotherm (relative to the corresponding symmetric ligand isotherm), whereas lattice anisotrophy raises it.

Binding Sites↗
PubMed2005

Screening for metal ligands by liquid chromatography--ligand-exchange--electrospray mass spectrometry.

Electrospray ionization mass spectrometry is applied for the selective detection of metal ligands after a post-column continuous-flow ligand-exchange reaction. The detection is based on the specific release of a reporter ligand from a metal-reporter ligand complex by a high affinity ligand. Constant infusion and direct-injection experiments are performed to optimize the method. The on-line coupling of a liquid chromatographic separation prior to the continuous flow ligand-exchange reaction enables the screening for high affinity ligands in complex samples. The feasibility of the method is demonstrated by using several ligands with a different affinity for either Cu(II) or Zn(II) ions. The selectivity of the ligand-exchange detection method can be tuned by the choice of the reporter ligand. This is demonstrated by using either 2,2'-bipyridyl or 5-methyl-1,10-phenanthroline as reporter ligands.

Chromatography, Liquid↗
PubMed1991

Bivalent ligand dissociation kinetics from receptor-bound immunoglobulin E: evidence for a time-dependent increase in ligand rebinding at the cell surface.

The bivalent ligand N,N'-bis[[epsilon-[(2,4- dinitrophenyl)amino]caproyl]-L-tyrosyl]cystine [(DCT)2-Cys] binds and cross-links anti-dinitrophenyl (DNP) immunoglobulin E (IgE)-receptor complexes on the cell surface of rat basophilic leukemia cells. The rate of dissociation of this bound ligand was monitored by using a fluorescence method under two different conditions. In one case the monovalent ligand DCT was added in large excess to prevent the dissociating ligand from rebinding to unoccupied antibody combining sites. Under these conditions, dissociation of the bivalent ligand from IgE-sensitized cells proceeds to completion with kinetics that are well described by two rate constants that are independent of the time of preincubation of the bivalent ligand with the cells. In the second case, dissociation of (DCT)2-Cys from cell-bound anti-DNP IgE was monitored in the presence of a large excess of anti-DNP IgE in solution that acts as a sink to absorb the dissociated ligand. Under these conditions, the bivalent ligand becomes more resistant to dissociation as the preincubation time of the bivalent ligand with the cells is increased. An increasing fraction of the bound ligand does not dissociate on a measurable time scale in the presence of this sink. The results indicate that cell-associated IgE-receptor complexes undergo a time-dependent change that facilitates the reformation of the cross-linked state when one end of the ligand dissociates to break up the existing cross-link. The possible physical basis and functional implications of these results are discussed.

Animals↗
PubMed2000

Understanding the orientation and dynamic motion of planar heterocyclic N-donor ligands by exploiting the symmetry properties of mixed-ligand mu-oxorhenium(V) dinuclear complexes.

Factors influencing the orientation and dynamic motions of planar N-donor heterocyclic ligands (L) are of interest since such features have broad relevance in metallobiochemistry [Marzilli, L. G.; Marzilli, P. A.; Alessio, E. Pure Appl. Chem. 1998, 70, 961-968]. We found that mu-oxorhenium(V) dinuclear complexes [ReOCl2LsLt]-O-[ReOCl2LsLt] bearing either symmetrical (L = py = pyridine; 3,5-lut = 3,5-lutidine) or lopsided (L = Me3-Bzm = 1,5,6-trimethylbenzimidazole) cis L ligands are particularly useful for studying these factors. NMR data showed that terminal (Lt) and stacked (Ls) ligands were exchanged by approximately 180 degrees rotation about the Re-O-Re bond system. Such exchange occurred, however, between degenerate chiral conformers. Here we report a combined X-ray structural and solution NMR investigation of the AA + CC (racemic) and AC (meso) forms of two mixed-ligand mu-oxorhenium dimers that bear one lopsided and one symmetrical ligand on each Re atom, namely, Re2O3-Cl4(py)2(Me3Bzm)2 (1rac and 1meso) and Re2O3Cl4(3,5-lut)2(Me3Bzm)2 (2rac and 2meso). The presence of two different cis L ligands in 1 and 2 breaks the local symmetry at each Re atom, so that, in the racemic dimers, the exchange of terminal and stacked ligands leads to nondegenerate conformers. Overall, NMR data showed that the unsymmetrical dimers 1 and 2 undergo two dynamic processes contemporaneously, namely, 180 degrees rotation about the Re-N(py or 3,5-lut) bond and coupled rotation about the Re-O-Re/Re-N bonds. Both processes reach the slow exchange limit below -80 degrees C. Rotation of py in 1 occurs faster than that of 3,5-lut in 2; this difference is attributed to the higher steric demands of 3,5-lut compared to py. For both dimers NMR data provided compelling evidence of the preferred conformers in solution, including ligand orientations. The low-T solution structure of 1meso and 2meso is chiral, the same as that found in the solid state for 2meso, where the Me3Bzm on one Re atom is stacked with the 3,5-lut on the other Re atom. The remaining Me3Bzm and 3,5-lut, one on each Re atom, are both terminal. In solution the coupled Re-O-Re/Re-N rotations interconvert the two halves of each meso dimer to yield the same overall stable chiral conformation. For the racemic dimers, however, this process does not interconvert one enantiomer into the other, but instead interconverts two rotamers, R1 and R2, each of which is chiral. We found that, in the case of both 1rac and 2rac, the conformer with stacking symmetrical ligands (R1) is roughly 1 order of magnitude more stable than that with stacking Me3Bzm ligands (R2). Moreover, the solution conformation of R1 is the same as that found in the solid state of 1rac. Solution- and solid-state data indicate that the key interaction favoring the observed conformations is very likely the electrostatic attraction between the delta+ H2 atoms on the Me3Bzm ligands and the negative O and Cl groups in the core of the dimers. Finally, for both meso and racemic dimers we were also able to elucidate the preferred pathways of the coupled dynamic motions and establish that, very likely, the two halves of the dimers swing back and forth by approximately 130 degrees through the anti eclipsed form.

Crystallography, X-Ray↗
PubMed2000

Selective upregulation of fibroblast Fas ligand expression, and prolongation of Fas/Fas ligand-mediated skin allograft survival, by retinoic acid: the skin as a retinoide-inducible immune privilege site.

Fas/Fas ligand-mediated lymphocyte apoptosis has been implicated in the suppression of immune responses and may cause immune privilege. Human corneas exhibit immune privilege and can be transplanted across allogeneic barriers without immunosuppressive therapy, perhaps, because corneal keratinocytes express Fas ligand. To characterize Fas and Fas ligand expression in skin, we examined expression by murine keratinocytes, dermal fibroblasts, melanocytes, and human umbilical endothelial cells. We also studied the regulation of Fas and Fas ligand in skin cells by retinoic acid, vitamin D3, and dexamethasone as well as various cytokines. Among the molecules and cells tested, retinoic acid selectively upregulated the expression of Fas ligand molecule by fibroblasts. Retinoic acid-induced Fas ligand+ fibroblasts killed Fas+ target cells, and this killing was blocked by anti-Fas ligand antibody. The function of Fas ligand on dermal fibroblasts in vivo was tested in a cutaneous allograft system. Histoincompatible BALB/C mouse (H-2d) donor skin was grafted on to allogeneic C57BL/6 mice (H-2b). Daily local injection of retinoic acid blocked inflammation and extended graft survival for more than 10 d. Injection of retinoic acid into Fas ligand mutated gld/gld donor skin did not prevent leukocyte infiltration into the allograft or prolong graft survival. These experiments indicate that, in skin, retinoic acid selectively increases Fas ligand expression by fibroblasts and that retinoic acid has potent Fas/Fas ligand-dependent immunosuppressive activity.

Animals↗