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Quantitative evaluation of weak nonbonded Se...F interactions and their remarkable nature as orbital interactions.

To evaluate weak intramolecular nonbonded Se...F interactions recently characterized for a series of o-selenobenzyl fluoride derivatives (Iwaoka et al., Chem. Lett. 1998, 969-970), the temperature dependence of the nuclear spin coupling between Se and F (J(Se...F)) was investigated for 2-(fluoromethyl)phenylselenenyl cyanate (1a) and bis[2-(fluoromethyl)phenyl] diselenide (1e) in CD2Cl2 and CD3CN. A significant increase in the magnitude of J(Se...F) was observed for both 1a and 1e upon lowering temperature, whereas the values of J(Se...F) for the corresponding trifluoromethyl compounds slightly reduced or remained unchanged at low temperatures. Application of the rapid equilibrium model between two possible conformers revealed that conformer A with an intramolecular Se...F interaction is more stable in enthalpy (DeltaH) by 1.23 kcal/mol for 1a (in CD2Cl2) and by 0.85 and 0.83 kcal/mol for 1e (in CD2Cl2 and CD3CN, respectively) than conformer B, which does not have close Se...F contact. The negligible solvent effects for 1e suggested marginal electrostatic nature of the Se...F interactions. Instead, importance of the n(F) -->sigma*(Se-X) orbital interaction was suggested by quantum chemical (QC) calculations and the natural bond orbital (NBO) analysis.

Journal Article↗

Crystal engineering for topochemical polymerization of muconic esters using halogen-halogen and CH/pi interactions as weak intermolecular interactions.

We now report the molecular and crystal structure design of muconic ester derivatives on the basis of crystal engineering using halogen-halogen contacts and CH/pi interactions. The solid-state photoreaction pathway of the dibenzyl (Z,Z)-muconates as the 1,3-diene dicarboxylic acid monomers depends on the structure of the ester groups. The substitution of a halogen atom for the aromatic hydrogen of a benzyl group induces topochemical polymerization to produce stereoregular polymers in a crystalline form, whereas the unsubstituted benzyl derivative isomerizes to yield the corresponding E,E isomer under similar conditions. The topochemical polymerization process is directly confirmed by the fact that the single-crystal structures before and after the polymerization are very similar to each other. From the crystal structure analysis for a series of substituted benzyl (Z,Z)- and (E,E)-muconates, it has been revealed that the planar diene moieties are closely packed to form a columnar structure in the crystals. The stacking of the polymerizable monomers is characterized by a stacking distance of 4.9-5.2 A along the columns. This structure is supported by a halogen-halogen interaction between the chlorine or bromine atoms introduced at the p position of the benzyl groups in addition to an aromatic stacking due to the CH/pi interaction between the benzylic methylene hydrogens and aromatic rings. The design of a monomer packing corresponds to the type and position of the introduced halogen atom and also the polymorphs. To make a stacking distance of 5 A using both halogen-halogen and CH/pi interactions as supramolecular synthons is important for the molecular design of muconic ester derivatives appropriate for topochemical polymerization.

Journal Article↗

Why are silyl ethers conformationally different from alkyl ethers? Chair-chair conformational equilibria in silyloxycyclohexanes and their dependence on the substituents on silicon. The wider roles of eclipsing, of 1,3-repulsive steric interactions, and of attractive steric interactions.

An NMR study of the diaxial/diequatorial chair equilibrium in a range of silylated derivatives of trans-1,4- and trans-1,2-dihydroxycyclohexane is reported and discussed with a view to explaining unusually large populations of chair conformations with axial substituents, noted previously for some monosilyloxycyclohexanes and in some silylated sugars. X-ray diffraction studies of three bis-triphenylsilyloxycyclohexanes are reported and show both axial and equatorial silyloxy groups with the exocyclic bonds eclipsed. Eclipsing is also suggested by molecular mechanics (MM3) calculations on such derivatives. Both axial and equatorial tertiary silyl groups have 1,3-repulsive interactions with whatever substituents or hydrogen atoms are at the two adjacent equatorial positions, and these are relieved by rotation toward the eclipsed conformation of the exocyclic C-O bond. The three substituents on silicon interact attractively with the nine atoms at the 3, 4, and 5-positions of the cyclohexane ring and calculations suggest that these stabilizing interactions are significantly greater in the axial than in the equatorial conformation. An equatorial C-OSiR(3) bond with one or two equatorial neighbors has a restricted potential energy well that becomes much broader when the bond is axial without any equatorial neighbors in the alternative chair. Adjacent silyl groups in the 1,2-disubstituted series interact in a stabilizing way overall in all conformations, this being particularly marked in the diaxial conformation of the more complex ethers. These factors lead to unusually large axial populations.

Journal Article↗

Effective disruption of phosphoprotein-protein surface interaction using Zn(II) dipicolylamine-based artificial receptors via two-point interaction.

Protein phosphorylation is ubiquitously involved in living cells, and it is one of the key events controlling protein-protein surface interactions, which are essential in signal transduction cascades. We now report that the small molecular receptors bearing binuclear Zn(II)-Dpa can strongly bind to a bis-phosphorylated peptide in a cross-linking manner under neutral aqueous conditions when the distance between the two Zn(II) centers can appropriately fit in that of the two phosphate groups of the phosphorylated peptide. The binding property was quantitatively determined by ITC (isothermal titration calorimetry), induced CD (circular dichroism), and NMR. On the basis of these findings, we demonstrated that these types of small molecules were able to effectively disrupt the phosphoprotein-protein interaction in a phosphorylated CTD peptide and the Pin1 WW domain, a phosphoprotein binding domain, at a micromolar level. The strategy based on a small molecular disruptor that directly interacts with phosphoprotein is unique and should be promising in developing a designer inhibitor for phosphoprotein-protein interaction.

Amino Acid Sequence↗

A threshold for charge transfer in aromatic interactions? A quantitative study of pi-stacking interactions.

[structure: see text] Attractive interactions between substituted arenes in the parallel displaced configuration have been quantitatively studied using triptycene-derived molecular conformational reporters. Charge-transfer bands are observed for models where the interactions are between strong donor and acceptors. Substituent effects on the strength of the aromatic interaction follow opposite trends for strongly electron-deficient arenes and mildly perturbed arenes. The free energy of interactions for models with strong electron donors and acceptors does not follow a linear correlation in the Hammett plot. Electrostatic models alone do not account for the nonlinearity of the free energy-substituents plot.

Electrons↗

Use of NMR binding interaction mapping techniques to examine interactions of chiral molecules with molecular micelles.

NMR spectroscopy was used to investigate the association of four chiral molecules with the molecular micelle poly(sodium N-undecanoyl-l-leucylvalinate) (poly(SULV)). Adding poly(SULV) to the background electrolyte in electrokinetic chromatography (EKC) allows enantiomeric resolution to be achieved because enantiomers interact differentially with the chiral centers on the micelle headgroups as they both move in the electric field. Pulsed field gradient diffusion experiments were used to measure molecular micelle association constants for enantiomers of each analyte. These association constants were consistent with EKC elution order for the compounds 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BNP), 1,1'-bi-2-naphthol (BOH), and Troger's base. In addition, nuclear Overhauser enhancement spectroscopy, nuclear Overhauser effect difference, and intermolecular cross relaxation diffusion experiments were used to generate binding interaction maps for each chiral analyte. These maps showed that BNP and BOH inserted into the surfactant headgroup's major chiral groove and interacted predominately with the leucine chiral center. (+)-Troger's base was also found to insert into the major chiral groove. However, this compound instead interacted with the valine chiral atom. In diffusion experiments with long diffusion times, the linearized diffusion plots for each analyte-molecular micelle mixture showed curvature characteristic of intermolecular cross relaxation. The magnitude of this effect scaled linearly with the analytes' free energies of binding.

Chemistry, Physical↗

Adult attachment and marital interaction as predictors of whole family interactions during the transition to parenthood.

This study examined the role of parental adult attachment and couples' prenatal and postnatal marital interactions in predicting the quality of family interactions 24 months after the birth of the couple's first child. Father's prenatal marital withdrawal and mother's postnatal marital withdrawal were associated with less adaptive family interactions at 24 months. Families with fathers who had an insecure attachment, as assessed by the Adult Attachment Interview, showed less positive and more negative interactions at 24 months, but only when there were higher levels of negative escalation in the couple's marriage prenatally. Findings are discussed in terms of the importance of exploring the transition to parenthood at the broader family level.

Adolescent↗

Localization of p0071-interacting proteins, plakophilin-related armadillo-repeat protein-interacting protein (PAPIN) and ERBIN, in epithelial cells.

PAPIN has six PDZ domains and interacts with p0071, a catenin-related protein. Recent studies have revealed that catenins determine the subcellular localization of some PDZ proteins. We have examined whether the localization of PAPIN is determined by p0071 in epithelial cells. PAPIN was localized not only on the lateral membrane but also on the apical membrane, where p0071 was absent. The targeting to both membranes was mediated by the middle region of PAPIN and did not require the p0071-interacting PDZ domain. In cells that came into contact, PAPIN was diffusely distributed on the plasma membrane, while p0071 was concentrated at immature cell-cell contacts. When epithelial cells were exposed to the low concentration of calcium, p0071 was internalized, whereas PAPIN remained on the plasma membrane. We also confirmed that the interaction with p0071 was not essential for the membrane targeting of ERBIN, a recently identified p0071- and ErbB2-binding protein. PAPIN, p0071, and ERBIN formed a complex in 293T cells. Furthermore, ERBIN and ErbB2 were colocalized with PAPIN on the lateral membrane. These findings suggest that PAPIN, p0071, and ERBIN come to the cell-cell contacts independently and interact with each other on the lateral membrane.

Adaptor Proteins, Signal Transducing↗

Glucocorticoid--receptor interactions. Studies of the negative co-operativity induced by steroid interactions with a secondary, hydrophobic, binding site.

The effects of steroids on the binding of [1,2-3H]dexamethasone and [1,2-3H]progesterone to the glucocorticoid receptor of rat thymus cytosol were studied. Although both glucocorticoid agonists and antagonists competed with [1,2-3H]dexamethasone for binding to the receptor under equilibrium conditions, only glucocorticoid antagonists of partial agonists, at micromolar concentrations, were capable of accelerating the rate of dissociation of previously bound [1,2-3H]dexamethasone from the receptor. Antagonists or partial agonists also enhanced the rate of dissociation of [1,2-3H]progesterone from the glucocorticoid receptor, with identical specificity and concentration--response characteristics. These effects are attributed to the presence on the receptor of a secondary, low-affinity, binding site for glucocorticoid antagonists, the occupancy of which produces negatively co-operative interactions with the primary glucocorticoid-binding site. In contrast with the interactions with the primary site, the interactions of steroids with the negatively co-operative site appear to be primarily hydrophobic in nature, and the site resembles the steroid-binding site of progestin-binding proteins in its specificity, though not its affinity. The results also suggest that the initial interactions of both glucocorticoid agonists and antagonists with the receptor under equilibrium conditions are with one primary site on a receptor existing in one conformation only.

Animals↗

Interaction of rat liver glucocorticoid receptor with adenosine 5'-triphosphate. Characterization of interaction by use of ATP-sepharose affinity chromatography.

An interaction between rat liver glucocorticoid--receptor complex and immobilized ATP was identified. Rat liver cytosol preparations were incubated with [3H]triamcinolone acetonide for 4 h at 4 degrees C and partially purified by precipitation with (NH4)2SO4 before use. The resulting glucocorticoid--receptor complex could be selectively adsorbed on to columns of ATP--Sepharose. The freshly prepared cytosol [3H]triamcinolone acetonide--receptor complex had very little affinity for binding to the ATP--Sepharose column, but acquired this ability on temperature- or salt-activation. The presence of 10 mM-sodium molybdate during this salt- or temperature-dependent activation blocked the binding of the receptor complex to ATP--Sepharose. The interaction is reversible, since it can be disrupted by high-salt conditions. A competitive binding assay, using free nucleotides in samples to be chromatographed, revealed a preferential interaction between ATP and the glucocorticoid--receptor complex. Buffer containing ATP was also used to elute the glucocorticoid--receptor complex from ATP--Sepharose columns successfully. When ATP was added to the preparations containing [3H]triamcinolone acetonide--receptor complexes, the steroid specificity or sedimentation properties of the complex remained unaltered. Our results demonstrate an interaction between rat liver glucocorticoid--receptor complex and immobilized ATP and suggest a role of this nucleotide in receptor function.

Adenosine Triphosphate↗

A novel higher plant protein tyrosine phosphatase interacts with SNF1-related protein kinases via a KIS (kinase interaction sequence) domain.

A novel protein phosphatase in Arabidopsis thaliana was identified by database searching. This protein, designated AtPTPKIS1, contains a protein tyrosine phosphatase (PTP) catalytic domain and a kinase interaction sequence (KIS) domain. It is predicted to interact with plant SNF1-related kinases (SnRKs), representing central regulators of metabolic and stress responses. AtPTPKIS1 has close homologues in other plant species, both dicots and monocots, but is not found in other kingdoms. The tomato homologue of AtPTPKIS1 was expressed as a recombinant protein and shown to hydrolyse a generic phosphatase substrate, and phosphotyrosine residues in synthetic peptides. The KIS domain of AtPTPKIS1 was shown to interact with the plant SnRK AKIN11 both in vivo in the yeast two-hybrid system, and in vitro in a GST-fusion 'pull down' assay. The genomes of Arabidopsis and other plants contain further predicted proteins related to AtPTPKIS1, which could also interact with SnRKs and act in novel regulatory and signalling pathways.

Amino Acid Sequence↗

Protein-protein interaction in transport: periplasmic histidine-binding protein J interacts with P protein.

A component of the high-affinity histidine transport system in Salmonella typhimurium, the periplasmic histidine-binding protein J, interacts with another transport component, the P protein. A mutant J protein, with a defective interaction site but intact histidine-binding site, can function in histidine transport if an appropriate compensating mutation is introduced in the P protein. The interaction between the J and P proteins is an obligatory step in transport. The significance of this interaction and of the involvement of the P protein in multiple transport functions is discussed.

Bacterial Proteins↗

The regulatory subunit of Escherichia coli aspartate carbamoyltransferase may influence homotropic cooperativity and heterotropic interactions by a direct interaction with the loop containing residues 230-245 of the catalytic chain.

A recent x-ray structure of aspartate carbamoyltransferase (carbamoyl-phosphate: L-aspartate carbamoyl-transferase, EC 2.1.3.2) with phosphonoacetamide bound [Gouaux, J. E. & Lipscomb, W. N. (1990) Biochemistry 29, 389-402] shows an interaction between Asp-236 of the catalytic chain and Lys-143 of the regulatory chain. Asp-236 is part of the loop containing residues 230-245 (240s) of the catalytic chain that undergoes a significant conformational change between the tight and the relaxed states of the enzyme. Furthermore, side-chain interactions between the 240s loop and other portions of the enzyme have been shown to be important for the low activity and low affinity of the tight state and the high activity and high affinity of the relaxed state. To determine whether the intersubunit link between Lys-143 of the regulatory chain and Asp-236 of the catalytic chain is important for either homotropic cooperativity and/or the heterotropic interactions in aspartate carbamoyltransferase, site-specific mutagenesis was used to replace Asp-236 with alanine. The mutant enzyme exhibits full activity and a loss of both homotropic cooperativity and heterotropic interactions. Furthermore, the aspartate concentration at half the maximal observed specific activity is reduced by approximately 8-fold. The mutant enzyme exhibits normal thermal stability but drastically altered reactivity toward p-hydroxymercuribenzoate. The catalytic subunit of the mutant and wild-type enzymes have very similar properties. These results, in conjunction with previous experiments, suggest that the intersubunit link involving Asp-236 is involved in the stabilization of the 240s loop in its tight-state position and that the regulatory subunits exert their effect on the catalytic subunits by influencing the position of the 240s loop.

Alanine↗

Characterization of the interaction between DARPP-32 and protein phosphatase 1 (PP-1): DARPP-32 peptides antagonize the interaction of PP-1 with binding proteins.

The catalytic subunit of PP-1 (PP-1C) is potently inhibited (IC50, approximately 1 nM) by DARPP-32 (dopamine- and cAMP-regulated phosphoprotein, M(r) 32,000), inhibitor-1, and inhibitor-2. The NH2-terminal 50 amino acid residues of DARPP-32 and inhibitor-1 are similar, and phosphorylation of a common threonine residue (Thr-34/Thr-35) is necessary for inhibition of PP-1C. We have characterized further the interaction between DARPP-32 and PP-1C. Using synthetic peptides derived from the NH2-terminal region of DARPP-32, residues 6-11, RKKIQF, have been shown to be required for inhibition of PP-1C. Peptides containing this motif were able to antagonize the inhibition of PP-1C by phospho-DARPP-32 and phosphoinhibitor-1. The inhibition of PP-1C by inhibitor-2, but not by okadaic acid, microcystin, or calyculin A, was also attentuated by these antagonist peptides. These results together with results from other studies support a model in which two subdomains of phospho-DARPP-32 interact with PP-1C. The region encompassing phospho-Thr-34 appears to interact with the active site of the enzyme blocking enzyme activity. The region encompassing the RKKIQF motif binds to a domain of PP-1C removed from the active site. Amino acid sequence analysis indicates that basic and hydrophobic features of the RKKIQF motif are conserved in the binding domains of certain PP-1C targeting proteins, suggesting that interaction of inhibitor proteins and targeting proteins may be mutually exclusive.

Amino Acid Sequence↗

Role of the catalytic serine in the interactions of serine proteinases with protein inhibitors of the serpin family. Contribution of a covalent interaction to the binding energy of serpin-proteinase complexes.

The contribution of a covalent bond to the stability of complexes of serine proteinases with inhibitors of the serpin family was evaluated by comparing the affinities of beta-trypsin and the catalytic serine-modified derivative, beta-anhydrotrypsin, for several serpin and non-serpin (Kunitz) inhibitors. Kinetic analyses showed that anhydrotrypsin had little or no ability to compete with trypsin for binding to alpha 1-proteinase inhibitor (alpha 1PI), plasminogen activator inhibitor 1 (PAI-1), antithrombin (AT), or AT-heparin complex when present at up to a 100-fold molar excess over trypsin. By contrast, equimolar levels of anhydrotrypsin blocked trypsin binding to non-serpin inhibitors. Equilibrium binding studies of inhibitor-enzyme interactions monitored by inhibitor displacement of the fluorescence probe, p-aminobenzamidine, from the enzyme active site, confirmed that the binding of serpins to anhydrotrypsin was undetectable in the case of alpha 1PI or AT (KI > 10(-5) M), of low affinity in the case of AT-heparin complex (KI 7-9 x 10(-6) M), and of moderate affinity in the case of PAI-1 (KI 2 x 10(-7) M). This contrasted with the stoichiometric high affinity binding of the serpins to trypsin as well as of the non-serpin inhibitors to both trypsin and anhydrotrypsin. Maximal KI values for serpin-trypsin interactions of 1 to 8 x 10(-11) M, obtained from kinetic analyses of association and dissociation rate constants, indicated that the affinity of serpins for trypsin was minimally 4 to 6 orders of magnitude greater than that of anhydrotrypsin. Anhydrotrypsin, unlike trypsin, failed to induce the characteristic fluorescence changes in a P9 Ser-->Cys PAI-1 variant labeled with a nitrobenzofuran fluorescent probe (NBD) which were shown previously to report the serpin conformational change associated with active enzyme binding. These results demonstrate that a covalent interaction involving the proteinase catalytic serine contributes a major fraction of the binding energy to serpin-trypsin interactions and is essential for inducing the serpin conformational change involved in the trapping of enzyme in stable complexes.

Animals↗

The molecular interaction of Fas and FAP-1. A tripeptide blocker of human Fas interaction with FAP-1 promotes Fas-induced apoptosis.

Fas (APO-1/CD95), which is a member of the tumor necrosis factor receptor superfamily, is a cell surface receptor that induces apoptosis. A protein tyrosine phosphatase, Fas-associated phosphatase-1 (FAP-1), that was previously identified as a Fas binding protein interacts with the C-terminal 15 amino acids of the regulatory domain of the Fas receptor. To identify the minimal region of the Fas C-terminal necessary for binding to FAP-1, we employed an in vitro inhibition assay of Fas/FAP-1 binding using a series of synthetic peptides as well as a screen of random peptide libraries by the yeast two-hybrid system. The results showed that the C-terminal three amino acids (SLV) of human Fas were necessary and sufficient for its interaction with the third PDZ (GLGF) domain of FAP-1. Furthermore, the direct cytoplasmic microinjection of this tripeptide (Ac-SLV) resulted in the induction of Fas-mediated apoptosis in a colon cancer cell line that expresses both Fas and FAP-1. Since t(S/T)X(V/L/I) motifs in the C termini of several other receptors have been shown to interact with PDZ domain in signal transducing molecules, this may represent a general motif for protein-protein interactions with important biological functions.

Adaptor Proteins, Signal Transducing↗

Characterization of the interactions between the small GTPase Cdc42 and its GTPase-activating proteins and putative effectors. Comparison of kinetic properties of Cdc42 binding to the Cdc42-interactive domains.

The small GTPase Cdc42 interacts with multiple factors to transduce diverse intracellular signals. The factors that preferentially recognize the GTP-bound, active state of Cdc42 include a panel of GTPase-activating proteins (GAPs), the Cdc42/Rac interactive binding (CRIB) motif-containing molecules, and the RasGAP domain containing IQGAP1 and IQGAP2. In the present study, we have determined the kinetic parameters underlying the functional interactions between the Cdc42-binding domains of some of these factors and Cdc42 by monitoring the continuous release of gammaPi and have compared the ability of the domains to bind to Cdc42. The catalytic efficiencies (Kcat/Km) of the GAP domains of Bcr, 3BP-1, and p190 on Cdc42 are found to be 60-, 160-, and over 500-fold less than that of Cdc42GAP, respectively, and the differences are due, to a large part, to differences in Km. The Km values of the GAP domains compare well to the binding affinity to the guanylyl imidodiphosphate-bound Cdc42, suggesting a rapid equilibrium reaction mechanism. The affinity of the Cdc42-binding domains of the CRIB motif of Wiskott-Aldrich Syndrome protein and p21(cdc42/rac)-activated kinase 1, and the RasGAP-related domain of IQGAP1, which all inhibit the intrinsic rate of GTP hydrolysis of Cdc42, are found to be 4, 0.7, and 0.08 microM, respectively. These quantitative analysis provide insight that Cdc42GAP functions as an effective negative regulator of Cdc42 by fast, relatively tight binding to the GTP-bound Cdc42, whereas IQGAP1 interacts with Cdc42 as a putative effector with over 10-fold higher affinity than the CRIB domains and GAPs, and suggest that various GAPs and effectors employ distinct mechanism to play roles in Cdc42-mediated signaling pathways.

Binding Sites↗

Pathway of complex formation between DNA and three subunits of CBF/NF-Y. Photocross-linking analysis of DNA-protein interaction and characterization of equilibrium steps of subunit interaction and dna binding.

In this study, we used a photocross-linking method to identify specific contact of CCAAT-binding factor (CBF) subunits in a CBF-DNA complex. The analysis showed that all three subunits in the CBF-DNA complex were cross-linked to DNA and that CBF-B and CBF-C were cross-linked more strongly than CBF-A. None of the CBF-A and CBF-C subunits, which together formed a CBF-A/CBF-C heterodimer, were cross-linked without CBF-B; in contrast, CBF-B was cross-linked in the absence of CBF-A/CBF-C. No subunit of heterotrimeric CBF containing DNA-binding domain mutant of either CBF-B or CBF-C was cross-linked to DNA, and interestingly, cross-linking of CBF-B that occurred without CBF-A/CBF-C was inhibited in presence of mutant CBF-C/CBF-A heterodimer. Altogether, these results indicated that the specific DNA contact surface of each CBF subunit is generated as a result of interaction between CBF-B and CBF-A/CBF-C heterodimer and that the three CBF subunits interact interdependently with DNA to form a CBF-DNA complex. Equilibrium interactions among the three CBF subunits and between CBF subunits and DNA were studied by electrophoretic mobility shift assay. This showed that at equilibrium DNA-binding conditions, the CBF-A/CBF-C heterodimer is very stable, but association between CBF-B and CBF-A/CBF-C is very weak. The nature of the association of CBF-B with CBF-A/CBF-C was also revealed by studying the inhibition of CBF-DNA complex formation by the mutant CBF-B. This study indicated that the association between CBF-B and CBF-A/CBF-C is stabilized upon interaction with DNA, a process likely to favor formation of a high-affinity CBF-DNA complex.

Bromodeoxyuridine↗