Phytotropins: Conformational requirements for the abolition of the root geotropic response

Compounds of the phytotropin class have been assessed for possible conformational requirements with respect to their ability to aftect the root geotropic response. It is shown that part of the molecule may need to adopt a planar configuration, and evidence is adduced which indicates that the remainder of the molecule may also have conformational requirements which need further definition. It is suggested that molecules which favour a conformation such that the aromatic ring which bears the carboxyl function is out of plane with the remainder of the molecule may have activity. Coplanarity of the carboxyl group with the ring to which it is attached is not a prerequisite for activity.     

Auxins: On the nature of the receptor site and molecular requirements for auxin activity

Suggested structural requirements for auxin activity are defined in terms of the receptor site with which the auxins interact. It is suggested that the site may be planar but for the portion which accepts the oxygen atoms of the carboxylic acid, and that compounds which have appropriate atoms covering postulated critical areas will have auxin activity. It is postulated that the area which accepts the indole nucleus is electrophilic in nature.     

Phytotropins: III. NAPHTHYLPHTHALAMIC ACID BINDING SITES ON MAIZE COLEOPTILE MEMBRANES AS POSSIBLE RECEPTOR SITES FOR PHYTOTROPIN ACTION

Certain members of the phytotropin class of auxin transport inhibitors are shown to bind with high affinity to the known naphthylphthalamic acid binding sites in maize (Zea mays) coleoptiles. The binding site is, thus, a phytotropin binding site. In general, the degree of binding correlates with the phytotropin structure activity rules and with physiological activities of model compounds. It is argued that the binding site may be a receptor, and it also may be the receptor involved in the control of the auxin transport process. The possibility is raised that the binding sites may be intrinsic receptors for endoanalog(s) of the phytotropins.     

A conformational study of the topographical requirements of a phytotropin recognition site on the naphthylphthalamic acid receptor

Phytotropins are a group of chemicals which have the ability to abolish the gravitropic response in plants by inhibiting the polar movement of auxin in the plant. They have other physiological properties such as inhibiting the phototropic response of stems. They bind to the naphthylphthalamic acid receptor and may elicit their physiological responses by this means. Most phytotropins consist of a benzoic acid moiety substituted at the ortho position by a bridging group connected to a second aryl group. Conformational energy calculations were performed on a subset of phytotropins. The calculations yielded a single, low energy conformation common to each molecule and thus identified three dimensional requirements for binding to the receptor. Electrostatic potential calculations, in the vicinity of the benzoic acid moiety, identified recognition and binding requirements for this group. Similar calculations for the second aryl group indicated that some similarity exists between the electrostatic potentials of molecules which bind most tightly to the receptor. The revised binding model was assessed by consideration of a second series of molecules showing phytotropic activity. The model was consistent with the biological activities of these molecules.     

Phytotropin-induced root phototropism in maize

Phytotropins, even those not absorbing in the visible region of the spectrum, can induce a phototropic response in maize ( Zea mays L. cv. PX-75) roots when illuminated unilaterally with white light. The most active phytotropin, 2-(1-pyrenoyl) benzoic acid (PBA) can elicit a full response at 10 μ M , while the other active molecules, 2-carboxyphenyl-3-phenylpropane-1,3-dione (CPD), 2-carboxyphenyl-3-phenyl-1,2-pyrazole (CPP), 1-N-naphthylphthalamic acid (NPA) and erythrosin elicit a full response at 100 μ M . The less active phytotropins BBA and fluorescein give a reduced response. It is suggested that the observed effect cannot be explained solely on the basis of auxin transport inhibition. There is a photoreceptor in the extension zone of the root, which may be associated in some way with the receptor for NPA. The results are consistent with the proposal that the phototropic process may form part of the root gravitropic response mechanism.     

The Structure-taste Relationships of Aspartyl Dipeptide Esters

The molecular features common to sweet-tasting dipeptide esters are described. The molecular features of sweet amino acids were represented by the Fischer projection formulas and sweet peptides were related to the sweet amino acids through the Fischer projection formulas of the peptides. It was concluded that a peptide is sweet when it takes the formula 5a, whereas when it takes the formula 5b it is not sweet. It was also concluded that a third binding site (R₁ in 5a) besides the postulated AH–B system in a sweet molecule is necessary for an intense sweetness potency. The location of the site in the molecule relative to the AH–B system is important, as well as the shape and size of this site, because the third binding site is considered to participate in hydrophobic interaction with a similar binding site on the taste receptor. Increased sweetness is observed when these requirements are satisfied.     

Structural Requirements for the Action of Neurohypophyseal Hormones upon the Isolated Amphibian Urinary Bladder

The response of the isolated amphibian urinary bladder to thirty-four structural analogs of arginine vasotocin was determined in an effort to define the physiological significance of specific structural groups on the hormone molecule. All but one of the analogs tested possessed full intrinsic activity in this system but varied greatly in their affinity for the receptor site. An analysis of the effect of changes in hydrogen ion concentration upon the response of the bladder to oxytocin was performed in order to determine the number and nature of the ionizable groups involved in hormone receptor interaction. Two ionizable groups with apparent pK's of 7.1 and 7.75 were found to be important in determining the magnitude of the hormonal response. On the basis of the results it was postulated that hormone-receptor interaction can be considered a two-step process: (a) The binding or attachment of hormone to receptor site through ionic, hydrogen, and hydrophobic bonds and (b) a disulfide interchange reaction between hormonal disulfide and receptor sulfhydryl. The latter step is considered to be the reaction which initiates the chain of events leading to the observed change in permeability.     

Binding of N-Acetylglucosamine (GlcNAc) β1-6-branched Oligosaccharide Acceptors to β4-Galactosyltransferase I Reveals a New Ligand Binding Mode

N-Acetyllactosamine is the most prevalent disaccharide moiety in the glycans on the surface of mammalian cells and often found as repeat units in the linear and branched polylactosamines, known as i- and I-antigen, respectively. The β1-4-galactosyltransferase-I (β4Gal-T1) enzyme is responsible for the synthesis of the N-acetyllactosamine moiety. To understand its oligosaccharide acceptor specificity, we have previously investigated the binding of tri- and pentasaccharides of N-glycan with a GlcNAc at their nonreducing end and found that the extended sugar moiety in these acceptor substrates binds to the crevice present at the acceptor substrate binding site of the β4Gal-T1 molecule. Here we report seven crystal structures of β4Gal-T1 in complex with an oligosaccharide acceptor with a nonreducing end GlcNAc that has a β1-6-glycosidic link and that are analogous to either N-glycan or i/I-antigen. In the crystal structure of the complex of β4Gal-T1 with I-antigen analog pentasaccharide, the β1-6-branched GlcNAc moiety is bound to the sugar acceptor binding site of the β4Gal-T1 molecule in a way similar to the crystal structures described previously; however, the extended linear tetrasaccharide moiety does not interact with the previously found extended sugar binding site on the β4Gal-T1 molecule. Instead, it interacts with the different hydrophobic surface of the protein molecule formed by the residues Tyr-276, Trp-310, and Phe-356. Results from the present and previous studies suggest that β4Gal-T1 molecule has two different oligosaccharide binding regions for the binding of the extended oligosaccharide moiety of the acceptor substrate.     

The selectivity of tyrosine 280 of human 11beta-hydroxysteroid dehydrogenase type 1 in inhibitor binding

11beta-Hydroxysteroid dehydrogenase type 1 is a homodimer where the carboxyl terminus of one subunit covers the active site of the dimer partner. Based on the crystal structure with CHAPS, the carboxyl terminal tyrosine 280 (Y280) has been postulated to interact with the substrate/inhibitor at the binding pocket of the dimer partner. However, the co-crystal structure with carbenoxolone argues against this role. To clarify and reconcile these findings, here we report our mutagenesis data and demonstrate that Y280 is not involved in substrate binding but rather plays a selective role in inhibitor binding. The involvement of Y280 in inhibitor binding depends on the inhibitor chemical structure. While Y280 is not involved in the binding of carbenoxolone, it is critical for the binding of glycyrrhetinic acid.     

Etoxadrol-meta-isothiocyanate: a potent, enantioselective, electrophilic affinity ligand for the phencyclidine-binding site

Etoxadrol-meta-isothiocyanate (2S,4S,6S-2-ethyl-2-(3-isothiocyanatophenyl)-2-piperidyl)1,3-dioxolane, 4a) has been synthesized and characterized as an irreversible ligand for the phencyclidine (PCP)-binding site. It is the first chiral electrophilic affinity ligand for this site to have been described. This affinity ligand is based upon etoxadrol, a 1,3-dioxolane known to have PCP-like effects in vivo and in vitro. Etoxadrol-meta-isothiocyanate was found to be four-five times more potent in vitro than metaphit (1-[1-(3- isothiocyanatophenyl)cyclohexyl]piperidine), the only previously known electrophilic affinity ligand for the PCP-binding site. The binding was shown to be highly enantioselective for etoxadrol-meta-isothiocyanate (4a). The 2R,4R,6R-enantiomer of 4a was essentially inactive. The ability of the 2S,4S,6S-enantiomer (4a) to interact with the benzodiazepine, muscarinic, and mu opioid receptor systems was also examined, and it was found not to interact with these receptor systems. It seems likely that 4a will prove to be a valuable tool in the study of structure and function of the PCP-binding site.     

Synthesis and receptor binding characteristics of [D-Ala2, cysteamine 5] enkephalin, a thiol-containing probe for structural elements of opiate receptors

For the elucidation of structural elements in the opiate receptors, a thiol-containing enkephalin analog [D-Ala2, cysteamine 5]enkephalin, and its dimeric analog were synthesized and evaluated in the radio-ligand receptor binding assays using rat brain membranes. The dimeric analog was very potent in both delta and mu assays. Comparison of receptor affinities of the thiol-containing enkephalin with those of standard mu or delta receptor specific ligands suggested that the mu receptor contains an essential thiol group which may interact with the thiol group at the C-terminus of the enkephalin analog. It also appears that no metal-ion site, postulated for the delta receptors, is present in the delta binding site.     

Different types of opiate agonists interact distinguishably with mu, delta and kappa opiate binding sites

The present studies were undertaken to evaluate whether different types of opiate agonists interact in a distinguishable manner with mu, delta and kappa opiate binding sites. Two approaches were employed: (a) the well known effects of metal ions on opiate agonist binding affinities of subsite selective ligands were studied at mu, delta and kappa sites in rat brain homogenates. Binding parameters were obtained by simultaneous computeranalysis of displacement curves using the prototypic ligands dihydromorphine (DHM), (D-Ala2, D-Leu5) enkephalin (DADL) and ethylketocyclazocine (EKC) of the mu, delta and kappa binding sites respectively. The results show that the effects of metal ions depend not only on the binding site, but also on the ligand under investigation. (b) The interaction of the delta agonist DADL with the mu agonist DHM was investigated at mu binding sites by characterizing the type of competition occurring between the two ligands. The interaction was of the noncompetitive type. It therefore appears that the various opiate agonists either interact preferentially with different parts of a larger receptor site area or bind to topographically distinct sites on a single receptor molecule which are coupled allosterically.     

Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1)

The degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. However, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. In order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (DPE1; a 4-α-glucanotransferase) converts two molecules of maltotriose to a molecule of maltopentaose, which can now be acted on by the degradative enzymes, and one molecule of glucose that can be exported. We have determined the structure of the Arabidopsis plastidial DPE1 (AtDPE1), and, through ligand soaking experiments, we have trapped the enzyme in a variety of conformational states. AtDPE1 forms a homodimer with a deep, long, and open-ended active site canyon contained within each subunit. The canyon is divided into donor and acceptor sites with the catalytic residues at their junction; a number of loops around the active site adopt different conformations dependent on the occupancy of these sites. The “gate” is the most dynamic loop and appears to play a role in substrate capture, in particular in the binding of the acceptor molecule. Subtle changes in the configuration of the active site residues may prevent undesirable reactions or abortive hydrolysis of the covalently bound enzyme-substrate intermediate. Together, these observations allow us to delineate the complete AtDPE1 disproportionation cycle in structural terms.     

A theoretical study of torsional flexibility in the active site of aspartic proteinases: Implications for catalysis

We have performed ab initio Hartree-Fock self-consistent field calculations on the active site of endothiapepsin. The active site was modeled as a formic acid/formate anion moiety (representing the catalytic aspartates, Asp-32 and -215) and a bound water molecule. Residues Gly-34, Ser-35, Gly-217, and Thr-218, which all form hydrogen bonds to the active site, were modeled using formamide and methanol molecules. The water molecule, which is generally believed to function as the attacking nucleophile in catalysis, was allowed to bind to the active site in four distinct configurations. The geometry of each configuration was optimized using two basis sets (4-31G and 4-31G*). The results indicate that in the native enzyme the nucleophilic water is bound in a catalytically inert configuration. However, by rotating the carboxyl group of Asp-32 by about 90° the water molecule can be reorientated to attack the scissile bond of the substrate. A model of the bound enzyme-substrate complex was constructed from the crystal structure of a difluorostatone inhibitor complexed with endothiapepsin. This model suggests that the substrate itself initiates the reorientation of the nucleophilic water immediately prior to catalysis by forcing the carboxyl group of Asp-32 to rotate. The theoretical results predict that the active site of endothiapepsin undergoes a large distortion during substrate binding and this observation has been used to explain some of the kinetics results which have been reported for mutant aspartic proteinases.     

Insulin-binding peptide. Design and characterization

The design and characterization of a six-amino acid-containing peptide that binds insulin is described. The amino acid sequence of the insulin-binding peptide (IBP) was determined from the strand of DNA complementary to the strand of DNA coding for the insulin molecule in the domain of the insulin monomer believed to interact with the insulin receptor. The IBP (Cys-Val-Glu-Glu-Ala-Ser) binds specifically to insulin in a saturable manner with a Kd of 3 nM. This binding process is time dependent and slightly temperature dependent, and the peptide appears to interact with insulin near the carboxyl terminus of the B-chain of insulin. Incubation of insulin with the peptide decreases insulin binding to the insulin receptor by 50%, with no effect on the affinity of insulin for the receptor and no effect on cellular insulin-stimulated deoxyglucose uptake. A polyclonal antibody produced against the IBP will inhibit specific insulin binding to intact cells by approximately 50%, with no effects on insulin-stimulated glucose uptake. From this data, we suggest that there are at least two domains of the insulin molecule through which it interacts with its receptor, the "binding region" of insulin, which is the domain blocked by the IBP, and the "message region" of insulin, through which insulin not only binds to the receptor, but also generates the cellular signal.     

Evidence for the Importance of a Carboxyl Group in the Binding of Ligands to the D2 Dopamine Receptor

A series of group specific modifying reagents were tested for their effects on [3H]spiperone binding to brain D2 dopamine receptors to identify amino acid residues at the binding site of the D2 dopamine receptor that are critical for ligand binding. The dependence of ligand binding to the receptor on the pH of the incubation medium was also examined. N-Acetylimidazole, 5,5'-dithiobis(2-nitrobenzoic acid), 1,2-cyclohexanedione, and acetic anhydride had no specific effect on [3H]spiperone binding, indicating the lack of participation of tyrosine, free sulphydryl, arginine, or primary amino groups in ligand binding to the receptor. N,N'-Dicyclohexylcarbodiimide (DCCD) potently reduced the number of [3H]spiperone binding sites, indicating that a carboxyl group is involved in ligand binding to the receptor. The effects of DCCD could be prevented by prior incubation of the receptor with D2 dopamine receptor selective compounds. The pH-binding profile for [3H]spiperone binding indicated the importance of an ionising group of pKa 5.2 for ligand binding which may be the same carboxyl group. Diethyl pyrocarbonate, the histidine modifying reagent, also inhibited [3H]spiperone binding, reducing the affinity of the receptor for this ligand but the effects were not at the ligand binding site. From the effects of pH changes on ligand binding some evidence was obtained for a second ionising group (pKa 7.0) that specifically affects the binding of substituted benzamide drugs to the receptor. It is concluded that the D2 dopamine receptor binding site contains separate but over-lapping binding regions for antagonists such as spiperone and substituted benzamide drugs. The former region contains an important carboxyl group; the latter region contains another group that may be a second carboxyl group or a histidine.     

Monoclonal antibody to human cytochrome c: Effect on electron-transfer reactions

A monoclonal antibody has been produced to an antigenic site on human cytochrome c which includes amino acid number 58 (isoleucine). This area is on the bottom back of the cytochrome, removed from the postulated binding/reaction sites for oxidase and reductase, but in the area of the molecule where an appreciable change in conformation is seen on oxidation-reduction. In spectrophotometric assays, where binding of cytochrome c to the oxidase or reductase is rate-limiting, the antibody gave stimulation of the reductase reaction under some conditions, where the oxidase reaction was inhibited. Also variation of the pH of the reaction medium resulted in differential effects on the oxidase and reductase reactions. Different effects of the antibody were seen when the oxidase was assayed polarographically, as compared to the spectrophotometric measurements. The data show that the binding/reaction sites on cytochrome c for the oxidase and reductase must be different. They suggest that binding of antibody may affect conformational changes in the whole molecule, distorting the binding/reaction sites. Conformational changes may be involved as a control mechanism in cytochrome c-mediated electron-transfer reactions.     

The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer,demonstrates the exquisite nature of enzyme specificity

Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.     

Allele-specific activation of genetically engineered receptors.

The binding of agonists and antagonists to the beta-adrenergic receptor (beta AR) is postulated to involve an ionic interaction between the amine group of the ligand and the carboxylate side chain of Asp113 in the third hydrophobic domain of the receptor. To explore the importance of this interaction in the binding of ligands to the beta AR, a Ser residue was substituted for Asp113, and the ability of this mutant receptor to respond to compounds which could potentially interact with the hydroxyl side chain of the Ser residue was assessed. The mutant receptor was fully activated by catechol-containing esters and ketones, compounds which did not activate the wild-type beta AR. The demonstration that the molecular substitution of a single amino acid residue can alter the ligand binding specificity of the beta AR provides evidence that the chemical nature of this residue is a critical determinant in the recognition site of the receptor. Further, the ability to modify the specificity of a receptor by the replacement of amino acids at the binding site demonstrates the potential for the rational design of drugs which function specifically at genetically engineered receptors.     

Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

The interleukin-1 receptor (IL-1R) is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1) ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD) simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.