Transformation of 2,4,6-trinitrotoluene (TNT) by Raoultella terrigena.

Manufacture of nitroorganic explosives generates toxic wastes leading to contamination of soils and waters, especially groundwater. For that reason bacteria living in environments highly contaminated with 2,4,6-trinitrotoluene (TNT) and other nitroorganic compounds were investigated for their capacity for TNT degradation. One isolate, Raoultella terrigena strain HB, removed TNT at concentrations between 10 and 100 mg l(-1) completely from culture supernatants under optimum aerobic conditions within several hours. Only low concentrations of nutrient supplements were needed for the cometabolic transformation process. Radioactivity measurements with ring-labelled (14)C-TNT detected about 10-20% of the initial radioactivity in the culture supernatant and the residual 80-90% as water-insoluble organic compounds in the cellular pellet. HPLC analysis identified aminodinitrotoluenes (2-ADNT, 4-ADNT) and diaminonitrotoluenes (2,4-DANT) as the metabolites which remained soluble in the culture medium and azoxy-dimers as the main products in the cell extracts. Hence, the new isolate could be useful for the removal of TNT from contaminated waters.

Accurate prediction of the bound conformation of galanthamine in the active site of Torpedo californica acetylcholinesterase using molecular docking.

The alkaloid (-)-galanthamine is known to produce significant improvement of cognitive performances in patients with the Alzheimer's disease. Its mechanism of action involves competitive and reversible inhibition of acetylcholinesterase (AChE). Herein, we correctly predict the orientation and conformation of the galanthamine molecule in the active site of AChE from Torpedo californica (TcAChE) using a combination of rigid docking and flexible geometry optimization with a molecular mechanics force field. The quality of the predicted model is remarkable, as indicated by the value of the RMS deviation of approximately 0.5A when compared with the crystal structure of the TcAChE-galanthamine complex. A molecular model of the complex between TcAChE and a galanthamine derivative, SPH1107, with a long chain substituent on the nitrogen has been generated as well. The side chain of this ligand is predicted to extend along the enzyme active site gorge from the anionic subsite, at the bottom, to the peripheral anionic site, at the top. The docking procedure described in this paper can be applied to produce models of ligand-receptor complexes for AChE and other macromolecular targets of drug design.

Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs.

The 3D structure of a complex of the anti-Alzheimer drug galanthamine with Torpedo californica acetylcholinesterase is reported. Galanthamine, a tertiary alkaloid extracted from several species of Amarylidacae, is so far the only drug that shows a dual activity, being both an acetylcholinesterase inhibitor and an allosteric potentiator of the nicotinic response induced by acetylcholine and competitive agonists. The X-ray structure, at 2.5A resolution, shows an unexpected orientation of the ligand within the active site, as well as unusual protein-ligand interactions. The inhibitor binds at the base of the active site gorge, interacting with both the acyl-binding pocket and the principal quaternary ammonium-binding site. However, the tertiary amine group of galanthamine does not directly interact with Trp84. A docking study using the program AUTODOCK correctly predicts the orientation of galanthamine in the active site. The docked lowest-energy structure has a root mean square deviation of 0.5A with respect to the corresponding crystal structure of the complex. The observed binding mode explains the affinities of a series of structural analogs of galanthamine and provides a rational basis for structure-based drug design of synthetic derivatives with improved pharmacological properties. Proteins 2001;42:182-191.

Tolperisone: evaluation of the lidocaine-like activity by molecular modeling.

Tolperisone (1), a muscle relaxant with lidocaine-like activity, was compared to lidocaine (2) by molecular modeling methods. Conformational search analysis has been employed to find the global minima of these compounds along with numerous low energy conformations from which specific conformers were extracted that show good superimposition of the structural features important for protein binding. Two additional compounds, mepi- (3) and bupivacaine (4), were included in the analysis to validate the method as these ligands show very close structural and pharmacological relationship to lidocaine (2) and are assumed to bind to an identical site. As a result we find conformers of all four ligands that have exactly the same position and orientation of the potential sites for hydrogen bonding with the rest of the molecule showing close comparison of the three-dimensional geometry. Semiempirical calculations furthermore reveal good agreement of the electrostatic potentials of these conformations indicating similar interactions with a receptor. We conclude that tolperisone (1) and lidocaine (2) despite their chemical divergence can still attach to identical protein binding sites.

Epitope mapping employing antibodies raised against short synthetic peptides: a study of the nicotinic acetylcholine receptor.

Antibodies were raised against eight synthetic peptides matching preselected portions of the amino acid sequence of nicotinic acetylcholine receptor (nAChR) from Torpedo marmorata. To increase the probability of obtaining antibodies specific for the exact sequence of the immunizing peptide, peptides of only five to seven amino acids in length were employed. Even under these limiting conditions some of the polyclonal rabbit immune sera showed cross-reactivity with other peptides and/or other sequence regions of the receptor. Further studies with polyclonal and monoclonal sera suggested that conformation and charge pattern rather than linear sequence are the essential determinants of antibody epitopes. Application of antibodies for topological studies therefore requires that the antibody specificity for a particular region of the antigen has been firmly established. Epitope mapping with the eight anti-peptide immune sera provides information on the accessibility to antibody of matching sequences within the receptor molecule. We find the sequence portions alpha 81-85, alpha 127-132, and alpha 190-195 to be freely accessible both at membrane-bound and at purified receptor. Binding of anti-alpha 387-392 serum does not prove accessibility of this region as the serum cross-reacts strongly with peptide fragments corresponding to the regions alpha 165-200 and beta 190-200 of nAChR from Torpedo californica. To permit binding of anti-alpha 137-142 immune serum, treatment of the receptor with endoglycosidase is required, showing that Asn-141 indeed is glycosylated in native nAChR. The homologous sequence of the other subunits differing only in one sequence position from alpha 137-142 is not accessible in native nAChR to antibody, indicating clear differences in folding of the receptor polypeptides. Sequence portions alpha 395-401 and alpha 161-166 must first be exposed by appropriate treatment to permit binding of respective serum. These results and previous epitope mapping studies by other laboratories are discussed with respect to the limited sequence specificity of antibodies.

Antibodies as probes of the structure and function of the nicotinic acetylcholine receptor.

Structural and functional studies of the nicotinic acetylcholine receptor from Torpedo marmorata are discussed as examples for the distinct differences in properties of antibodies raised against a native antigen as compared to antibodies raised against short or long synthetic peptides.

A monoclonal antibody interfering with binding and response of the acetylcholine receptor.

Employing a monoclonal antibody raised against the receptor protein, we have probed the mechanism of ligand interaction of the nicotinic acetylcholine receptor from Torpedo marmorata. Antibody WF6 specifically binds to alpha-subunits of the receptor with a stoichiometry of one molecule per receptor monomer. At saturating concentrations, WF6 blocks half of the binding sites for acetylcholine, all of the binding sites for alpha-neurotoxins, and none of the binding sites for representative cholinergic antagonists (with the exception of alpha-toxins) at the receptor. In the presence of saturating concentrations of antibody WF6, acetylcholine (or its agonists) cannot induce T1+ influx into Torpedo membrane vesicles. Rapid oversaturation of the receptor by agonist also cannot overcome this blockade of channel gating. The observed competition patterns of WF6 and representative cholinergic ligands with the receptor are evidence for separate binding sites for groups of ligands and for a network of allosterically linked effector regions at the receptor. The blockade by saturating concentrations of WF6 of the agonist-induced channel gating supports the conclusion that two molecules of agonist are required to activate the receptor-integral ion channel.

Antibodies against preselected peptides to map functional sites on the acetylcholine receptor.

Rabbit immune sera and mouse monoclonal antibodies were raised against the synthetic peptide Tyr-Cys-Glu-Ile-Ile-Val matching in sequence residues 127-132 of the alpha-subunit of all nicotinic acetylcholine receptors sequenced so far. Representative cholinergic ligands did not interfere with the binding of these antibodies to the receptor from Torpedo marmorata, indicating that this sequence is not part of the binding sites for cholinergic ligands. The applicability of antigenic sites analysis to the mapping of functional sites on receptor proteins is discussed.

Antibodies directed against functional sites on the acetylcholine receptor from Torpedo marmorata.

Antibodies directed against functional sites on the acetylcholine receptor from Torpedo marmorata have been obtained by the following two procedures: (i) Our library of monoclonal antibodies raised against the whole receptor protein was screened for antibodies competing with cholinergic agonists, antagonists and local anesthetics for receptor binding, (ii) antibodies were raised against short peptides matching the sequence of predetermined sites on the receptor protein. In this way, a topographic map of the functional sites on the receptor surface can be constructed.

Synthesis and properties of NBD-n-acylcholines, fluorescent analogs of acetylcholine.

We have synthesized a homologous series of fluorescent analogs of acetylcholine, N-7-(4-nitrobenzo-2-oxa-1,3-diazolyl)-omega-amino-n-alkanoic acid beta (N,N,N-trialkylammonium) ethylesters (NBD-n-acylcholines) and report here on their physiological and biochemical properties. All NBD-n-acylcholines trimethylated at the cholinergic nitrogen are agonists of acetylcholine at the frog neuromuscular junction. Their potencies in depolarizing frog muscle cells decrease with decreasing chain length. The affinities of binding to the purified receptor from Electrophorus electricus also decrease with decreasing chain length with a large drop in affinity for the derivatives n = 4 and n = 3. The rate constants of association to acetylcholine receptor and to acetylcholine esterase are of the order of 10(8) M-1 S-1 and do not vary significantly with the chain length of the NBD-n-acylcholines. In contrast, the dissociation rate constants decrease with increasing chain length. The quenching of fluorescence of NBD-n-acylcholines accompanying binding to purified receptor and esterase from E. electricus appears to be due to the formation of a hydrogen bond between the omega-amino group as donor and an unidentified acceptor group in a hydrophobic pocket of the protein. With their advantageous fluorescence properties, their simple pharmacology, and their clear structure-function relationships, these compounds are useful tools for the study of cholinergic mechanisms.

Equilibrium binding of acetylcholine to the membrane-bound acetylcholine receptor.

We have studied the binding of acetylcholine to membrane-bound acetylcholine receptor from Torpedo marmorata employing a highly accurate airfuge assay procedure. At equilibrium the receptor displays two classes of acetylcholine binding sites; these interact with only weak positive cooperativity. As a further difference to binding data deduced from electrophysiological dose/response curves, the equilibrium constants for the two classes of sites (Kd1 = 25 nM, Kd2 = 8 nM) are orders of magnitude lower than the concentration required for half-maximal response. Both the weaker-than-expected cooperativity of sites and the high binding affinities are likely to be due to desensitisation of the receptor during the period of incubation. The positively cooperative interaction of acetylcholine binding sites is only observed with membrane preparations obtained in the presence of appropriate chelating, sulfhydryl-blocking and active-serine-blocking agents. Aged membrane preparations loose the ability of site interactions while only small changes in the total number of binding sites are observed. In the absence of divalent ions, the affinity of binding of acetylcholine to the receptor is reduced. To assess the significance of the binding data obtained, several alternative reaction schemes for non-random binding to two sites at the receptor are considered. In addition, the effects of possible sources of experimental error on the shape of Scatchard plots are analysed.

Agonist-activated ionic channels in acetylcholine receptor reconstituted into planar lipid bilayers.

Planar lipid bilayers were formed with the mixed chain phospholipid 1-stearoyl-3-myristolglycero-2-phosphocholine. Acetylcholine receptor membrane fragments or the purified receptor protein was incorporated into these bilayers by fusing receptor-containing vesicles with the planar membranes a few degrees below the lipid phase transition temperature. Single-channel currents activated by nicotinic agonists in the reconstituted system resembled those observed in intact rat and frog muscle membrane as measured by the patch clamp technique. The observed channel characteristics did not depend on the degree of receptor purification. Thus, the receptor-enriched fragments and those depleted of nonreceptor peripheral peptides, the purified receptor monomer/dimer mixtures, and the isolated receptor monomer as defined by gel electrophoresis all shared similar electrochemical properties in the synthetic lipid bilayer. The agonist-activated ionic channel seems, therefore, to be contained within the receptor monomer.