Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM4

Ligand-gated ion channels (LGICs) significantly modulate anesthetic effects. Their exact molecular structure remains unknown. This has led to ambiguity regarding the proper amino acid alignment within their 3D structure and, in turn, the location of any anesthetic binding sites. Current controversies suggest that such a site could be located in either an intra- or intersubunit locale within the transmembrane domain of the protein. Here, we built a model of the glycine alpha one receptor (GlyRa1) based on the open-state structures of two new high-resolution ion channel templates from the prokaryote, Gloebacter violaceus (GLIC). Sequence scoring suggests reasonable homology between GlyRa1 and GLIC. Three of the residues notable for modulating anesthetic action are on transmembrane segments 1-3 (TM1-3): (ILE229, SER 267, and ALA 288). They line an intersubunit interface, in contrast to previous models. However, residues from the fourth transmembrane domain (TM4) that are known to modulate a variety of anesthetic effects are quite distant from this putative anesthetic binding site. While this model can account for a large proportion of the physicochemical data regarding such proteins, it cannot readily account for the alterations on anesthetic effects that are due to mutations within TM4.     

Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor

It is well known that G protein-coupled receptors are prime targets for drug discovery. At the present time there is only one protein from this class that has an X-ray crystal structure, bovine rhodopsin. Crystal structures of rhodopsin have become invaluable templates for the modeling of class-A G protein-coupled receptors as they likely represent the overall topology of this family of proteins. However, because of low sequence homology within the class and the inherent mobility of integral membrane proteins, it is unlikely that this single structural template reflects the ensemble of conformations accessible for any given receptor. We have devised a procedure based upon comparative modeling that uses induced fit modeling coupled with binding site expansion. The modeling protocol enables an ensemble approach to binding mode prediction. The utility of models for β-2 adrenergic receptor will be discussed.     

A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor

GABA(C) (rho) receptors are members of the Cys-loop superfamily of neurotransmitter receptors, which includes nicotinic acetylcholine (nACh), 5-HT(3), and glycine receptors. As in other members of this family, the agonist binding site of GABA(C) receptors is rich in aromatic amino acids, but while other receptors bind agonist through a cation-pi interaction to a tryptophan, the GABA(C) binding site has tyrosine at the aligning positions. Incorporating a series of tyrosine derivatives at position 198 using unnatural amino acid mutagenesis reveals a clear correlation between the cation-pi binding ability of the side chain and EC(50) for receptor activation, thus demonstrating a cation-pi interaction between a tyrosine side chain and a neurotransmitter. Comparisons among four homologous receptors show variations in cation-pi binding energies that reflect the nature of the cationic center of the agonist.     

SeqFold – fully automated fold recognition and modeling software – evaluation and application

SeqFold is a fold recognition program based on sequence-similarity detection aided by predicted secondary structure [1–3]. Critical validation and evaluation of SeqFold fold recognition performance based on the latest Critical Assessment of protein Structure Prediction (CASP2) targets has been performed. It has revealed that four out of seven CASP2 threading targets were assigned a correct fold using this method. SeqFold has also been applied to the problem of fold recognition for leptin. Mice with a defective leptin gene are extremely obese and diabetic. Leptin does not exhibit clear sequence homology to any protein with known structure. SeqFold predicts that leptin belongs to the class of short-chain four-helical cytokines. The structure of leptin, which has recently been solved by X-ray crystallography, reveals that leptin is a long-chain four-helical cytokine. The 3D model of leptin demonstrates that SeqFold alignment-based homology modeling captures essential features of the leptin structure. Received: 25 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Cyclodextrin‐Templated Porphyrin Nanorings

α‐ and β‐Cyclodextrins have been used as scaffolds for the synthesis of six‐ and seven‐legged templates by functionalizing every primary CH₂OH with a 4‐pyridyl moiety. Although these templates are flexible, they are very effective for directing the synthesis of macrocyclic porphyrin oligomers consisting of six or seven porphyrin units. The transfer of chirality from the cyclodextrin templates to their nanoring hosts is evident from NMR and circular dichroism spectroscopy. Surprisingly, the mean effective molarity for binding the flexible α‐cyclodextrin‐based template within the six‐porphyrin nanoring (74 M ) is almost as high as for the previously studied rigid hexadentate template (180 M ). The discovery that flexible templates are effective in this system, and the availability of a template with a prime number of binding sites, open up many possibilities for the template‐directed synthesis of larger macrocycles.     

Identification of the druggable concavity in homology models using the PLB index

Identification of the druggable concavity, in which drug-like molecules are highly inclined to bind, is an important step in structure-based drug design. We previously proposed an index named PLB (propensity for ligand binding), which is based on the amino acid composition characteristically observed at the small molecule binding sites in the X-ray structures of the complexes between proteins and drug-like small molecules. The PLB index was proven to be useful in identifying the druggable concavities in the quality X-ray structures of proteins. Here, we apply the PLB to predicting the druggable concavity in target proteins using the structures of homologous proteins constructed by homology modeling. In this study, we assembled a set of reference proteins that were accurately determined by X-ray analysis in forms of complexes with drug-like small molecules. Homology models for the reference protein were constructed using multiple homologous proteins as templates. The PLB index was then used to predict the druggable concavity. If the template protein in a complex with a drug-like small molecule was used, the druggable concavity was predicted well, with a prediction rate of 78%. When only the apo protein was available as the template, the practical prediction rate was 71%. Interestingly, even when the percent sequence identity between the reference and template proteins was lower than 30, the PLB index could successfully identify the druggable concavity in some cases. This study demonstrates the practical value of applying the PLB index to identifying the drugabble concavity in the homology model.     

Simulation of conformational changes occurring when a protein interacts with its receptor

In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subjected to additional modeling refinements to improve the side chain geometry. Comparing the theoretical and experimental complexes in term of structural and energetic factors is resulted that the refined theoretical complexes became more similar to the experimental ones. We applied the same procedure within an homology modeling experiment, using as templates the experimental structures of human interleukin-1beta (IL-1beta) unbound and bound with its receptor, to build models of the homologous proteins from mouse and trout in unbound and bound conformations and to simulate the interaction with the related receptors. Our results suggest that homology modeling techniques are sensitive to differences between bound and unbound conformations, and that modeling with accuracy the side chains in the complex improves the interaction and molecular recognition. Moreover, our refinement procedure could be used in protein-protein interaction studies and, also, applied in conjunction with rigid-body docking when is not available the protein-bound conformation.     

Ginkgolides and glycine receptors: a structure-activity relationship study

Ginkgolides from the Ginkgo biloba tree are diterpenes with a cage structure consisting of six five-membered rings and a unique tBu group. They exert a variety of biological properties. In addition to being antagonists of the platelet activating factor receptor (PAFR), it has recently been shown that native ginkgolides are potent and selective antagonists of the inhibitory glycine receptor. Forty new ginkgolide derivatives have been prepared in good to high yields on milligram scales and investigated for their antagonistic properties at homomeric alpha 1 glycine receptors, thus providing the first structure-activity relationship study of ginkgolides at glycine receptors. A high-throughput screening assay showed that native ginkgolide C was the most potent ligand, and that manipulation of any of the hydroxyl groups led to loss of activity at alpha 1 glycine receptors.     

Molecular Modeling of the Binding of the Allosteric Inhibitor Optactin at a New Binding Site in Neuraminidase A from <Emphasis Type="Italic">Streptococcus pneumoniae</Emphasis>

Neuraminidase A (NanA) from the pathogenic bacteria Streptococcus pneumoniae catalyzes the cleavage of terminal sialic acid residues from oligosaccharide receptors on the surface of human respiratory epithelium cells and is considered to be the key virulence factor. The search for new regulatory ligand-binding sites in the structure of this enzyme is of fundamental interest and can reveal new targets to design drugs for treating pneumonia, meningitis, and other human infectious diseases. The low molecular weight compound optactin has been recently shown to inhibit the activity of the homologous Neuraminidase B (NanB). Furthermore, optactin binds at a separate site of the protein structure, which is topologically different from the catalytic center. The bioinformatic and structural analysis using the pocketZebra method was used to annotate a new, previously unknown site in the NanA structure. This new site is analogous to the optactin binding site in NanB and characterized by the high content of subfamily-specific positions, what indicates the importance of this site for the enzyme function. Molecular modeling was used to study optactin binding at the allosteric sites of the homologous neuraminidases NanA and NanB. Tyr250, Thr251, Lys334, Gln494, Lys499, Lys597, Thr657, and Glu658 residues were shown to stabilize the optactin molecule in the NanB structure, with water molecules playing an important role in the coordination of the ligand. Molecular modeling has shown that optactin binding by NanA is complicated due to substitutions in the subfamily-specific positions of the allosteric center. The peculiarities of the structural organization of the new NanA binding site facilitate the targeted search for complementary ligands that can selectively regulate the activity of this enzyme.     

Molecular modeling and mutagenesis reveals a tetradentate binding site for Zn2+ in GABA(A) alphabeta receptors and provides a structural basis for the modulating effect of the gamma subunit

Gamma-aminobutyric acid type A receptors (GABA(A)-R) containing alpha1beta2gamma2 subunits are weakly inhibited by Zn2+, whereas receptors containing only the alpha1beta2 subunits are strongly inhibited. We built homology models of the ion pores of alpha1beta2 and alpha1beta2gamma2 GABA(A)-R using coordinates of the nicotinic acetylcholine receptor as a template. Threading the GABA(A)-R beta2 sequence onto this template placed the 17' histidine and the 20' glutamate residues at adjacent locations in the mouth of the pore, such that a nearly ideal tetradentate site for Zn2+ was formed from two histidine and two glutamate residues between adjacent beta subunits in the alpha1beta2 GABA(A)-R. Following optimization with CHARMM, the distance between the alpha-carbons of the adjacent histidine residues was approximately 9.2 A, close to the ideal distance for a Zn2+ binding site. Loss of inhibition by Zn2+ in alpha1beta2gamma2 GABA(A)-R can be explained by the geometry of these residues in the arrangement alpha1beta2gamma2alpha1beta2, in which the nearest C-alpha-C-alpha distance between the histidine residues is 15.5 A, too far apart for an energetically optimal Zn2+ binding site. We then mutated the gamma subunit at the 17' and/or 20' positions. Zn2+ inhibition was not restored in alpha1beta2gamma2 (I282H) receptors. A novel finding is that the modeling shows the native 20' lysine in gamma2 can compete with Zn2+ for binding to the inserted 17' histidine. Sensitivity to Zn2+ was restored in the double mutant receptor, alpha1beta2gamma2 (I282H; K285E), in which the competition with lysine was removed and a more favorable Zn2+ binding site was formed.     

Water‐Soluble Molecularly Imprinted Nanoparticles (MINPs) with Tailored,Functionalized, Modifiable Binding Pockets

Construction of receptors with binding sites of specific size, shape, and functional groups is important to both chemistry and biology. Covalent imprinting of a photocleavable template within surface–core doubly cross‐linked micelles yielded carboxylic acid‐containing hydrophobic pockets within the water‐soluble molecularly imprinted nanoparticles. The functionalized binding pockets were characterized by their binding of amine‐ and acid‐functionalized guests under different pH values. The nanoparticles, on average, contained one binding site per particle and displayed highly selective binding among structural analogues. The binding sites could be modified further by covalent chemistry to modulate their binding properties.     

A tetradecanuclear copper dimeric macrocyclic complex with a body-centred heptanuclear core-structure and magnetism

2,6-Diformyl-4-methylphenol and 1,3-diamino-2-hydroxypropane template condense in the presence of Cu(NO(3))(2) and azide to produce a 3 : 3 macrocyclic ring containing an unprecedented grouping of seven copper(ii) ions within the macrocyclic cavity, with the seventh metal completing a body-centred heptanuclear lattice.     

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling.     

Optimal attachment position and linker length promote native-like character of cavitand-based template-assembled synthetic proteins (TASPs)

We have designed, synthesised and characterised a series of template-assembled de novo four-helix bundles, each differing in the linker length between the template and the peptides. The helix is based on an earlier peptide sequence: EELLKKLEELLKKLG (first-generation sequence), which was designed to link the hydrophilic/hydrophobic interface of the helices. Increasing or decreasing the linker length by one glycine residue had a significant effect on the structure and properties of the template-assembled synthetic proteins (TASPs). Here, the effect of the linker length is further probed by linking the peptides closer to the hydrophobic face by using the second-generation sequence, AEELLKKLEELLKKG, in an effort to improve the packing between the helices and to better understand the helical bundles. The peptides were synthesised with 0-4 Gly linker residues and linked onto a cavitand template. The proteins were found to be alpha-helical, stable to guanidine hydrochloride (GuHCl) and to unfold cooperatively. However, their stabilities toward GuHCl, propensity to self-aggregate and structural specificity differed. The two-glycine variant of the second-generation series demonstrated the highest stability and most native-like character of all the mononeric TASPs in both the first- and second-generation series. The structural specificity of this two glycine variant is comparable to that of other known native-like de novo proteins. Molecular dynamics simulations showed that the two-glycine variant contains helices that are tilted with respect to the cavitand template and may account for its unique properties.     

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.     

Tailored polymer-supported templates in dynamic combinatorial libraries: simultaneous selection, amplification and isolation of synthetic receptors

The thermodynamically controlled synthesis and isolation of macrocyclic receptors from dynamic combinatorial libraries has been achieved in a single step using a polymer-supported template. The templates were cinchona alkaloids which show interesting enantio- and diastereoselective molecular recognition events in libraries based on pseudo-dipeptide building blocks. The synthetic routes used to derivatise the alkaloids and attach them to polymer supports minimised any influence of the tethering linkage on the templating activity. Systematic studies have been carried out to probe how the polymer morphology and the template loading affect the selectivity and isolation yield of the macrocyclic receptors. Molecular recognition between solid-phase bound templates and selected receptors also enabled their affinity-type chromatographic separation.     

Biaryl amino acid templates in place of D-Pro-L-Pro in cyclic beta-hairpin cationic antimicrobial peptidomimetics

The turn-forming D-Pro-L-Pro template has been frequently used to promote regular beta-hairpin conformations in cyclic protein epitope mimetics. Here the use of three isomeric biaryl templates has been studied as alternatives to D-Pro-L-Pro in the preparation of beta-hairpin peptidomimetics. The o,o'- o,m'- and m,m'-isomers of carboxymethyl- and aminomethyl-substituted biaryl templates have been incorporated into novel macrocyclic mimics of the naturally occurring cationic antimicrobial peptide protegrin I. The presence of the o-carboxymethyl-o'-aminomethyl-biaryl template within the macrocyclic peptide resulted in the appearance of slowly interconverting atropisomers. Although none of the resulting mimetics adopted stable beta-hairpin structures in aqueous solution, they all nevertheless retained a significant antimicrobial activity against Gram positive and Gram negative bacteria. These mimetics provide interesting starting points for an optimization program in the search for potent and novel antimicrobial compounds.     

A common motif in G-protein-coupled seven transmembrane helix receptors

Summary G-protein-coupled receptors all share the seven transmembrane helix motif similar to bacteriorhodopsin. This similarity was exploited to build models for these receptors. From an analysis of a multi-sequence alignment of 225 G-protein-coupled receptors belonging to the rhodopsin-like superfamily, conclusions could be drawn about functional residues. Seven residues in the transmembrane regions are conserved throughout all aligned receptors. These residues cluster at the cytosolic side of the transmembrane helices and are for all rhodopsin-like G-protein-coupled receptors implied in signal transduction. An analysis of correlated mutations reveals a number of residues, both in the helices and in the cytosolic loops, that might be important in the signal transduction pathway in subfamilies of this receptor family.     

Molecular modeling of A1 and A2A adenosine receptors: comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies

Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors. The homology models of adenosine A1 and A2A receptors were constructed. The high-resolution X-ray structure of bovine rhodopsin and crystal structure of beta2-adrenergic receptor were used as templates. The binding sites of the A1 and A2A ARs were constructed by using data obtained from mutagenesis experiments as well as docking simulations of the respective AR antagonsists DPCPX and XAC. To compare rhodopsin- and beta2-adrenergic-based models, the binding mode of A1 (KW-3902, LUF-5437) and A2A (KW-6002, ZM-241385) ARs antagonists were also examined. The differences in the binding ability of both models were noted during the study. The beta2-adrenergic-based A2A AR model was much more capable to stabilize the ligand in the binding site cavity than the corresponding rhodopsin-based A2A AR model, however, such differences were not so clear in case of A1 AR models. It was suggested that for the A1 AR it is possible to use the crystal structure of rhodopsin as a template as well as beta2-adrenergic receptor, but for A2A AR, with the now available beta2-adrenergic receptor X-ray structure, docking studies should be avoided on the rhodopsin-based model. However, taking into account that the beta2AR shares about 31% of the residues with the AR in comparison to 21% in case of bRho, we suggest using beta2-adrenergic-based models for the A1 and A2A ARs for further in silico ligand screening also because of their generally better ability to stabilize ligands inside the binding pocket.     

Structure-directing role of molecules containing benzyl rings in the synthesis of a large-pore aluminophosphate molecular sieve: an experimental and computational study

We describe the synthesis of AlPO-5 and SAPO-5 materials (AFI topology) using five different tertiary amines or quaternary ammonium ions containing one or two benzyl rings as structure-directing agents (SDAs). All of the molecules successfully direct the crystallization of AlPO-5; however, only the most efficient templates are able to crystallize SAPO-5. The observed differences in template efficiency can be rationalized in terms of the interaction energy between these molecules and the AFI framework. In ranking the template molecules, we notice that a well-defined molecular shape enhances the templating ability, but molecules that are too rigid are not able to adapt to the AlPO framework, yielding an inferior templating ability. Results of atomic-level modeling show that templates with one benzyl ring self-assemble in the main AFI channel by forming dimers with the benzyl rings parallel to each other; templates with two benzyl rings assemble instead into longer chains in which the benzyl ring of one molecule faces the ring of the subsequent one. Both mono- and dibenzyl templates show a high space-filling ability in AFI. Kinetic and thermodynamic factors that might affect the structure-directing activity of the molecules are examined.