New alignment strategy for transmembrane proteins.

In this paper an algorithm which locates helical transmembrane segments is described. It is shown that given the location of transmembrane helices of a protein, corresponding helices in another membrane related protein can be pinpointed. The method seems to be extremely insensitive to sequence identity but highly sensitive to the property of a sequence to assume transmembrane helical structure. As an example, using the present method, a sequence alignment between bacteriorhodopsin and human rhodopsin is carried out and it provides a good starting point for homology modeling of this G-protein coupled receptor. It is difficult to obtain this particular alignment using the traditional methods because of poor sequence homology. There are indications that hint at the broader range of applicability of the presented method.

In vitro studies on the role of the peripheral-type benzodiazepine receptor in steroidogenesis.

In vitro studies using isolated cells, mitochondria and submitochondrial fractions demonstrated that in steroid synthesizing cells, the peripheral-type benzodiazepine receptor (PBR) is an outer mitochondrial membrane protein, preferentially located in the outer/inner membrane contact sites, involved in the regulation of cholesterol transport from the outer to the inner mitochondrial membrane, the rate-determining step in steroid biosynthesis. Mitochondrial PBR ligand binding characteristics and topography are sensitive to hormone treatment suggesting a role of PBR in the regulation of hormone-mediated steroidogenesis. Targeted disruption of the PBR gene in Leydig cells in vitro resulted in the arrest of cholesterol transport into mitochondria and steroid formation; transfection of the mutant cells with a PBR cDNA rescued steroidogenesis demonstrating an obligatory role for PBR in cholesterol transport. Molecular modeling of PBR suggested that it might function as a channel for cholesterol. This hypothesis was tested in a bacterial system devoid of PBR and cholesterol. Cholesterol uptake and transport by these cells was induced upon PBR expression. Amino acid deletion followed by site-directed mutagenesis studies and expression of mutant PBRs demonstrated the presence in the cytoplasmic carboxy-terminus of the receptor of a cholesterol recognition/interaction amino acid consensus sequence. This amino acid sequence may help for recruiting the cholesterol coming from intracellular sites to the mitochondria.

Peripheral benzodiazepine receptor in cholesterol transport and steroidogenesis.

Steroidogenesis begins with the metabolism of cholesterol to pregnenolone by the inner mitochondrial membrane cytochrome P450 side-chain cleavage (P450scc) enzyme. The rate of steroid formation, however, depends on the rate of cholesterol transport from intracellular stores to the inner mitochondrial membrane and loading of P450scc with cholesterol. In previous in vitro studies, we demonstrated that a key element in the regulation of cholesterol transport is the mitochondrial peripheral-type benzodiazepine receptor (PBR). We also showed that the polypeptide diazepam binding inhibitor (DBI), an endogenous PBR ligand, stimulates cholesterol transport and promotes loading of cholesterol to P450scc in vitro, and that its presence is vital for hCG-induced steroidogenesis by Leydig cells. Based on these data and the observations that i) the mitochondrial PBR binding and topography are regulated by hormones; ii) the 18-kDa PBR protein is functionally coupled to the mitochondrial contact site voltage-dependent anion channel protein; iii) the 18-kDa PBR protein is a channel for cholesterol, as shown by molecular modeling and in vitro reconstitution studies; iv) targeted disruption of the PBR gene in steroidogenic cells dramatically reduces the ability of the cells to transport cholesterol in the mitochondria and produce steroids; v) endocrine disruptors, with known anisteroidogenic effect, inhibit PBR ligand binding; and vi) in vivo reduction of adrenal PBR expression results in reduced circulating glucocorticoid levels, we conclude that PBR is an indispensable element of the steroidogenic machinery.

Methionyl-tRNA synthetase from Escherichia coli. Absence of interaction between the metal ion and the purine ring of ATP in the L-methionine activation site.

Enhancement of the nuclear relaxation rates by manganese has been used to derive manganese--purine-ring distances in the activation site of methionyl-tRNA synthetase. This is possible with the help of an abortive complex between the enzyme, methionine, adenosine, pyrophosphate and manganese which simulates an intermediate species of the activation reaction. It is found that the distances between the manganese ion and the purine ring are too high (greater than 0.8 nm) to allow interaction between them. Thus, metal-purine interaction is involved neither in the catalytic mechanism nor in the stabilization of abortive synergistic complexes [S. Blanquet, G. Fayat and J. P. Waller (1975) J. Mol. Biol. 94, 1-15].

Solution structure of human corticotropin releasing factor by 1H NMR and distance geometry with restrained molecular dynamics.

The structure of human corticotropin releasing factor (hCRF) has been determined by proton nuclear magnetic resonance (1H NMR) in a mixed-solvent system of 66% trifluoroethanol/34% H2O at pH 3.8 and 37 degrees C. Nearly complete resonance assignment was achieved by using standard two-dimensional methods. Distance restraints for structure calculations were obtained by qualitative analysis of intra- and inter-residue nuclear Overhauser effects. Structures were obtained from the distance restraints by distance geometry, followed by refinement using molecular dynamics and were completed with amide hydrogen exchange data. The structure of hCRF in this solvent comprises an extended N-terminal tetrapeptide connected to a well-defined alpha-helix between residues 6 and 36. The first half of the alpha-helix (residues 6-20) is clearly amphipathic. The five carboxy-terminal residues are predominantly disordered.

MolStruc: a force field calculation program allowing interactive modifications of the force field parameters.

To analyze the influence of parameters and functions on the energy and geometry obtained through different force field calculations, we have developed program MolStruc. This software allows the user to choose between two sets of functions and parameters, MM2 and AMBER. The MM2 option of the program was developed to compute the coulombic energy in a dipole or monopole approximation. To establish comparisons between the energy values, the coulombic contribution is computed in the same way in the Amber and MM2 options of the program. The force field parameters can be handled interactively (through addition or modification). The program was used to study molecules of a representative sample displaying most of the problems encountered in molecular mechanics (MM).

A 3D model of the peripheral benzodiazepine receptor and its implication in intra mitochondrial cholesterol transport.

A three-dimensional (3D) model of the peripheral benzodiazepine receptor (PBR) has been built using molecular dynamics simulations. The transmembrane domain of the receptor has been modeled as five alpha-helices, which are not long enough to cross the entire bilayer membrane but correspond approximately to only one phospholipid layer. The receptor model has also been tested as a cholesterol carrier, and molecular dynamics simulations have shown that it could indeed accommodate a cholesterol molecule within the five helices. All three known PBR sequences have been modeled, and no significant difference has been found between them.

Solution conformation of human neuropeptide Y by 1H nuclear magnetic resonance and restrained molecular dynamics.

The solution structure of human neuropeptide Y has been solved by conventional two-dimensional NMR techniques followed by distance-geometry and molecular-dynamics methods. The conformation obtained is composed of two short contiguous alpha-helices comprising residues 15-26 and 28-35, linked by a hinge inducing a 100 degree angle. The first helix (15-26) is connected to a polyproline stretch (residues 1-10) by a tight hairpin (residues 11-14). The helices and the polyproline stretch are packed together by hydrophobic interactions. This structure is related to that of the homologous avian pancreatic polypeptide and bovine pancreatic polypeptide. The C- and N-terminii, known to be involved in the biological activity for respectively the receptor binding and activation, are close together in space. The side chains of residues Arg33, Arg35 and Tyr36 on the one hand, and Tyr1 and Pro2 on the other, form a continuous solvent-exposed surface of 4.9 mm2 which is supposed to interact with the receptor for neuropeptide Y.

Determination of the three-dimensional structure of CC chemokine monocyte chemoattractant protein 3 by 1H two-dimensional NMR spectroscopy.

MCP-3 is a beta chemokine consisting of 76 amino acid residues. It has been described to be involved in the activation of all leukocytic cells, activation mediated by the presence of multiple binding sites on the target cells. Its three-dimensional structure has been studied by making use of two-dimensional 1H NMR spectroscopy. MCP-3 exhibits the same monomeric structure as the other chemokines, i.e., a three-stranded antiparallel beta sheet covered on one face by an alpha helix. Although it belongs to the same subfamily as RANTES (Chung et al., 1995; Faitbrother et al., 1994) and hMIP-1beta (Lodi et al., 1994), the MCP-3 dimer is folded like IL-8 with the so-called alphabeta sandwich structural motif. Structural and sequence analysis gives clear indications suggesting that the other MCP chemokines may have the same quaternary structure, contrary to the other beta chemokines.

Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program.

G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur program allows one to interactively visualise and/or modify the sequences, transmembrane areas, alignments, models and results of mutagenesis experiments in an integrated environment. This integration increases the ease of modelling GPCRs: visualisation and manipulation improvements enable easier databank interrogation and interpretation. Unique program features include: (i) automatic construction of 'Snake-like' diagrams or hyperlinked GPCR molecular models to HTML or VRML and (ii) automatic access to a mutagenesis data server through the Internet. The novel algorithms or methods involved are presented, followed by the overall complementary features of the program. Finally, we present two applications of the program: (i) an automatic construction of GPCR snake-like diagrams for the GPCRDB WWW server, and (ii) a preparation of the modelling of the 5HT receptor subtypes. The interest of the direct access to mutagenesis results through an alignment and a molecular model are discussed. The Viseur program, which runs on SGI workstations, is freely available and can be used for preparing the modelling of integral membrane proteins or as an alignment editor tool.

Comparative conformations of uridine and pseudouridine and their derivatives.

Stimulated by the suggestion that pseudouridine psi-39 in yeast tRNAPhe could be in a syn conformation [R. E. Hurd and B. R. Reid (1977) Nucleic Acid Research 4, 2747-2755], we have made a comparative study of the solution conformations of psi and U derivatives, using the proton-proton Overhauser effect. Rotation around the glycosidic bond is observed for pseudouridine and 3 psi MP as well as for uridine and 3'UMP. However pseudouridine an 3 psi MP are mostly syn, whereas uridine, 3'-UMP and 5'UMP are mostly anti. There is no evidence for a correlation between sugar conformation and orientation around the glycosidic bond. The results are confirmed by relaxation measurements. They are discussed in the light of earlier studies. They tend to support the suggestion of Hurd and Reid. They raise the question of the orientation of the pseudouridine found elsewhere in tRNA (e.g. in the T psi C loop).

Solution structure of P01, a natural scorpion peptide structurally analogous to scorpion toxins specific for apamin-sensitive potassium channel.

The venom of the North African scorpion Androctonus mauretanicus mauretanicus possesses numerous highly active neurotoxins that specifically bind to various ion channels. One of these, P05, has been found to bind specifically to calcium-activated potassium channels and also to compete with apamin, a toxin extracted from bee venom. Besides the highly potent ones, several of these peptides (including that of P01) have been purified and been found to possess only a very weak, although significant, activity in competition with apamin. The amino acid sequence of P01 shows that it is shorter than P05 by two residues. This deletion occurs within an alpha-helix stretch (residues 5-12). This alpha-helix has been shown to be involved in the interaction of P05 with its receptor via two arginine residues. These two arginines are absent in the P01 sequence. Furthermore, a proline residue in position 7 of the P01 sequence may act as an alpha-helix breaker. We have determined the solution structure of P01 by conventional two-dimensional 1H nuclear magnetic resonance and show that 1) the proline residue does not disturb the alpha-helix running from residues 5 to 12; 2) the two arginines are topologically replaced by two acidic residues, which explains the drop in activity; 3) the residual binding activity may be due to the histidine residue in position 9; and 4) the overall secondary structure is conserved, i.e., an alpha-helix running from residues 5 to 12, two antiparallel stretches of beta-sheet (residues 15-20 and 23-27) connected by a type I' beta-turn, and three disulfide bridges connecting the alpha-helix to the beta-sheet.

Identification of residues involved in neurotensin binding and modeling of the agonist binding site in neurotensin receptor 1.

The neurotensin receptor 1 (NTR1) subtype belongs to the family of G protein-coupled receptors and mediates most of the known effects of the neuropeptide including modulation of central dopaminergic transmission. This suggested that nonpeptide agonist mimetics acting at the NTR1 might be helpful in the treatment of Parkinson's disease and schizophrenia. Here, we attempted to define the molecular interactions between neurotensin-(8-13), the pharmacophore of neurotensin, and the rat NTR1. Mutagenesis of the NTR1 identified residues that interact with neurotensin. Structure-activity studies with neurotensin-(8-13) analogs identified the peptide residues that interact with the mutated amino acids in the receptor. By taking these data into account, computer-assisted modeling techniques were used to build a tridimensional model of the neurotensin-(8-13)-binding site in which the N-terminal tetrapeptide of neurotensin-(8-13) fits in the third extracellular loop and the C-terminal dipeptide binds to residues at the junction between the extracellular and transmembrane domains of the receptor. Interestingly, the agonist binding site lies on top of the previously described NTR1-binding site for the nonpeptide neurotensin antagonist SR 48692. Our data provide a basis for understanding at the molecular level the agonist and antagonist binding modes and may help design nonpeptide agonist mimetics of the NTR1.

Glycerated hemoglobin, alpha 2A beta 2(82) (EF6) N epsilon-glyceryllysine. A new post-translational modification occurring in erythrocyte bisphosphoglyceromutase deficiency.

A new minor Hb fraction initially designated Hbx, has been found in the hemolysate of an erythremic patient that we have previously described with a complete erythrocyte bisphosphoglycerate mutase (EC 5.4.2.4) deficiency. Hbx (3.5% of the total) was detected by isoelectric focusing and exhibited electrophoretic and chromatographic properties similar to those of several variants of the Hb central cavity. By density fractionation of red cells, it was demonstrated that Hbx was an aging hemoglobin as in the case of glycated Hb A1c. Functional studies revealed a low oxygen affinity and almost complete inhibition of the allosteric effect of the organic phosphate effectors. Structural studies demonstrated an absence of tryptic cleavage between the peptides beta T9 and beta T10 suggesting the presence of an adduct on Lys beta 82 or on a neighboring residue. Fast atom bombardment mass spectrometry and a specific enzymatic assay with glyoxylate reductase demonstrated that the beta 82 adduct was a glycerate moiety. It was concluded that Hbx was a glycerylated Hb, alpha 2A beta 2(82) (EF6) N epsilon-glyceryllysine, to our knowledge the first example of glycerylated protein. The mechanism of formation of glyceryl Hb, which was found in the four studied subjects with a bisphosphoglyceromutase deficiency, remains to be determined.

Solution structure of P05-NH2, a scorpion toxin analog with high affinity for the apamin-sensitive potassium channel.

The venom of the scorpion Androctonus mauretanicus mauretanicus contains a toxin--P05--which is structurally and functionally similar to scorpion leiurotoxin I (87% sequence identity), a blocker of the apamin-sensitive Ca(2+)-activated K+ channels. P05, a 31-residue polypeptide cross-linked by three disulfide bridges, also possesses binding and physiological properties similar to those of the bee venom toxin apamin (18 residues, two disulfides). However, the amino acid sequences of these two polypeptides are dissimilar, except for a common Arg-Arg-Cys-Gln motif which is located on an alpha-helix. P05-NH2, a synthetic analog of P05, unlike native P05, was found to bind irreversibly to the apamin receptor. The solution structure of P05-NH2 has been solved by conventional two-dimensional NMR techniques followed by distance geometry and energy minimization. The obtained conformation is composed of two and an half turns of alpha-helix (residues 5-14) connected by a tight turn to a two-stranded antiparallel beta-sheet (sequences 17-22 and 25-29). This beta-sheet has a right-handed twist as usual for such secondary structures. The beta-turn connecting the two strands belongs to type II'. This structure is homologous to all scorpion toxin structures known so far as well as to insect defensins. The three arginines known to be involved in the pharmacological activity, i.e., Arg6, Arg7, and Arg13, are all located on the solvent-exposed side of the helix and form a positively charged surface which includes Gln9. The calculated electrostatic potential is highly asymmetric with the greatest positive potential centered on the Arg-rich alpha-helix side.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure-activity relationship study of a scorpion toxin with high affinity for apamin-sensitive potassium channels by means of the solution structure of analogues.

Scorpion venoms contain numerous toxic polypeptides displaying various pharmacological activities. These toxins interact with ion channels of excitable membranes. Long toxins (60-70 amino acids) are known to interact with sodium channels, whereas most of the short toxins (31-37 amino acids) found their toxicity in modifying the potassium channel functions. A family of short scorpion toxins are known to interact specifically with apamin-sensitive calcium-activated potassium channels. Structure-activity relationship studies of these toxins have demonstrated that a short region located on the solvent-exposed side of an alpha-helix is involved in the interaction with their receptor. Two positions, i.e. residues 6 and 7 in the sequence, are essential for the full activity of these molecules. We have synthesized analogues of these toxins and demonstrated that the three-dimensional structure is not affected by these mutations, and thus that the observed variations of activity are only due to the chemical function carried by the side chain. This interaction between the toxins and their receptor is thus purely electrostatic.

Mutagenesis and modeling of the neurotensin receptor NTR1. Identification of residues that are critical for binding SR 48692, a nonpeptide neurotensin antagonist.

The two neurotensin receptor subtypes known to date, NTR1 and NTR2, belong to the family of G-protein-coupled receptors with seven putative transmembrane domains (TM). SR 48692, a nonpeptide neurotensin antagonist, is selective for the NTR1. In the present study we attempted, through mutagenesis and computer-assisted modeling, to identify residues in the rat NTR1 that are involved in antagonist binding and to provide a tentative molecular model of the SR 48692 binding site. The seven putative TMs of the NTR1 were defined by sequence comparison and alignment of bovine rhodopsin and G-protein-coupled receptors. Thirty-five amino acid residues within or flanking the TMs were mutated to alanine. Additional mutations were performed for basic residues. The wild type and mutant receptors were expressed in COS M6 cells and tested for their ability to bind 125I-NT and [3H]SR 48692. A tridimensional model of the SR 48692 binding site was constructed using frog rhodopsin as a template. SR 48692 was docked into the receptor, taking into account the mutagenesis data for orienting the antagonist. The model shows that the antagonist binding pocket lies near the extracellular side of the transmembrane helices within the first two helical turns. The data identify one residue in TM 4, three in TM 6, and four in TM 7 that are involved in SR 48692 binding. Two of these residues, Arg327 in TM 6 and Tyr351 in TM 7, play a key role in antagonist/receptor interactions. The former appears to form an ionic link with the carboxylic group of SR 48692, as further supported by structure-activity studies using SR 48692 analogs. The data also show that the agonist and antagonist binding sites in the rNTR1 are different and help formulate hypotheses as to the structural basis for the selectivity of SR 48692 toward the NTR1 and NTR2.