Regulation of circadian gene expression in liver by systemic signals and hepatocyte oscillators.

The mammalian circadian timing system has a hierarchical structure, in that a master pacemaker located in the suprachiasmatic nuclei (SCN) coordinates slave oscillators present in virtually all body cells. In both the SCN and peripheral organs, the rhythm-generating oscillators are self-sustained and cell-autonomous, and it is likely that the molecular makeup of master and slave oscillators is nearly identical. However, due to variations in period length, the phase coherence between peripheral oscillators in intact animals must be established by daily signals emanating directly or indirectly from the SCN master clock. The synchronization of individual cellular clocks in peripheral organs is probably accomplished by immediate-early genes that interpret the cyclic systemic signals and convey this phase information to core clock components. This model predicts that circadian gene expression in peripheral organs can be influenced either by systemic signals emanating from the SCN master clock, local oscillators, or both. We developed a transgenic mouse strain in which hepatocyte clocks are only operative when the tetracycline analog doxycycline is added to the food or drinking water. The genome-wide mapping of genes whose cyclic expression in liver does not depend on functional hepatocyte oscillators unveiled putative signaling pathways that may participate in the phase entrainment of peripheral clocks.

An evaluation of potassium ions as endothelium-derived hyperpolarizing factor in porcine coronary arteries.

In the rat hepatic artery, the endothelium-derived hyperpolarizing factor (EDHF) was identified as potassium. Potassium hyperpolarizes the smooth muscles by gating inward rectified potassium channels and by activating the sodium-potassium adenosine triphosphatase (Na(+)-K(+)ATPase). Our goal was to examine whether potassium could explain the EDHF in porcine coronary arteries. On coronary strips, the inhibition of calcium-dependent potassium channels with 100 nM apamin plus 100 microM charibdotoxin inhibited the endothelium-dependent relaxations, produced by 10 nM substance P and 300 nM bradykinin and resistant to nitro-L-arginine and indomethacin. The scavenging of potassium with 2 mM Kryptofix 2.2.2 abolished the endothelium-dependent relaxations produced by the kinins and resistant to nitro-L-arginine and indomethacin. Forty microM 18alpha glycyrrethinic acid or 50 microM palmitoleic acid, both uncoupling agents, did not inhibit these kinin relaxations. Therefore, EDHF does not result from an electrotonic spreading of an endothelial hyperpolarization. Barium (0.3 nM) did not inhibit the kinin relaxations resistant to nitro-L-arginine and indomethacin. Therefore, EDHF does not result from the activation of inward rectified potassium channels. Five hundred nM ouabain abolished the endothelium-dependent relaxations resistant to nitro-L-arginine and indomethacin without inhibiting the endothelium-derived NO relaxation. The perifusion of a medium supplemented with potassium depolarized and contracted a coronary strip; however, the short application of potassium hyperpolarized the smooth muscles. These results are compatible with the concept that, in porcine coronary artery, the EDHF is potassium released by the endothelial cells and that this ion hyperpolarizes and relaxes the smooth muscles by activating the Na(+)-K(+)ATPase.

Single binding versus single channel recordings: a new approach to study ionotropic receptors.

The observation of ligand binding to a single molecule has become feasible with recent developments in laser-based fluorescence microscopy. We have simulated such single ligand-binding events for the nicotinic acetylcholine receptor in order to provide comparisons with single channel events under pulsed agonist conditions. The binding events would be more complex than ionic events due to multiple interconversions between different conformational states at the same degree of ligation. Nevertheless, recording of such events could provide valuable new information concerning the role of ligand binding in stabilizing conformational changes and the degree of functional nonequivalence of the binding sites.

Myasthenic nicotinic receptor mutant interpreted in terms of the allosteric model.

An extended Monod-Wyman-Changeux allosteric-type model is applied to human muscle nicotinic acetylcholine receptors expressed in HEK cells, for both the normal form and the high-affinity human myasthenic mutant, epsilon T264P. The model is based on a concerted transition between the basal (resting) B state and the active (open-channel) A state, with the equilibrium in the absence of ligand determined by the allosteric constant, L0 = [B0]/[A0]. For wild-type receptors the model with L0 = 9 x 10(8) provides a satisfactory representation of published patch-clamp recordings that yields a distribution of open-channel dwell times with a single peak at 0.7 ms. For the epsilon T264P mutant, the model with L0 = 100 accounts for the trimodal distribution reported for open-channel dwell times, with peaks at 0.15, 3.8 and 60 ms that correspond to non-, mono- and bi-liganded receptors, respectively. Possible applications of the allosteric model to other myasthenic mutants are considered.

A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions.

Nicotinic acetylcholine receptors are transmembrane oligomeric proteins that mediate interconversions between open and closed channel states under the control of neurotransmitters. Fast in vitro chemical kinetics and in vivo electrophysiological recordings are consistent with the following multi-step scheme. Upon binding of agonists, receptor molecules in the closed but activatable resting state (the Basal state, B) undergo rapid transitions to states of higher affinities with either open channels (the Active state, A) or closed channels (the initial Inactivatable and fully Desensitized states, I and D). In order to represent the functional properties of such receptors, we have developed a kinetic model that links conformational interconversion rates to agonist binding and extends the general principles of the Monod-Wyman-Changeux model of allosteric transitions. The crucial assumption is that the linkage is controlled by the position of the interconversion transition states on a hypothetical linear reaction coordinate. Application of the model to the peripheral nicotine acetylcholine receptor (nAChR) accounts for the main properties of ligand-gating, including single-channel events, and several new relationships are predicted. Kinetic simulations reveal errors inherent in using the dose-response analysis, but justify its application under defined conditions. The model predicts that (in order to overcome the intrinsic stability of the B state and to produce the appropriate cooperativity) channel activation is driven by an A state with a Kd in the 50 nM range, hence some 140-fold stronger than the apparent affinity of the open state deduced previously. According to the model, recovery from the desensitized states may occur via rapid transit through the A state with minimal channel opening, thus without necessarily undergoing a distinct recovery pathway, as assumed in the standard 'cycle' model. Transitions to the desensitized states by low concentration 'pre-pulses' are predicted to occur without significant channel opening, but equilibrium values of IC50 can be obtained only with long pre-pulse times. Predictions are also made concerning allosteric effectors and their possible role in coincidence detection. In terms of future developments, the analysis presented here provides a physical basis for constructing more biologically realistic models of synaptic modulation that may be applied to artificial neural networks.

Electrotonic propagation of kinin-induced, endothelium-dependent hyperpolarizations in pig coronary smooth muscles.

The kinins, substance P and bradykinin, cause endothelium-dependent hyperpolarizations in smooth muscles of the pig coronary artery. We tested whether the propagation, in the media, of these hyperpolarizations is passive or whether the hyperpolarizations are regenerated in the smooth muscle cells. The space constants measured in response to the kinin endothelium-dependent stimulations were compared to those obtained by electrical field stimulation. The space constant is 2.6 +/- 0.2 mm (n = 13) measured for substance P and 2.2 +/- 0.2 mm (n = 12) for bradykinin. The space constants established by electrical field stimulation-induced hyperpolarization are 3 +/- 0.2 mm (n = 7) for strips with intact endothelium and 2.7 +/- 0.3 mm (n = 7) for strips with removed endothelium. These results show that the space constants obtained for the kinin stimulations are not larger than those caused by electrical field stimulation. This suggests that the kinin-induced hyperpolarizations propagate, in the media, in a passive, electronic manner, therefore the hypothesis of regenerated kinin hyperpolarizations is unlikely.

Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin.

We have begun to use molecular dynamics to simulate the kinetics of nitric oxide rebinding to myoglobin after photodissociation. Rebinding was simulated using a potential function that switches smoothly between a nonbinding potential and a binding potential as a function of the position and orientation of the ligand, with no barrier arising from the crossing of potential surfaces of different electron spin. In 96 of 100 trajectories, the ligand rebound in < 15 ps. The kinetic progress curve was obtained by determining the time in each trajectory at which the ligand rebound and then calculating the fraction of unbound ligands as a function of time. The curve can be well reproduced by a simple model based on the dynamics of a Langevin particle moving on a one-dimensional potential of mean force calculated from nonreactive protein trajectories. The rate of escape from the energy well adjacent to the heme is in good agreement with the value calculated from experimental data, suggesting that a multiple-well model provides a plausible explanation for the nonexponential rebinding kinetics. A transition-state analysis suggests that protein conformational relaxation coupled to the displacement of the iron from the heme plane is an unlikely cause for the nonexponential rebinding of nitric oxide.

Functional consequences of mutations at the allosteric interface in hetero- and homo-hemoglobin tetramers.

A seminal difference exists between the two types of chains that constitute the tetrameric hemoglobin in vertebrates. While alpha chains associate weakly into dimers, beta chains self-associate into tightly assembled tetramers. While heterotetramers bind ligands cooperatively with moderate affinity, homotetramers bind ligands with high affinity and without cooperativity. These characteristics lead to the conclusion that the beta 4 tetramer is frozen in a quaternary R-state resembling that of liganded HbA. X-ray diffraction studies of the liganded beta 4 tetramers and molecular modeling calculations revealed several differences relative to the native heterotetramer at the "allosteric" interface (alpha 1 beta 2 in HbA) and possibly at the origin of a large instability of the hypothetical deoxy T-state of the beta 4 tetramer. We have studied natural and artificial Hb mutants at different sites in the beta chains responsible for the T-state conformation in deoxy HbA with the view of restoring a low ligand affinity with heme-heme interaction in homotetramers. Functional studies have been performed for oxygen equilibrium binding and kinetics after flash photolysis of CO for both hetero- and homotetramers. Our conclusion is that the "allosteric" interface is so precisely tailored for maintaining the assembly between alpha beta dimers that any change in the side chains of beta 40 (C6), beta 99 (G1), and beta 101 (G3) involved in the interface results in increased R-state behavior. In the homotetramer, the mutations at these sites lead to the destabilization of the beta 4 hemoglobin and the formation of lower affinity noncooperative monomers.

NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1.

The three-dimensional solution structure of a complex between the DNA binding domain of the chicken erythroid transcription factor GATA-1 and its cognate DNA site has been determined with multidimensional heteronuclear magnetic resonance spectroscopy. The DNA binding domain consists of a core which contains a zinc coordinated by four cysteines and a carboxyl-terminal tail. The core is composed of two irregular antiparallel beta sheets and an alpha helix, followed by a long loop that leads into the carboxyl-terminal tail. The amino-terminal part of the core, including the helix, is similar in structure, although not in sequence, to the amino-terminal zinc module of the glucocorticoid receptor DNA binding domain. In the other regions, the structures of these two DNA binding domains are entirely different. The DNA target site in contact with the protein spans eight base pairs. The helix and the loop connecting the two antiparallel beta sheets interact with the major groove of the DNA. The carboxyl-terminal tail, which is an essential determinant of specific binding, wraps around into the minor groove. The complex resembles a hand holding a rope with the palm and fingers representing the protein core and the thumb, the carboxyl-terminal tail. The specific interactions between GATA-1 and DNA in the major groove are mainly hydrophobic in nature, which accounts for the preponderance of thymines in the target site. A large number of interactions are observed with the phosphate backbone.

Critical residues responsible for self-association differences of hemoglobin alpha and beta chains: analysis by molecular modeling.

Although the alpha and beta chains of adult human hemoglobin (Hb A) are very similar, when isolated the individual chains display marked differences in the propensities to form homotetramers: alpha chains alone associate weakly into dimers, while beta chains form relatively stable tetramers. We have examined the origin of this difference using computer-based model building and energy minimization. For oxyhemoglobin (R state) structures, interfaces have been compared for energy minimized alpha 2 beta 2, beta 4, and hypothetical alpha 4 tetramers. For the alpha 1-beta 1 interface (also designated as the X-interface) 19 alpha chain and 19 beta chain residues were identified that each contribute at least 1% to the energy of the contact in Hb A. This interface has a high degree of pseudo-symmetry, with identical residues at 6 of these positions for both chains. The geometry of the X-interface is similar for the homotetramers, with all 6 of these residues retained at the interface in beta 4 and 4 of the 6 found at the interface in alpha 4, although the alpha-alpha interface involves fewer contacts and less buried surface area. For the alpha 1-beta 2 interface (also designated as the Z-interface) 10 alpha chain and 10 beta chain residues are identified as contributing at least 1% to the energy of the contact in Hb A; about half of the contact residues are identical for corresponding positions of alpha and beta chains and most of these residues are retained at the interfaces in the two types of homotetramers, but with fewer alpha-alpha contacts.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural modeling of the human erythrocyte bisphosphoglycerate mutase.

Using the crystallographic structure of yeast monophosphoglycerate mutase (MPGM) as a framework we constructed a three-dimensional model of the homologous human erythrocyte bisphosphoglycerate mutase (BPGM). The modeling procedure consisted of substituting 117 amino acid residues and positioning 19 C-terminal residues (unresolved in the X-ray structure) by empirical methods, followed by energy minimization. Among several differences in the active site region the most significant appears to be the replacement of Ser11 in MPGM by Gly in BPGM. The C-terminal segment, which contains mainly basic amino acids, lines the cavity of the active site. The seven amino acid residues, which have been shown to be essential for the three catalytic functions of the human BPGM, interact with the amino acids in the protein core, near the active site. In addition, a cluster of several positively charged residues, particularly arginines, has been identified at the entrance of the active site; this cluster may serve as a secondary binding site for polyanionic substrates or cofactors, as required by a two-binding-site model of the catalytic activities. This model is in agreement with recent studies of an inactive BPGM variant substituent at an Arg position situated in this positively charged cluster. The position of Cys20 in the model constructed suggests that this residue is responsible for inactivation of the enzyme by sulfhydryl reagents. Subunit interfaces have also been constructed for BPGM by analogy with MPGM and suggest that, in addition to the known dimerization of BPGM, tetramerization may occur under certain conditions.

Steric and hydrophobic determinants of the solubilities of recombinant sickle cell hemoglobins.

Models for the structure of the fibers of deoxy sickle cell hemoglobin (Hb Hb S, beta 6 Glu-->Val) have been obtained from X-ray and electron microscopic studies. Recent molecular dynamics calculations of polymer formation give new insights on the various specific interactions between monomers. Site-directed mutagenesis with expression of the Hb S beta subunits in Escherichia coli provides the experimental tools to test these models. For Hb S, the beta 6 Val residue is intimately involved in a specific lateral contact, at the donor site, that interacts with the acceptor site of an adjacent molecule composed predominantly of the hydrophobic residues Phe 85 and Leu 88. Comparing natural and artificial mutants indicates that the solubility of deoxyHb decreases in relation to the surface hydrophobicity of the residue at the beta 6 position with Ile > Val > Ala. We also tested the role of the stereospecific adjustment between the donor and acceptor sites by substituting Trp for Glu at the beta 6 location. Among these hydrophobic substitutions and under our experimental conditions, only Val and Ile were observed to induce polymer formation. The interactions for the Ala mutant are too weak whereas a Trp residue inhibits aggregation through steric hindrance at the acceptor site of the lateral contact. Increasing the hydrophobicity at the axial contact between tetramers of the same strand also contributes to the stability of the double strand. This is demonstrated by associating the beta 23 Val-->Ile mutation at the axial contact with either the beta 6 Glu-->Val or beta 6 Glu-->Ile substitution in the same beta subunit.(ABSTRACT TRUNCATED AT 250 WORDS)

Hemoglobin Saint Mandé [beta 102 (G4) Asn----Tyr]. Functional studies and structural modeling reveal an altered T state.

Oxygen equilibrium studies of purified hemoglobin Saint Mandé (Hb SM) [beta 102 (G4) Asn----Tyr] reveal a decreased oxygen affinity and cooperativity but to a lesser extent than found for Hb Kansas (beta 102 Thr). The low affinity of Hb SM depends on environmental conditions: eliminating chloride or raising the pH greatly elevated the ratio of p50 of Hb SM to that of Hb A. The alkaline Bohr effect is reduced by about 40%. The effects of anions (chloride, organophosphates) binding to deoxy Hb SM are also reduced. These data indicate that the functional properties of Hb SM are intermediary between Hb A and Hb Kansas. In addition, molecular graphics modeling of Hb SM in the oxy and deoxy structures indicate the possibility of a new hydrogen bond in the T state between beta(1)102 Tyr and alpha(2)42 Tyr. Stabilisation of the T state in this manner is a plausible explanation for several of the effects observed.

Comparative molecular modeling of Amphioxus calcium vector protein with calmodulin and troponin C.

Calcium vector protein (CaVP), a new protein isolated from Amphioxus muscle, binds in a Ca2(+)-regulated manner to a 27 kd target protein, named CaVPT, whose function has not been elucidated yet. CaVP bears significant sequence homology to both calmodulin and skeletal muscle troponin C, especially in the C-terminal half of the molecule, which presumably contains the two functional Ca2(+)-binding sites. The N-terminal half contains two abortive EF-hands and is intramolecularly crosslinked with a disulfide bond. Using the crystallographic structures of calmodulin and striated muscle troponin C as a framework, we constructed two different three-dimensional models of CaVP and modeled the intramolecular disulfide bridge. The modeling based upon the coordinates of calmodulin yields a Ca2(+)-filled sites configuration in the N-terminal half of the molecule, even though no Ca2+ is bound in this half, whereas the troponin C-derived model generates a Ca2(+)-empty sites configuration. The models predict that neither is the Ca2(+)-filled nor in the Ca2(+)-empty sites conformation is there any steric and/or energetic obstacle for the formation of the disulfide bridge and that the disulfide bond is poorly accessible to reducing reagents. The optical properties of the Trp and Tyr residues of CaVP indicate that the calmodulin-derived model represents the most plausible prediction.

Enhanced polymerization of recombinant human deoxyhemoglobin beta 6 Glu----Ile.

Polymerization of the deoxy form of sickle cell hemoglobin (Hb S; beta 6 Glu----Val) involves both hydrophobic and electrostatic intermolecular contacts. These interactions drive the mutated molecules into long fibrous rods composed of seven pairs of strands. X-ray crystallography of Hb S and electron microscopy image reconstruction of the fibers have revealed the remarkable complementarity between one of the beta 6 valines of each molecule (the donor site) and an acceptor site at the EF corner of a neighboring tetramer. This interaction constitutes the major lateral contact between the two strands in a pair. To estimate the relative importance of this key hydrophobic contact in polymer formation we have generated a polymerizing Hb with isoleucine at the beta 6 position (beta E6I) by site-directed mutagenesis. The mutated beta chains were produced in Escherichia coli and reassembled into functional tetramers with native alpha chains. Compared to native Hb S, the beta E6I mutant polymerizes faster and with a shortened delay time in 1.8 M phosphate buffer, indicating an increased stability of the nuclei preceding fiber growth. The solubility of the beta E6I mutant Hb is half that of native Hb S. Computer modeling of the donor-acceptor interaction shows that the presence of an isoleucine side chain at the donor site induces increased contacts with the receptor site and an increased buried surface area, in agreement with the higher hydrophobicity of the isoleucine residue. The agreement between the predicted and experimental differences in solubility suggests that the transfer of the beta 6 valine or isoleucine side chain from water to a hydrophobic environment is sufficient to explain the observations.

The modelling of nucleophilic and electrophilic additions to organometallic complexes using molecular graphics techniques.

A new formalism has been developed in order to evaluate intermolecular interaction energies for inorganic and organometallic complexes in the framework of the extended Hückel method. In order to provide the shortest possible response time on an interactive computer graphics facility, this model should require the minimum amount of computer time, which explains why approximate procedures are used to evaluate electrostatic, charge transfer and exchange repulsion components. When applying this model to typical examples of electrophilic addition reactions to organometallic complexes, it is found that it is essential to take account of charge transfer interactions, the electrostatic component alone being not sufficient, even qualitatively, for a proper description of the reaction mechanism. The results, presented as color-coded dot molecular surfaces, show a very good agreement with experiment as to the site of attack, namely (i) on metal for the electrophilic attack on Fe(cp)2, Fe(CO)5 and X(cp)(CO)2, X = Co, Rh; (ii) on the cp ligand for the nucleophilic attack on Co(cp)2+ and Rh(cp)2+; (iii) on bz for the nucleophilic attack on Fe(cp)(bz)+. Finally, modellizations of the nucleophilic attack on a coordinated olefin and of the relation between structure and acidic properties of zeolites are presented and discussed.