Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA†

Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain

α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors produce postsynaptic current by transmitting an agonist-induced structural change in the ligand-binding domain (LBD) to the transmembrane channel. Receptors carrying T686S/A substitutions in their LBDs produce weaker glutamate-evoked currents than wild-type (WT) receptors. However, the substitutions induce little differences in the crystal structures of their LBDs. To understand the structural mechanism underlying reduced activities of these AMPAR variants, we analyzed the structural dynamics of WT, T686S, and T686A variants of LBD using nuclear magnetic resonance. The HD exchange studies of the LBDs showed that the kinetic step where the ligand-binding cleft closes was changed by the substitutions, and the substitution-induced population shift from cleft-closed to cleft-open structures is responsible for the reduced activities of the variants. The chemical shift analyses revealed another structural equilibrium between cleft-locked and cleft-partially-open conformations. The substitution-induced population shift in this equilibrium may be related to slower desensitization observed for these variants.

Computational study of synthetic agonist ligands of ionotropic glutamate receptors

Neurological glutamate receptors are among the most important and intensely studied protein ligand binding systems in humans. They are crucial for the functioning of the central nervous system and involved in a variety of pathologies. Apart from the neurotransmitter glutamate, several artificial, agonistic and antagonistic ligands are known. Of particular interest here are novel photoswitchable agonists that would open the field of optogenetics to glutamate receptors. The receptor proteins are complex, membrane-bound multidomain oligomers that undergo large scale functional conformational changes, making detailed studies of their atomic structure challenging. Therefore, a thorough understanding of the microscopic details of ligand binding and receptor activation remains elusive in many cases. This topic has been successfully addressed by theoretical studies in the past and in this paper, we present extensive molecular dynamics simulation and free energy calculation results on the binding of AMPA and an AMPA derivative, which is the basis for designing light-sensitive ligands. We provide a two-step model for ligand binding domain activation and predict binding free energies for novel compounds in good agreement to experimental observations.

Role of conformational dynamics in α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor partial agonism

We have investigated the range of cleft closure conformational states that the agonist-binding domains of the α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors occupy when bound to a series of willardiine derivatives using single-molecule FRET. These studies show that the agonist-binding domain exhibits varying degrees of dynamics when bound to the different willardiines with differing efficacies. The chlorowillardiine- and nitrowillardiine-bound form of the agonist-binding domain probes a narrower range of cleft closure states relative to the iodowillardiine bound form of the protein, with the antagonist (αS)-α-amino-3-[(4-carboxyphenyl)methyl]-3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinepropanoic acid (UBP-282)-bound form exhibiting the widest range of cleft closure states. Additionally, the average cleft closure follows the order UBP-282 > iodowillardiine > chlorowillardiine > nitrowillardiine-bound forms of agonist-binding domain. These single-molecule FRET data, along with our previously reported data for the glutamate-bound forms of wild type and T686S mutant proteins, show that the mean currents under nondesensitizing conditions can be directly correlated to the fraction of the agonist-binding domains in the "closed" cleft conformation. These results indicate that channel opening in the AMPA receptors is controlled by both the ability of the agonist to induce cleft closure and the dynamics of the agonist-binding domain when bound to the agonist.

Coupled control of desensitization and gating by the ligand binding domain of glutamate receptors

The kinetics of ligand gated ion channels are tuned to permit diverse roles in cellular signaling. To follow high-frequency excitatory synaptic input, postsynaptic AMPA-type glutamate receptors must recover rapidly from desensitization. Chimeras between AMPA and the related kainate receptors demonstrate that the ligand binding domains alone control the lifetime of the desensitized state. Mutation of nonconserved amino acids in the lower lobe (domain 2) of the ligand binding domain conferred slow recovery from desensitization on AMPA receptors, and fast recovery on kainate receptors. Single-channel recordings and a correlation between the rate of deactivation and the rate of recovery across panels of mutant receptors revealed that domain 2 also controls ion channel gating. Our results demonstrate that the same mechanism that ensures fast recovery also sharpens the response of AMPA channels to synaptically released glutamate.

Glutamate receptor ion channels: structure, regulation, and function

The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors.

Energy transfer ligands of the GluR2 ligand binding core

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory signaling in the central nervous system. When a ligand binds to the extracellular domain of iGluRs, local conformational changes ensue and this motion is translated to the transmembrane domain, inducing channel opening. We have used an isolated ligand binding domain, GluR2-S1S2J (GluR2), as a model system to study the protein-ligand complex by steady-state and time-resolved intrinsic tryptophan fluorescence measurements. Specifically, we determined that the widely used and structurally characterized antagonist, 6,7-dinitroquinoxaline-2,3-dione (DNQX), acts as an efficient fluorescence energy transfer (FET) acceptor for Trp. Consistent with crystallographic data, our results indicate that the four native tryptophans are within Forster's radius (R(o) approximately 33 A) of the bound ligand. Additionally, we demonstrate the broader value of this technique by identifying an original FET ligand, 3-nitrotyrosine (3NY), for GluR2 (R(o) approximately 24 A; apparent dissociation constant K(d) approximately 170 microM). Estimated average donor-acceptor (Trp-ligand) distances extracted from tryptophan excited-state decays are similar for both ligands (approximately 24 A), suggesting that 3NY binds in the structurally characterized ligand binding cleft. Moreover, an alternative competition assay utilizing Trp --> DNQX quenching for detection of ligand binding in GluR2 is described.

On the mechanisms of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor binding to glutamate and kainate

The alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) subtype of ionotropic glutamate receptors mediates much of the fast excitatory neurotransmission in the central nervous system. The ability of these receptors to shape such responses appears to be due in part to dynamic processes induced by agonists in the ligand-binding domain. Previous studies employing fluorescence spectroscopy and whole cell recording suggest that agonist binding is followed by sequential transitions to one or more distinct conformational states. Here, we used hydrogen-deuterium exchange to determine the mechanisms of binding of glutamate and kainate (full and partial agonists, respectively) to a soluble ligand-binding domain of GluR2. Our results provide a structural basis for sequential state models of agonist binding and the free energy changes of the associated state-to-state transitions. For glutamate, a multi-equilibrium binding reaction was discerned involving distinct ligand docking, domain isomerization, and lobe-locking steps. In contrast, kainate binding involves a simpler dock-isomerization process in which the isomerization equilibrium is shifted dramatically toward open domain conformations. In light of increasing evidence that the stability, in addition to the extent, of domain closure is a critical component of the channel activation mechanism, the differences in domain opening and closing equilibria detected for glutamate and kainate should be useful structural measures for interpreting the markedly different current responses evoked by these agonists.

Hydrophobic side chain dynamics of a glutamate receptor ligand binding domain

Ionotropic glutamate receptors are ligand-gated ion channels that mediate much of the fast excitatory neurotransmission in the central nervous system. The extracellular ligand binding core (S1S2) of the GluR2 subtype of ionotropic glutamate receptors can be produced as a soluble protein with properties essentially identical to the corresponding domain in the intact, membrane-bound protein. Using a variety of biophysical techniques, much has been learned about the structure and dynamics of S1S2 and the relationship between its ligand-induced conformational changes and the function of the receptor. It is clear that dynamic processes are essential to the function of ionotropic glutamate receptors. We have isotopically labeled side chain methyls of GluR2 S1S2 and used NMR spectroscopy to study their dynamics on the ps-ns and mus-ms time scales. Increased disorder is seen in regions that are part of the key dimer interface in the intact protein. When glutamate is bound, the degree of ps-ns motion is less than that observed with other ligands, suggesting that the physiological agonist binds to a preformed binding site. At the slower time scales, the degree of S1S2 flexibility induced by ligand binding is greatest for willardiine partial agonists, least for antagonists, and intermediate for full agonists. Notable differences among bound ligands are in the region of the protein that forms a hinge between two lobes that close upon agonist binding, and along the beta-sheet in Lobe 2. These motions provide clues as to the functional properties of partial agonists and to the conformational changes associated with lobe closure and channel activation.

Global and local mobility of apocalmodulin monitored through fast-field cycling relaxometry

Calmodulin (CaM) is a ubiquitous eukaryotic protein with two conformationally independent domains that can bind up to two calcium ions each. In the calcium-bound state, CaM is able to regulate a vast number of cellular activities by binding to a multiplicity of target proteins in different modes. Its versatility has been ascribed to its anomalously high flexibility. The calcium-free form (apoCaM), which is the resting state of CaM in cells, is also able to functionally bind a number of protein targets, but its dynamics has received less attention. At variance with the calcium-bound form, the crystal structure of apoCaM shows a compact organization of the two domains, but NMR measurements could not detect any contact between them, thus indicating the presence of mobility in solution. The mobility of apoCaM is here investigated through protein proton relaxation rate measurements performed with a high-sensitivity fast-field cycling relaxometer. Such measurements provide direct access to the spectral density function and show that 1), the reorientation time is in agreement with a closed form of the protein; but 2), the collective order parameter is much smaller than for other well folded compact proteins, indicating that a remarkably large side-chain mobility must be present.

Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments

In the analysis of the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment, chemical exchange parameters, such as rate of exchange and population of the exchanging species, are typically optimized using equations that predict experimental relaxation rates recorded as a function of effective field strength. In this process, the effect of chemical exchange during the CPMG pulses is typically assumed to be the same as during the free-precession. This approximation may introduce systematic errors into the analysis of data because the number of CPMG pulses is incremented during the constant-time relaxation period, and the total pulse duration therefore varies as a function of the effective field strength. In order to estimate the size of such errors, we simulate the time-dependence of magnetization during the entire constant time period, explicitly taking into account the effect of the CPMG pulses on the spin relaxation rate. We show that in general the difference in the relaxation dispersion profile calculated using a practical pulse width from that calculated using an extremely short pulse width is small, but under certain circumstances can exceed 1 s(-1). The difference increases significantly when CPMG pulses are miscalibrated.

Structure of the S1S2 glutamate binding domain of GLuR3

Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system. Determining the structural differences between the binding sites of different subtypes is crucial to our understanding of neuronal circuits and to the development of subtype specific drugs. The structures of the binding domain (S1S2) of the GluR3 (flip) AMPA receptor subunit bound to glutamate and AMPA and the GluR2 (flop) subunit bound to glutamate were determined by X-ray crystallography to 1.9, 2.1, and 1.55 A, respectively. Overall, the structure of GluR3 (flip) S1S2 is very similar to GluR2 (flop) S1S2 (backbone RMSD of 0.30 +/- 0.05 for glutamate-bound and 0.26 +/- 0.01 for AMPA-bound). The differences in the flip and flop isoforms are subtle and largely arise from one hydrogen bond across the dimer interface and associated water molecules. Comparison of the binding affinity for various agonists and partial agonists suggest that the S1S2 domains of GluR2 and GluR3 show only small differences in affinity, unlike what is found for the intact receptors (with the exception of one ligand, Cl-HIBO, which has a 10-fold difference in affinity for GluR2 vs. GluR3).

Mechanisms of antagonism of the GluR2 AMPA receptor: structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain

Ionotropic glutamate receptors mediate the majority of vertebrate excitatory synaptic transmission. The development of selective antagonists for glutamate receptor subtypes is of interest in the treatment of a variety of neurological disorders. This study presents the crystal structure of the binding domain of GluR2 bound to two antagonists (UBP277 and UBP282) that are derivatives of the natural product, willardiine. The antagonists bind to one lobe of the protein with interactions similar to agonists. Interaction with the second lobe differs between the two antagonists, resulting in a different position of the uracil ring and different orientations of the bilobed structure. UBP277 binding produces a stable lobe orientation that is similar to the apo state, but the binding of UBP282 produces the largest hyperextension of the lobes yet reported for an AMPA receptor. The carboxyethyl (UBP277) and carboxybenzyl (UBP282) substituents in the N(3) position keep the lobes separated by a "foot-in-the-door" mechanism and the internal dynamics are minimal compared to the CNQX-bound form of the protein (which makes minimal contacts with one of the two lobes). In contrast to the antagonists CNQX and DNQX, UBP277 and UBP282 produce complexes with higher thermal stability, but affinities that are more than 100-fold lower. These structures support the idea that antagonism is associated with the overall orientation of the lobes rather than with specific interactions, and antagonism can rise either from specific interactions with both lobes ("foot-in-the-door" mechanism) or from the lack of extensive interactions with one of the two lobes.

Mechanism of partial agonism at the GluR2 AMPA receptor: Measurements of lobe orientation in solution

The mechanism by which the binding of a neurotransmitter to a receptor leads to channel opening is a central issue in molecular neurobiology. The structure of the agonist binding domain of ionotropic glutamate receptors has led to an improved understanding of the changes in structure that accompany agonist binding and have provided important clues about the link between these structural changes and channel activation and desensitization. However, because the binding domain has exhibited different structures under different crystallization conditions, understanding the structure in the absence of crystal packing is of considerable importance. The orientation of the two lobes of the binding domain in the presence of a full agonist, an antagonist, and several partial agonists was measured using NMR spectroscopy by employing residual dipolar couplings. For some partial agonists, the solution conformation differs from that observed in the crystal. A model of channel activation based on the results is discussed.

Glutamate receptors as seen by light: spectroscopic studies of structure-function relationships

Ionotropic glutamate receptors are major excitatory receptors in the central nervous system and also have a far reaching influence in other areas of the body. Their modular nature has allowed for the isolation of the ligand-binding domain and for subsequent structural studies using a variety of spectroscopic techniques. This review will discuss the role of specific ligand:protein interactions in mediating activation in the a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype of glutamate receptors as established by various spectroscopic investigations of the GluR2 and GluR4 subunits of this receptor. Specifically, this review will provide an introduction to the insight gained from X-ray crystallography and nuclear magnetic resonance investigations and then go on to focus on studies utilizing vibrational spectroscopy and fluorescence resonance energy transfer to study the behavior of the isolated ligand-binding domain in solution and discuss the importance of specific ligand:protein interactions in the mechanism of receptor activation.

NMR spectroscopy of the ligand-binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists

Glutamate receptors mediate neuronal intercommunication in the central nervous system by coupling extracellular neurotransmitter-receptor interactions to ion channel conductivity. To gain insight into structural and dynamical factors that underlie this coupling, solution NMR experiments were performed on the bilobed ligand-binding core of glutamate receptor 2 in complexes with a set of willardiine partial agonists. These agonists are valuable for studying structure-function relationships because their 5-position substituent size is correlated with ligand efficacy and extent of receptor desensitization, whereas the substituent electronegativity is correlated with ligand potency. NMR results show that the protein backbone amide chemical shift deviations correlate mainly with efficacy and extent of desensitization. Pronounced deviations occur at specific residues in the ligand-binding site and in the two helical segments that join the lobes by a disulfide bond. Experiments detecting conformational exchange show that micro- to millisecond timescale motions also occur near the disulfide bond and vary largely with efficacy and extent of desensitization. These results thus identify regions displaying structural and dynamical dissimilarity arising from differences in ligand-protein interactions and lobe closure that may play a critical role in receptor response. Furthermore, measures of line broadening and conformational exchange for a portion of the ligand-binding site correlate with ligand EC(50) data. These results do not have any correlate in the currently available crystal structures and thus provide a novel view of ligand-binding events that may be associated with agonist potency differences.

Structural and single-channel results indicate that the rates of ligand binding domain closing and opening directly impact AMPA receptor gating

At most excitatory central synapses, glutamate is released from presynaptic terminals and binds to postsynaptic AMPA receptors, initiating a series of conformational changes that result in ion channel opening. Efficient transmission at these synapses requires that glutamate binding to AMPA receptors results in rapid and near-synchronous opening of postsynaptic receptor channels. In addition, if the information encoded in the frequency of action potential discharge is to be transmitted faithfully, glutamate must dissociate from the receptor quickly, enabling the synapse to discriminate presynaptic action potentials that are spaced closely in time. The current view is that the efficacy of agonists is directly related to the extent to which ligand binding results in closure of the binding domain. For glutamate to dissociate from the receptor, however, the binding domain must open. Previously, we showed that mutations in glutamate receptor subunit 2 that should destabilize the closed conformation not only sped deactivation but also altered the relative efficacy of glutamate and quisqualate. Here we present x-ray crystallographic and single-channel data that support the conclusions that binding domain closing necessarily precedes channel opening and that the kinetics of conformational changes at the level of the binding domain importantly influence ion channel gating. Our findings suggest that the stability of the closed-cleft conformation has been tuned during evolution so that glutamate dissociates from the receptor as rapidly as possible but remains an efficacious agonist.

The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain

Ionotropic glutamate receptors are ligand-gated transmembrane ion channels activated by the binding of glutamate. The free energy landscapes governing the opening/closing of the GluR2 S1S2 ligand-binding domain in the apo, DNQX-, and glutamate-bound forms are computed by using all-atom molecular dynamics simulations with explicit solvent, in conjunction with an umbrella sampling strategy. The apo S1S2 easily accesses low-energy conformations that are more open than observed in X-ray crystal structures. A free energy of 9-12 kcal/mol becomes available upon glutamate binding for driving conformational changes in S1S2 associated with receptor activation. Small-angle X-ray scattering profiles calculated from computed ensemble averages agree better with experimental results than profiles calculated from static X-ray crystal structures. Water molecules in the cleft may contribute to stabilizing the apo S1S2 in open conformations. Free energy landscapes were also computed for the glutamate-bound T686A and T686S S1S2 mutants, and the results elaborate on findings from experimental functional studies.

Backbone chemical shift assignment of a glutamate receptor ligand binding domain in complexes with five partial agonists

Backbone (1)H, (13)C, and (15)N chemical shifts are reported for complexes of a perdeuterated glutamate receptor ligand binding domain with kainate, willardiine, and 5-substituted fluoro-, bromo-, and iodowillardiine. These ligands are partial agonists that induce distinct current responses at post-synaptic neurons. The chemical shifts pave the way for numerous NMR studies to identify structural and dynamical determinants of receptor function.

The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data

Structural biology now plays a prominent role in addressing questions central to understanding how excitable cells function. Although interest in the insights gained from the definition and dissection of macromolecular anatomy is high, many neurobiologists remain unfamiliar with the methods employed. This primer aims to help neurobiologists understand approaches for probing macromolecular structure and where the limits and challenges remain. Using examples of macromolecules with neurobiological importance, the review covers X-ray crystallography, electron microscopy (EM), small-angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) and biophysical methods with which these approaches are often paired: isothermal titration calorimetry (ITC), equilibrium analytical ultracentifugation, and molecular dynamics (MD).

Structural aspects of AMPA receptor activation, desensitization and deactivation

Glutamate mediates most of the excitatory neurotransmission in the mammalian central nervous system by activating ionotropic glutamate receptors. Structural and functional studies of ionotropic glutamate receptors have offered detailed insight into the mechanism by which these integral membrane proteins function. In particular, advances in our understanding of the atomic structure of the agonist-binding domain have provided new opportunities to consider the conformational changes that take place in a functioning ligand-gated ion channel. Several recent studies have turned up important new ideas about the structural determinants of channel activation, deactivation and desensitization of AMPA receptors. Working hypotheses derived from this structural insight offer a rare opportunity to enrich and guide functional studies.

Dynamics of the S1S2 Glutamate Binding Domain of GluR2 Measured Using 19F NMR Spectroscopy

Ionotropic glutamate receptors mediate the majority of vertebrate excitatory synaptic transmission. Although the structure of the GluR2 binding domain (S1S2) is well known (agonist binding site between two lobes), little is known about the time scales of conformational transitions or the relationship between dynamics and function. (19)F NMR ((19)F-labeled tryptophan) spectroscopy was used to monitor motions in the S1S2 domain bound to ligands with varying efficacy and in the apo state. One tryptophan (Trp-671) undergoes chemical exchange in some but not all agonists, consistent with mus-ms motion. The dynamics can be correlated to ligand affinity, and a likely source of the motion is a peptide bond capable of transiently forming hydrogen bonds across the lobe interface. Another tryptophan (Trp-767) appears to monitor motions of the relative positions of the lobes and suggests that the relative orientation in the apo- and antagonist-bound forms can exchange between at least two conformations on the ms time scale.

Role of the chemical interactions of the agonist in controlling alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor activation

Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are the main excitatory neurotransmitter receptors in the mammalian central nervous system. Structures of the isolated ligand binding domain of this receptor have provided significant insight into the large-scale conformational changes, which when propagated to the channel segments leads to receptor activation. However, to establish the role of specific molecular interactions in controlling fine details such as the magnitude of the functional response, we have used a multiscale approach, where changes at specific moieties of the agonists have been studied by vibrational spectroscopy, while large-scale conformational changes have been studied using fluorescence resonance energy transfer (FRET) investigations. By exploiting the wide range of activations by the agonists, glutamate, kainate, and AMPA, for the wild type and Y450F and L650T mutants of the GluR2 subtype, and by using the multiscale investigation, we show that the strength of the interactions at the alpha-amine group of the agonist with the protein in all but one case tracks the extent of activation. Since the alpha-amine group forms bridging interactions at the cusp of the ligand binding cleft, this appears to be a critical interaction through which the agonist controls the extent of activation of the receptor.

In silico mutation of cysteine residues in the ligand-binding domain of an N-methyl-D-aspartate receptor

The precise nature of redox modulation of N-methyl-d-aspartate (NMDA) receptors is still unclear, although it is thought to be related to the formation and breaking of disulfide bonds. Recent structural data demonstrated the way in which disulfide bonds in the ligand-binding core of the NR1 subunit are arranged. However, the structures were not able to reconcile existing experimental data that examined the effects of mutating these cysteine residues. We have used molecular dynamics (MD) simulations of a series of in silico mutations to try and address this in terms of the current structure of the NR1 ligand-binding domain. A double mutation that removes the disulfide bridge between C744 and C798 gives rise to greater interlobe mobility which was predicted from the crystal structure information but, unexpectedly, also appears to predispose the receptor toward greater flexibility in the hinge region. Removal of the disulfide bond between C454 and C420 did not show any appreciable difference from the "wild-type" simulation, suggesting that removal of this would not change receptor properties, which is in agreement with experimental findings. Furthermore, the position of the C454 side chain could be characterized into discrete rotamers, which may reflect the observation of alternative density in the crystal structure for this residue. Simulations in which two of the disulfide bonds are removed via mutations to alanine (C420A and C436A) resulted in a tendency of the protein to adopt a partially closed conformation.

Internal Bulge and Tetraloop of the Catalytic Domain 5 of a Group II Intron Ribozyme Are Flexible: Implications for Catalysis

RNA molecules have an inherent flexibility that enables recognition of other interacting partners through potential disorder-order transitions, yet studies to quantify such motional dynamics remain few. With an increasing database of three-dimensional structures of biologically important RNA molecules, quantifying such motions becomes important to link structural deformations with function. One such system studied intensely is domain 5 (D5) from the self-splicing group II introns, which is at the heart of its catalytic machinery. We report the dynamics of a 36 nucleotide D5 from the Pylaiella littoralis group II intron in the presence and absence of magnesium ions, and at a range of temperatures (298K-318 K). Using high-resolution NMR experiments of heteronuclear nuclear Overhauser enhancement (NOE), spin-lattice (R(1)), and spin-spin (R(2)) (13)C relaxation rates, we determined the rotational diffusion tensor of D5 using the ROTDIF program modified for RNA dynamic analysis (ROTDIF_RNA). The D5 rotational diffusion tensor has an axial symmetric ratio (D(||)/D(perpendicular)) of 1.7+/-0.3, consistent with an estimated overall rotational correlation time of tau(m)=(2D(||)+4D(perpendicular))(-1) of 6.1(+/-0.3) ns at 298 K and 4.1(+/-0.2) ns at 318 K. The measured relaxation data were analyzed with the reduced spectral density mapping formalism using assumed values of the chemical shift anisotropy of the (13)C spins. Both the relaxation data and the values of the spectral density function reveal that the functional groups in D5 implicated in magnesium ion binding and catalysis (catalytic triad, internal bulge, and tetraloop regions) exhibit thermally induced motion on a wide variety of timescales. Because these motions parallel those observed in the intramolecular stem-loop of the U6 element within the spliceosome, we hypothesize that such extensive dynamic disorder likely facilitates D5 engaging both binding and catalytic regions of the ribozyme, and these may be a conserved feature of the catalytic machinery essential for catalysis.

"Four-dimensional" protein structures: examples from metalloproteins

The fact that an object, for example, a protein, possesses a three-dimensional structure seems an obvious concept. However, when the object is flexible, the concept is less obvious. Growing experimental data over several decades show that proteins are not rigid objects, but they may sample more or less wide ranges of different conformations. To stress this concept, we propose to call the range of sampled conformations the "fourth dimension" of the protein structure. Nuclear magnetic resonance is a precious technique to define this fourth dimension. Examples of conformational heterogeneity taken from the realm of metalloproteins and their functional implications are discussed.

Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists

Glutamate receptor (GluR) ion channels mediate fast synaptic transmission in the mammalian CNS. Numerous crystallographic studies, the majority on the GluR2-subtype AMPA receptor, have revealed the structural basis for binding of subtype-specific agonists. In contrast, because there are far fewer antagonist-bound structures, the mechanisms for antagonist binding are much less well understood, particularly for kainate receptors that exist as multiple subtypes with a distinct biology encoded by the GluR5-7, KA1, and KA2 genes. We describe here high-resolution crystal structures for the GluR5 ligand-binding core complex with UBP302 and UBP310, novel GluR5-selective antagonists. The crystal structures reveal the structural basis for the high selectivity for GluR5 observed in radiolabel displacement assays for the isolated ligand binding cores of the GluR2, GluR5, and GluR6 subunits and during inhibition of glutamate-activated currents in studies on full-length ion channels. The antagonists bind via a novel mechanism and do not form direct contacts with the E723 side chain as occurs in all previously solved AMPA and kainate receptor agonist and antagonist complexes. This results from a hyperextension of the ligand binding core compared with previously solved structures. As a result, in dimer assemblies, there is a 22 A extension of the ion channel linkers in the transition from antagonist- to glutamate-bound forms. This large conformational change is substantially different from that described for AMPA receptors, was not possible to predict from previous work, and suggests that glutamate receptors are capable of much larger movements than previously thought.

Glutamate receptors: variation in structure-function coupling

Fast excitatory synaptic transmission in the CNS relies almost entirely on the neurotransmitter glutamate and its family of ion channel receptors. An appreciation of the coupling between agonist binding and channel opening has advanced rapidly during the past five years, largely as a result of new structural information about the agonist-binding site. Recent studies suggest that despite many structural similarities different family members use different mechanisms to translate agonist binding into channel opening.

Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding

The binding modes of a set of known ionotropic glutamate receptor antagonist-ligands have been studied using homology modeling, molecular docking, molecular dynamics (MD) simulations and ab initio quantum mechanical calculations. The core structure of the studied ligands is the decahydroisoquinoline ring, which has a carboxylic acid group at position three and different negatively-charged substituents (R) at position six. The binding affinities of these molecules have been reported earlier. From the current study, the carboxylate group of the decahydroisoquinoline ring hydrogen bonds with Arg485, the amino group with Pro478 and Thr480, and the negatively charged substituent R interacts with the positively charged N-terminus of helix-F. The subtype selectivity of these ligands seems to be strongly dependent on the amino acid at position 650 (GluR2: leucine, GluR5: valine), which affects the conformation of the ligand and ligand-receptor interactions, but depends considerably on the size of the R-group of the ligand. In addition, the MD simulations also revealed that the relative positions of the S1 and S2 domains can alter significantly showing different "closure" and "rotational movements" depending on the antagonist-ligand that is bound. Accordingly, molecular docking of antagonist ligands into static crystal structures cannot sufficiently explain ligand binding and subtype selectivity.

Glutamate receptor ion channels

Glutamate receptor ion channels mediate excitatory responses at the majority of CNS synapses. They are the only ligand-gated ion channels for which multiple high-resolution crystal structures have been solved. Highlights of information gained from mechanistic studies based on the crystal structures of their ligand-binding domains include explanations for strikingly diverse phenomena. These include the basis for subtype-specific agonist selectivity; mechanisms for desensitization and allosteric modulation; and mechanisms for partial agonist activity. In addition, multiple lines of evidence, including low-resolution electron microscopic studies, suggest that native AMPA receptors combine with an auxiliary subunit which regulates activity and trafficking. Functional studies suggest that glutamate receptor gating is distinct from that of structurally related voltage-gated ion channels.