The hidden energetics of ligand binding and activation in a glutamate receptor

Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling

It is well-known that the potency of a drug is heavily associated with its kinetic and thermodynamic properties with the target. Nuclear receptors (NRs), as an important target family, play important roles in regulating a variety of physiological processes in vivo. However, it is hard to understand the drug-NR interaction process because of the closed structure of the ligand-binding domain (LBD) of the NR proteins, which apparently hinders the rational design of drugs with controllable kinetic properties. Therefore, understanding the underlying mechanism of the ligand-NR interaction process seems necessary to help NR drug design. However, it is usually difficult for experimental approaches to interpret the kinetic process of drug-target interactions. Therefore, in silico methods were utilized to explore the optimal binding/dissociation pathways of the NR ligands. Specifically, farnesoid X receptor (FXR) is considered here as the target system since it has been an important target for the treatment of bile acid metabolism-associated diseases, and a series of structures cocrystallized with diverse scaffold ligands were resolved. By using random acceleration molecular dynamics (RAMD) simulation and umbrella sampling (US), 5 main dissociation pathways (pathways I-V) were identified in 11 representative FXR ligands, with most of them (9/11) preferring to go through Pathway III and the remaining two favoring escaping from Pathway I and IV. Furthermore, key residues functioning in the three main dissociation pathways were revealed by the kinetic residue energy analysis (KREA) based on the US trajectories, which may serve as road-marker residues for rapid identification of the (un)binding pathways of FXR ligands. Moreover, the preferred pathways explored by RAMD simulations are in good agreement with the minimum free energy path identified by the US simulations with the Pearson R = 0.76 between the predicted binding affinity and the experimental data, suggesting that RAMD is suitable for applying in large-scale (un)binding-pathway exploration in the case of ligands with obscure binding tunnels to the target.

Structural dynamics of GluK2 kainate receptors in apo and partial agonist bound states

Kainate receptors (KARs) belong to the family of ionotropic glutamate receptors (iGluRs) and are tetrameric ligand-gated ion channels that regulate neurotransmitter release and excitatory synaptic transmission in the central nervous system. While KARs share overall architectures with other iGluR subfamilies, their dynamics are significantly different from those of other iGluRs. KARs are activated by both full and partial agonists. While there is less efficacy with partial agonists than with full agonists, the detailed mechanism has remained elusive. Here, we used cryo-electron microscopy to determine the structures of homomeric rat GluK2 KARs in the absence of ligands (apo) and in complex with a partial agonist. Intriguingly, the apo state KARs were captured in desensitized conformation. This structure confirms the KAR desensitization prior to activation. Structures of KARs complexed to the partial agonist domoate populate in domoate bound desensitized and non-active/non-desensitized states. These previously unseen intermediate structures highlight the molecular mechanism of partial agonism in KARs. Additionally, we show how N-glycans stabilized the ligand-binding domain dimer via cation/anion binding and modulated receptor gating properties using electrophysiology. Our findings provide vital structural and functional insights into the unique KAR gating mechanisms.

Allosteric Competition and Inhibition in AMPA Receptors

Excitatory neurotransmission is principally mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). Dysregulation of AMPARs is the cause of many neurological disorders and how therapeutic candidates such as negative allosteric modulators inhibit AMPARs is unclear. Here, we show that non-competitive inhibition desensitizes AMPARs to activation and prevents positive allosteric modulation. We dissected the noncompetitive inhibition mechanism of action by capturing AMPARs bound to glutamate and the prototypical negative allosteric modulator, GYKI-52466, with cryo-electron microscopy. Noncompetitive inhibition by GYKI-52466, which binds in the transmembrane collar region surrounding the ion channel, negatively modulates AMPARs by decoupling glutamate binding in the ligand binding domain from the ion channel. Furthermore, during allosteric competition between negative and positive modulators, negative allosteric modulation by GKYI-52466 outcompetes positive allosteric modulators to control AMPAR function. Our data provide a new framework for understanding allostery of AMPARs and foundations for rational design of therapeutics targeting AMPARs in neurological diseases.

Desensitization dynamics of the AMPA receptor

To perform their physiological functions, amino methyl propionic acid receptors (AMPARs) cycle through active, resting, and desensitized states, and dysfunction in AMPAR activity is associated with various neurological disorders. Transitions among AMPAR functional states, however, are largely uncharacterized at atomic resolution and are difficult to examine experimentally. Here, we report long-timescale molecular dynamics simulations of dimerized AMPAR ligand-binding domains (LBDs), whose conformational changes are tightly coupled to changes in AMPAR functional states, in which we observed LBD dimer activation and deactivation upon ligand binding and unbinding at atomic resolution. Importantly, we observed the ligand-bound LBD dimer transition from the active conformation to several other conformations, which may correspond with distinct desensitized conformations. We also identified a linker region whose structural rearrangements heavily affected the transitions to and among these putative desensitized conformations, and confirmed, using electrophysiology experiments, the importance of the linker region in these functional transitions.

Excitatory and inhibitory D-serine binding to the NMDA receptor

N-methyl-D-aspartate receptors (NMDARs) uniquely require binding of two different neurotransmitter agonists for synaptic transmission. D-serine and glycine bind to one subunit, GluN1, while glutamate binds to the other, GluN2. These agonists bind to the receptor's bi-lobed ligand-binding domains (LBDs), which close around the agonist during receptor activation. To better understand the unexplored mechanisms by which D-serine contributes to receptor activation, we performed multi-microsecond molecular dynamics simulations of the GluN1/GluN2A LBD dimer with free D-serine and glutamate agonists. Surprisingly, we observed D-serine binding to both GluN1 and GluN2A LBDs, suggesting that D-serine competes with glutamate for binding to GluN2A. This mechanism is confirmed by our electrophysiology experiments, which show that D-serine is indeed inhibitory at high concentrations. Although free energy calculations indicate that D-serine stabilizes the closed GluN2A LBD, its inhibitory behavior suggests that it either does not remain bound long enough or does not generate sufficient force for ion channel gating. We developed a workflow using pathway similarity analysis to identify groups of residues working together to promote binding. These conformation-dependent pathways were not significantly impacted by the presence of N-linked glycans, which act primarily by interacting with the LBD bottom lobe to stabilize the closed LBD.

Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy

Systematic and quantitative analysis of the reliability of formally exact methods that in silico calculate absolute protein-ligand binding free energies remains lacking. Here, we provide, for the first time, evidence-based information on the reliability of these methods by statistically studying 853 cases from 34 different research groups through meta-analysis. The results show that formally exact methods approach chemical accuracy (error = 1.58 kcal/mol), even if people are challenging difficult tasks such as blind drug screening in recent years. The geometrical-pathway-based methods prove to possess a better convergence ability than the alchemical ones, while the latter have a larger application range. We also reveal the importance of always using the latest force fields to guarantee reliability and discuss the pros and cons of turning to an implicit solvent model in absolute binding free-energy calculations. Moreover, based on the meta-analysis, an evidence-based guideline for in silico binding free-energy calculations is provided.

Genome-Wide Identification, Characterization, and Expression Analysis of Glutamate Receptor-like Gene (GLR) Family in Sugarcane

The plant glutamate receptor-like gene (GLR) plays a vital role in development, signaling pathways, and in its response to environmental stress. However, the GLR gene family has not been comprehensively and systematically studied in sugarcane. In this work, 43 GLR genes, including 34 in Saccharum spontaneum and 9 in the Saccharum hybrid cultivar R570, were identified and characterized, which could be divided into three clades (clade I, II, and III). They had different evolutionary mechanisms, the former was mainly on the WGD/segmental duplication, while the latter mainly on the proximal duplication. Those sugarcane GLR proteins in the same clade had a similar gene structure and motif distribution. For example, 79% of the sugarcane GLR proteins contained all the motifs, which proved the evolutionary stability of the sugarcane GLR gene family. The diverse cis-acting regulatory elements indicated that the sugarcane GLRs may play a role in the growth and development, or under the phytohormonal, biotic, and abiotic stresses. In addition, GO and KEGG analyses predicted their transmembrane transport function. Based on the transcriptome data, the expression of the clade III genes was significantly higher than that of the clade I and clade II. Furthermore, qRT-PCR analysis demonstrated that the expression of the SsGLRs was induced by salicylic acid (SA) treatment, methyl jasmonic acid (MeJA) treatment, and abscisic acid (ABA) treatment, suggesting their involvement in the hormone synthesis and signaling pathway. Taken together, the present study should provide useful information on comparative genomics to improve our understanding of the GLR genes and facilitate further research on their functions.

Patients' attitudes toward conventional and herbal treatments for depression and anxiety: A cross-sectional Israeli survey

BACKGROUND

As many patients view conventional antidepressants and anxiolytics negatively, it is not surprising that the willingness to apply these treatments is far from ideal, thus posing a critical barrier in promoting an effective and durable treatment.

AIM

The present study aimed to explore patients' attitudes toward conventional and herbal treatments for depression and anxiety, while considering cultural and demographic factors, to further elucidate the antecedes that putatively determine the treatment's outcome.

METHODS

During June 2017, a cross-sectional survey was conducted using stratified sampling from a large-scale Israeli volunteer online panel. The final sample included 591 Jewish Israeli adults that reported they were suffering from depression or anxiety.

RESULTS

A heterogeneous range of attitudes toward treatment was found: for example, a large group of patients did not utilize prescription medications (39%), a professional consultation (12.9%), or any form of treatment (17.4%). Interestingly, these patients were significantly more likely to support naturally-derived treatments and were less concerned with scientific proof. Further, adverse effects were demonstrated as a prominent factor in the choice of treatment. A higher incidence of adverse effects was associated with an increased willingness to consider an alternative herbal treatment. Noteworthy attitudes were found in orthodox-Jewish individuals, who showed similar consultation rates, but utilized more psychological, rather than pharmacological treatments.

CONCLUSIONS

It is proposed that patients' perspectives and cultural backgrounds are needed to be taken into consideration during the clinical assessment and choice of treatment. The findings imply that a particular emphasis should be placed on patients that discard conventional pharmacological options and on distinct cultural aspects. Several recommendations for revising the current policy are advocated to promote more culturally-informed and patient-oriented care.

Nicotinic receptors: From protein allostery to computational neuropharmacology

We propose an extension and further development of the Monod-Wyman-Changeux model for allosteric transitions of regulatory proteins to brain communications and specifically to neurotransmitters receptors, with the nicotinic acetylcholine receptor (nAChR) as a model of ligand-gated ion channels. The present development offers an expression of the change of the gating isomerization constant caused by pharmacological ligand binding in terms of its value in the absence of ligands and several "modulation factors", which vary with orthosteric ligand binding (agonists/antagonists), allosteric ligand binding (positive allosteric modulators/negative allosteric modulators) and receptor desensitization. The new - explicit - formulation of such "modulation factors", provides expressions for the pharmacological attributes of potency, efficacy, and selectivity for the modulatory ligands (including endogenous neurotransmitters) in terms of their binding affinity for the active, resting, and desensitized states of the receptor. The current formulation provides ways to design neuroactive compounds with a controlled pharmacological profile, opening the field of computational neuro-pharmacology.

Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels

Many physiologic effects of l-glutamate, the major excitatory neurotransmitter in the mammalian central nervous system, are mediated via signaling by ionotropic glutamate receptors (iGluRs). These ligand-gated ion channels are critical to brain function and are centrally implicated in numerous psychiatric and neurologic disorders. There are different classes of iGluRs with a variety of receptor subtypes in each class that play distinct roles in neuronal functions. The diversity in iGluR subtypes, with their unique functional properties and physiologic roles, has motivated a large number of studies. Our understanding of receptor subtypes has advanced considerably since the first iGluR subunit gene was cloned in 1989, and the research focus has expanded to encompass facets of biology that have been recently discovered and to exploit experimental paradigms made possible by technological advances. Here, we review insights from more than 3 decades of iGluR studies with an emphasis on the progress that has occurred in the past decade. We cover structure, function, pharmacology, roles in neurophysiology, and therapeutic implications for all classes of receptors assembled from the subunits encoded by the 18 ionotropic glutamate receptor genes. SIGNIFICANCE STATEMENT: Glutamate receptors play important roles in virtually all aspects of brain function and are either involved in mediating some clinical features of neurological disease or represent a therapeutic target for treatment. Therefore, understanding the structure, function, and pharmacology of this class of receptors will advance our understanding of many aspects of brain function at molecular, cellular, and system levels and provide new opportunities to treat patients.

Structural biology and thermodynamics of GluD receptors

Glutamate delta (GluD) receptors are a functionally enigmatic subfamily of ionotropic glutamate receptors. Despite sharing similar sequences and structures with AMPA, NMDA, and kainate receptors, GluD receptors do not bind glutamate nor function as ligand-gated ion channels. Binding d-serine and engaging in transsynaptic protein-protein interactions, GluD receptors are thought to undergo complex conformational rearrangements for non-ionotropic signaling that regulates synaptic plasticity. Recent structural, biochemical, and computational studies have elucidated multiple conformational and thermodynamic factors governing the unique properties of GluD receptors. Here, we review advances in biophysical insights into GluD receptors and discuss the structural thermodynamic relationships that underpin their neurobiological functions.

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

Absolute binding free energy calculations with explicit solvent molecular simulations can provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to find new drug candidates. However, these calculations can be complex to implement and perform. Here, we introduce the software BAT.py, a Python tool that invokes the AMBER simulation package to automate the calculation of binding free energies for a protein with a series of ligands. The software supports the attach-pull-release (APR) and double decoupling (DD) binding free energy methods, as well as the simultaneous decoupling-recoupling (SDR) method, a variant of double decoupling that avoids numerical artifacts associated with charged ligands. We report encouraging initial test applications of this software both to re-rank docked poses and to estimate overall binding free energies. We also show that it is practical to carry out these calculations cheaply by using graphical processing units in common machines that can be built for this purpose. The combination of automation and low cost positions this procedure to be applied in a relatively high-throughput mode and thus stands to enable new applications in early-stage drug discovery.

D-Serine Potently Drives Ligand-Binding Domain Closure in the Ionotropic Glutamate Receptor GluD2

Despite their classification as ionotropic glutamate receptors, GluD receptors are not functional ligand-gated ion channels and do not bind glutamate. GluD2 receptors bind D-serine and coordinate transsynaptic complexes that regulate synaptic plasticity. Instead of opening the ion channel pore, mechanical tension produced from closure of GluD2 ligand-binding domains (LBDs) drives conformational rearrangements for non-ionotropic signaling. We report computed conformational free energy landscapes for the GluD2 LBD in apo and D-serine-bound states. Unexpectedly, the conformational free energy associated with GluD2 LBD closure upon D-serine binding is greater than that for AMPA, NMDA, and kainate receptor LBDs upon agonist binding. This excludes insufficient force generation as an explanation for lack of ion channel activity in GluD2 receptors and suggests that non-ionotropic conformational rearrangements do more work than pore opening. We also report free energy landscapes for GluD2 LBD harboring a neurodegenerative mutation and demonstrate selective stabilization of closed conformations in the apo state.

A Computational Pipeline to Predict Cardiotoxicity: From the Atom to the Rhythm

RATIONALE

Drug-induced proarrhythmia is so tightly associated with prolongation of the QT interval that QT prolongation is an accepted surrogate marker for arrhythmia. But QT interval is too sensitive a marker and not selective, resulting in many useful drugs eliminated in drug discovery.

OBJECTIVE

To predict the impact of a drug from the drug chemistry on the cardiac rhythm.

METHODS AND RESULTS

In a new linkage, we connected atomistic scale information to protein, cell, and tissue scales by predicting drug-binding affinities and rates from simulation of ion channel and drug structure interactions and then used these values to model drug effects on the hERG channel. Model components were integrated into predictive models at the cell and tissue scales to expose fundamental arrhythmia vulnerability mechanisms and complex interactions underlying emergent behaviors. Human clinical data were used for model framework validation and showed excellent agreement, demonstrating feasibility of a new approach for cardiotoxicity prediction.

CONCLUSIONS

We present a multiscale model framework to predict electrotoxicity in the heart from the atom to the rhythm. Novel mechanistic insights emerged at all scales of the system, from the specific nature of proarrhythmic drug interaction with the hERG channel, to the fundamental cellular and tissue-level arrhythmia mechanisms. Applications of machine learning indicate necessary and sufficient parameters that predict arrhythmia vulnerability. We expect that the model framework may be expanded to make an impact in drug discovery, drug safety screening for a variety of compounds and targets, and in a variety of regulatory processes.

Glutamate receptors from diverse animal species exhibit unexpected structural and functional diversity

The identification of AMPA, kainate and NMDA glutamate receptor subtypes by Watkins and colleagues underlies much of our understanding of excitatory synaptic transmission in the central nervous system of animals. Ongoing large scale genome sequencing projects in species for which physiological analysis of receptor function is challenging are resulting in identification of numerous eukaryotic glutamate receptor ion channels in the animal kingdom of life. On the basis of sequence similarity, these are frequently classified into the three vertebrate subtypes, initially identified using subtype selective ligands. Recent work reveals unexpected ligand binding profiles for these newly identified glutamate receptors, for example, kainate receptors on which NMDA acts as a competitive antagonist, and high affinity homomeric glycine activated glutamate receptors. Structural studies reveal that only subtle changes in the ligand binding domain, often identified only in retrospect, underlie different patterns of ligand binding, and that the biology of glutamate receptors is more complex than first anticipated.

A National Survey of Integrated Vascular Surgery Residents' Experiences With and Attitudes About Quality Improvement During Residency

BACKGROUND

Integrated vascular surgery residency, or "0+5," programs provide education in the Accreditation Council for Graduate Medical Education (ACGME) competencies of Systems-Based Practice (SBP) and Practice-Based Learning and Improvement (PBLI), which include milestones related to quality improvement (QI). It is unclear what QI curricula are in place in 0+5 programs nationally or how 0+5 residents perceive the importance of QI.

OBJECTIVE

The purpose of this study is to assess current 0+5 residents' knowledge, experiences with, and attitudes about QI.

DESIGN

A survey was developed using the ACGME Common Program Requirements and Milestones pertaining to QI. All 0+5 residents from 2017 to 2018 academic year were emailed an electronic link to the survey. Descriptive statistics and cross-tabulations were calculated using Stata/MP version 13.1.

SETTING

All 0+5 vascular surgery residency programs in the United State (n = 52).

PARTICIPANTS

The survey was completed by 35% (n = 90/257) of 0+5 residents, representing 75% of 0+5 programs in the United States (n = 39/52).

RESULTS

Forty-one percent of respondents felt that applying QI methods is very important and 33% felt that QI education is very important for their future work, however, just 13% felt very prepared to lead a QI initiative. Residents' perceptions of preparedness to lead QI projects and the importance they attached to QI education were significantly influenced by their participation in a QI project (p = 0.003 and p = 0.038 respectively). Finally, just 8% (n = 6) of residents responded correctly to all 13 knowledge-based questions and these residents felt better prepared to lead a QI initiative compared to those who answered incorrectly (p = 0.002).

CONCLUSIONS

Most 0+5 residents report participation in a QI project during residency, however, few feel prepared to lead a QI initiative in practice. Furthermore, only half of PGY5 0+5 residents report achieving specific ACGME targets for graduation pertaining to QI. Current QI curricula in 0+5 programs may be inadequate in teaching fundamental QI concepts and achieving ACGME competency targets for graduation.

Pre/post effectiveness evaluation of updated additional risk minimisation measures for an orphan disease: Myozyme (alglucosidase alfa) Safety Information Packet

BACKGROUND

The alglucosidase alfa (Myozyme®) Safety Information Packet ("previous SIP") was updated to improve readability and content ("updated SIP"). We compared the previous and updated SIPs.

METHODS

A two-wave pre-post multicountry survey was conducted among health care professionals (HCPs) who prescribed or monitored patients on alglucosidase alfa in the largest European Union ("EU5") countries and Poland. Wave (W) 2 started 15 months after completion of W1 and the implementation of the updated SIP. Changes between the waves were analysed.

RESULTS

Forty-six HCPs (34 physicians/12 nurses) participated in W1 and 52 in W2 (42 physicians/10 nurses); 22 participated in both waves. Nonsignificant differences were observed between waves 1 and 2 for awareness (75.6% in W1 and 82.4% in W2) and receipt (77.7% in W1 and 74.5% in W2) of the SIP, reading (88.6% in W1 and 89.5% in W2) and usage (88.2% in W1 and 89.5% in W2) among receivers of the SIP, or the overall knowledge about immunological testing (61.1% in W1 vs 55.1% in W2). Frequency of performance of immunological testing was significantly higher in W2 than in W1 (50.3% vs 34.4%; P = .024) with a tendency for increases in the appropriate performance of all types of testing in W2.

CONCLUSIONS

Both versions of the SIP showed relatively high awareness, receipt, reading, and usage, with an overall trend for most measures to improve numerically in W2. The updated SIP did not require further changes.

Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution

Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.

High Conformational Variability in the GluK2 Kainate Receptor Ligand-Binding Domain

The kainate family of ionotropic glutamate receptors (iGluRs) mediates pre- and postsynaptic neurotransmission. Previously computed conformational potentials of mean force (PMFs) for iGluR ligand-binding domains (LBDs) revealed subtype-dependent conformational differences between α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartic acid (NMDA) iGluR subfamilies. Here we report PMFs for the kainate receptor GluK2 in apo and glutamate-bound states. Apo and glutamate-bound GluK2 LBDs preferentially access closed-cleft conformations. Apo GluK2 exhibits a surprisingly high degree of conformational flexibility, accessing open and closed states. Comparing across iGluR subtypes, these results are similar to glycine-binding GluN1 and GluN3A NMDA subunits and differ from glutamate-binding GluA2 and GluN2A subunits. To test the contribution of cross-lobe interactions on closed-cleft LBD stability, we computed PMFs for two GluK2 mutants, D462A and D656S. D462A, but not D656S, weakens closed-cleft conformations of the glutamate-bound LBD. Theoretical Boltzmann-weighted small-angle X-ray scattering profiles improve agreement with experimental results compared with calculations from the LBD crystal structure alone.

Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain

Ionotropic glutamate receptors (iGluRs) mediate the majority of excitatory neurotransmission in the brain. Their dysfunction is implicated in many neurological disorders, rendering iGluRs potential drug targets. Here, we performed a systematic analysis of the druggability of two major iGluR subfamilies, using molecular dynamics simulations in the presence of drug-like molecules. We demonstrate the applicability of druggability simulations by faithfully identifying known agonist and modulator sites on AMPA receptors (AMPARs) and NMDA receptors. Simulations produced the expected allosteric changes of the AMPAR ligand-binding domain in response to agonist. We also identified a novel ligand-binding site specific to the GluA3 AMPAR N-terminal domain (NTD), resulting from its unique conformational flexibility that we explored further with crystal structures trapped in vastly different states. In addition to providing an in-depth analysis into iGluR NTD dynamics, our approach identifies druggable sites and permits the determination of pharmacophoric features toward novel iGluR modulators.

Population Shift Mechanism for Partial Agonism of AMPA Receptor

α-amino-3-hydroxy-5-methyl-4-isoaxazolepropionic acid (AMPA) ionotropic glutamate receptors mediate fast excitatory neurotransmission in the central nervous system, and their dysfunction is associated with neurological diseases. Glutamate binding to ligand-binding domains (LBDs) of AMPA receptors induces channel opening in the transmembrane domains of the receptors. The T686A mutation reduces glutamate efficacy so that the glutamate behaves as a partial agonist. The crystal structures of wild-type and mutant LBDs are very similar and cannot account for the observed behavior. To elucidate the molecular mechanism inducing partial agonism of the T686A mutant, we computed the free-energy landscapes governing GluA2 LBD closure using replica-exchange umbrella sampling simulations. A semiclosed state, not observed in crystal structures, appears in the mutant during simulation. In this state, the LBD cleft opens slightly because of breaking of interlobe hydrogen bonds, reducing the efficiency of channel opening. The energy difference between the LBD closed and semiclosed states is small, and transitions between the two states would occur by thermal fluctuations. Evidently, glutamate binding to the T686A mutant induces a population shift from a closed to a semiclosed state, explaining the partial agonism in the AMPA receptor.

Increasing Vaccination: Putting Psychological Science Into Action

Vaccination is one of the great achievements of the 20th century, yet persistent public-health problems include inadequate, delayed, and unstable vaccination uptake. Psychology offers three general propositions for understanding and intervening to increase uptake where vaccines are available and affordable. The first proposition is that thoughts and feelings can motivate getting vaccinated. Hundreds of studies have shown that risk beliefs and anticipated regret about infectious disease correlate reliably with getting vaccinated; low confidence in vaccine effectiveness and concern about safety correlate reliably with not getting vaccinated. We were surprised to find that few randomized trials have successfully changed what people think and feel about vaccines, and those few that succeeded were minimally effective in increasing uptake. The second proposition is that social processes can motivate getting vaccinated. Substantial research has shown that social norms are associated with vaccination, but few interventions examined whether normative messages increase vaccination uptake. Many experimental studies have relied on hypothetical scenarios to demonstrate that altruism and free riding (i.e., taking advantage of the protection provided by others) can affect intended behavior, but few randomized trials have tested strategies to change social processes to increase vaccination uptake. The third proposition is that interventions can facilitate vaccination directly by leveraging, but not trying to change, what people think and feel. These interventions are by far the most plentiful and effective in the literature. To increase vaccine uptake, these interventions build on existing favorable intentions by facilitating action (through reminders, prompts, and primes) and reducing barriers (through logistics and healthy defaults); these interventions also shape behavior (through incentives, sanctions, and requirements). Although identification of principles for changing thoughts and feelings to motivate vaccination is a work in progress, psychological principles can now inform the design of systems and policies to directly facilitate action.

Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are key players in synaptic transmission and plasticity. They are composed of four subunits, each containing four functional domains, the quaternary packing and collective structural dynamics of which are important determinants of their molecular mechanism of function. With the explosion of structural studies on different members of the family, including the structures of activated open channels, the mechanisms of action of these central signaling machines are now being elucidated. We review the current state of computational studies on two major members of the family, AMPA and NMDA receptors, with focus on molecular simulations and elastic network model analyses that have provided insights into the coupled movements of extracellular and transmembrane domains. We describe the newly emerging mechanisms of activation, allosteric signaling and desensitization, as mainly a selective triggering of pre-existing soft motions, as deduced from computational models and analyses that leverage structural data on intact AMPA and NMDA receptors in different states.

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

The need for accurate yet efficient representation of the aqueous environment in biomolecular modeling has led to the development of a variety of generalized Born (GB) implicit solvent models. While many studies have focused on the accuracy of available GB models in predicting solvation free energies, a systematic assessment of the quality of these models in binding free energy calculations, crucial for rational drug design, has not been undertaken. Here, we evaluate the accuracies of eight common GB flavors (GB-HCT, GB-OBC, GB-neck2, GBNSR6, GBSW, GBMV1, GBMV2, and GBMV3), available in major molecular dynamics packages, in predicting the electrostatic binding free energies ( ΔΔ G_el) for a diverse set of 60 biomolecular complexes belonging to four main classes: protein-protein, protein-drug, RNA-peptide, and small complexes. The GB flavors are examined in terms of their ability to reproduce the results from the Poisson-Boltzmann (PB) model, commonly used as accuracy reference in this context. We show that the agreement with the PB of ΔΔ G_el estimates varies widely between different GB models and also across different types of biomolecular complexes, with R² correlations ranging from 0.3772 to 0.9986. A surface-based "R6" GB model recently implemented in AMBER shows the closest overall agreement with reference PB ( R² = 0.9949, RMSD = 8.75 kcal/mol). The RNA-peptide and protein-drug complex sets appear to be most challenging for all but one model, as indicated by the large deviations from the PB in ΔΔ G_el. Small neutral complexes present the least challenge for most of the GB models tested. The quantitative demonstration of the strengths and weaknesses of the GB models across the diverse complex types provided here can be used as a guide for practical computations and future development efforts.

Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics

Ionotropic glutamate receptors (iGluRs) mediate neurotransmission at the majority of excitatory synapses in the brain. Little is known, however, about how glutamate reaches the recessed binding pocket in iGluR ligand-binding domains (LBDs). Here we report the process of glutamate binding to a prototypical iGluR, GluA2, in atomistic detail using unbiased molecular simulations. Charged residues on the LBD surface form pathways that facilitate glutamate binding by effectively reducing a three-dimensional diffusion process to a spatially constrained, two-dimensional one. Free energy calculations identify residues that metastably bind glutamate and help guide it into the binding pocket. These simulations also reveal that glutamate can bind in an inverted conformation and also reorient while in its pocket. Electrophysiological recordings demonstrate that eliminating these transient binding sites slows activation and deactivation, consistent with slower glutamate binding and unbinding. These results suggest that binding pathways have evolved to optimize rapid responses of AMPA-type iGluRs at synapses.

Functional Validation of Heteromeric Kainate Receptor Models

Kainate receptors require the presence of external ions for gating. Most work thus far has been performed on homomeric GluK2 but, in vivo, kainate receptors are likely heterotetramers. Agonists bind to the ligand-binding domain (LBD) which is arranged as a dimer of dimers as exemplified in homomeric structures, but no high-resolution structure currently exists of heteromeric kainate receptors. In a full-length heterotetramer, the LBDs could potentially be arranged either as a GluK2 homomer alongside a GluK5 homomer or as two GluK2/K5 heterodimers. We have constructed models of the LBD dimers based on the GluK2 LBD crystal structures and investigated their stability with molecular dynamics simulations. We have then used the models to make predictions about the functional behavior of the full-length GluK2/K5 receptor, which we confirmed via electrophysiological recordings. A key prediction and observation is that lithium ions bind to the dimer interface of GluK2/K5 heteromers and slow their desensitization.

Energetics of Glutamate Binding to an Ionotropic Glutamate Receptor

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are responsible for the majority of excitatory transmission at the synaptic cleft. Mechanically speaking, agonist binding to the ligand binding domain (LBD) activates the receptor by triggering a conformational change that is transmitted to the transmembrane region, opening the ion channel pore. We use fully atomistic molecular dynamics simulations to investigate the binding process in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, an iGluR subtype. The string method with swarms of trajectories was applied to calculate the possible pathways glutamate traverses during ligand binding. Residues peripheral to the binding cleft are found to metastably bind the ligand prior to ligand entry into the binding pocket. Umbrella sampling simulations were performed to compute the free energy barriers along the binding pathways. The calculated free energy profiles demonstrate that metastable interactions contribute substantially to the energetics of ligand binding and form local minima in the overall free energy landscape. Protein-ligand interactions at sites outside of the orthosteric agonist-binding site may serve to lower the transition barriers of the binding process.

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.

Computational membrane biophysics: From ion channel interactions with drugs to cellular function

The rapid development of experimental and computational techniques has changed fundamentally our understanding of cellular-membrane transport. The advent of powerful computers and refined force-fields for proteins, ions, and lipids has expanded the applicability of Molecular Dynamics (MD) simulations. A myriad of cellular responses is modulated through the binding of endogenous and exogenous ligands (e.g. neurotransmitters and drugs, respectively) to ion channels. Deciphering the thermodynamics and kinetics of the ligand binding processes to these membrane proteins is at the heart of modern drug development. The ever-increasing computational power has already provided insightful data on the thermodynamics and kinetics of drug-target interactions, free energies of solvation, and partitioning into lipid bilayers for drugs. This review aims to provide a brief summary about modeling approaches to map out crucial binding pathways with intermediate conformations and free-energy surfaces for drug-ion channel binding mechanisms that are responsible for multiple effects on cellular functions. We will discuss post-processing analysis of simulation-generated data, which are then transformed to kinetic models to better understand the molecular underpinning of the experimental observables under the influence of drugs or mutations in ion channels. This review highlights crucial mathematical frameworks and perspectives on bridging different well-established computational techniques to connect the dynamics and timescales from all-atom MD and free energy simulations of ion channels to the physiology of action potentials in cellular models. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.

Structural Mechanisms of Gating in Ionotropic Glutamate Receptors

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate the majority of excitatory neurotransmission in the central nervous system. iGluRs open their ion channels in response to binding of the neurotransmitter glutamate, rapidly depolarize the postsynaptic neuronal membrane, and initiate signal transduction. Recent studies using X-ray crystallography and cryo-electron microscopy have determined full-length iGluR structures that (1) uncover the receptor architecture in an unliganded, resting state, (2) reveal conformational changes produced by ligands in order to activate iGluRs, open their ion channels, and conduct ions, and (3) show how activated, glutamate-bound iGluRs can adopt a nonconducting desensitized state. These new findings, combined with the results of previous structural and functional experiments, kinetic and molecular modeling, mutagenesis, and biochemical analyses, provide new views on the structural mechanisms of iGluR gating.

Semiclosed Conformations of the Ligand-Binding Domains of NMDA Receptors during Stationary Gating

NMDA receptors are tetrameric ligand-gated ion channels. In the continuous presence of saturating agonists, NMDA receptors undergo stationary gating, in which the channel stochastically switches between an open state that permits ion conductance and a closed state that prevents permeation. The ligand-binding domains (LBDs) of the four subunits are expected to have closed clefts in the channel-open state. On the other hand, there is little knowledge about the conformational status of the LBDs in the channel-closed state during stationary gating. To probe the latter conformational status, Kussius and Popescu engineered interlobe disulfide cross-links in NMDA receptors and found that the cross-linking produced stationary gating kinetics that differed only subtly from that produced by agonist binding. These authors assumed that the cross-linking immobilized the LBDs in cleft-closed conformations, and consequently concluded that throughout stationary gating, agonist-bound LBDs also stayed predominantly in cleft-closed conformations and made only infrequent excursions to cleft-open conformations. Here, by calculating the conformational free energies of cross-linked and agonist-bound LBDs, we assess whether cross-linking actually traps the LBDs in cleft-closed conformations and delineate semiclosed conformations of agonist-bound LBDs that may potentially be thermodynamically and kinetically important during stationary gating. Our free-energy results show that the cross-linked LBDs are not locked in the fully closed form; rather, they sample semiclosed conformations almost as readily as the agonist-bound LBDs. Several lines of reasoning suggest that LBDs are semiclosed in the channel-closed state during stationary gating. Our free-energy simulations suggest possible structural details of such semiclosed LBD conformations, including intra- and intermolecular interactions that serve as alternatives to those in the cleft-closed conformations.

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

Bromodomains, protein domains involved in epigenetic regulation, are able to bind small molecules with high affinity. In the present study, we report free energy calculations for the binding of seven ligands to the first BRD4 bromodomain, using the attach-pull-release (APR) method to compute the reversible work of removing the ligands from the binding site and then allowing the protein to relax conformationally. We test three different water models, TIP3P, TIP4PEw, and SPC/E, as well as the GAFF and GAFF2 parameter sets for the ligands. Our simulations show that the apo crystal structure of BRD4 is only metastable, with a structural transition happening in the absence of the ligand typically after 20 ns of simulation. We compute the free energy change for this transition with a separate APR calculation on the free protein and include its contribution to the ligand binding free energies, which generally causes an underestimation of the affinities. By testing different water models and ligand parameters, we are also able to assess their influence in our results and determine which one produces the best agreement with the experimental data. Both free energies associated with the conformational change and ligand binding are affected by the choice of water model, with the two sets of ligand parameters affecting their binding free energies to a lesser degree. Across all six combinations of water model and ligand potential function, the Pearson correlation coefficients between calculated and experimental binding free energies range from 0.55 to 0.83, and the root-mean-square errors range from 1.4-3.2 kcal/mol. The current protocol also yields encouraging preliminary results when used to assess the relative stability of ligand poses generated by docking or other methods, as illustrated for two different ligands. Our method takes advantage of the high performance provided by graphics processing units and can readily be applied to other ligands as well as other protein systems.

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.

Structural mechanisms of activation and desensitization in neurotransmitter-gated ion channels

Ion channels gated by neurotransmitters are present across metazoans, in which they are essential for brain function, sensation and locomotion; closely related homologs are also found in bacteria. Structures of eukaryotic pentameric cysteine-loop (Cys-loop) receptors and tetrameric ionotropic glutamate receptors in multiple functional states have recently become available. Here, I describe how these studies relate to established ideas regarding receptor activation and how they have enabled decades' worth of functional work to be pieced together, thus allowing previously puzzling aspects of receptor activity to be understood.

Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating

AMPA subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission and are implicated in numerous neurological diseases. Ionic currents through AMPA receptor channels can be allosterically regulated via different sites on the receptor protein. We used site-directed mutagenesis and patch-clamp recordings to probe the ion channel extracellular collar, the binding region for noncompetitive allosteric inhibitors. We found position and substitution-dependent effects for introduced mutations at this region on AMPA receptor gating. The results of mutagenesis suggested that the transmembrane domains M1, M3 and M4, which contribute to the ion channel extracellular collar, undergo significant relative displacement during gating. We used molecular dynamics simulations to predict an AMPA receptor open state structure and rationalize the results of mutagenesis. We conclude that the ion channel extracellular collar plays a distinct role in gating and represents a hub for powerful allosteric modulation of AMPA receptor function that can be used for developing novel therapeutics.

Gating Motions and Stationary Gating Properties of Ionotropic Glutamate Receptors: Computation Meets Electrophysiology

Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels essential to all aspects of brain function, including higher order processes such as learning and memory. For decades, electrophysiology was the primary means for characterizing the function of iGluRs and gaining mechanistic insight. Since the turn of the century, structures of isolated water-soluble domains and transmembrane-domain-containing constructs have provided the basis for formulating mechanistic hypotheses. Because these structures only represent sparse, often incomplete snapshots during iGluR activation, significant gaps in knowledge remain regarding structures, energetics, and dynamics of key substates along the functional processes. Some of these gaps have recently been filled by molecular dynamics simulations and theoretical modeling. In this Account, I describe our work in the latter arena toward characterizing iGluR gating motions and developing a formalism for calculating thermodynamic and kinetic properties of stationary gating. The structures of iGluR subunits have a highly modular architecture, in which the ligand-binding domain and the transmembrane domain are well separated and connected by flexible linkers. The ligand-binding domain in turn is composed of two subdomains. During activation, agonist binding induces the closure of the intersubdomain cleft. The cleft closure leads to the outward pulling of a linker tethered to the extracellular terminus of the major pore-lining helix of the transmembrane domain, thereby opening the channel. This activation model based on molecular dynamics simulations was validated by residue-specific information from electrophysiological data on cysteine mutants. A further critical test was made through introducing glycine insertions in the linker. Molecular dynamics simulations showed that, with lengthening by glycine insertions, the linker became less effective in pulling the pore-lining helix, leading to weaker stabilization of the channel-open state. In full agreement, single-channel recordings showed that the channel open probability decreased progressively as the linker was lengthened by glycine insertions. Crystal structures of ligand-binding domains showing different degrees of cleft closure between full and partial agonists suggested a simple mechanism for one subtype of iGluRs, but mysteries surrounded a second subtype, where the ligand-binding domains open to similar degrees when bound with either full or partial agonists. Our free energy simulations now suggest that broadening of the free energy basin for cleft closure is a plausible solution. A theoretical basis for these mechanistic hypotheses on partial agonisms was provided by a model for the free energy surface of a full receptor, where the stabilization by cleft closure is transmitted via the linker to the channel-open state. This model can be implemented by molecular dynamics simulations to predict thermodynamic and kinetics properties of stationary gating that are amenable to direct test by single-channel recordings. Close integration between computation and electrophysiology holds great promises in revealing the conformations of key substates in functional processes and the mechanisms of disease-associated mutations.

Mechanism of partial agonism in AMPA-type glutamate receptors

Neurotransmitters trigger synaptic currents by activating ligand-gated ion channel receptors. Whereas most neurotransmitters are efficacious agonists, molecules that activate receptors more weakly-partial agonists-also exist. Whether these partial agonists have weak activity because they stabilize less active forms, sustain active states for a lesser fraction of the time or both, remains an open question. Here we describe the crystal structure of an α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR) ligand binding domain (LBD) tetramer in complex with the partial agonist 5-fluorowillardiine (FW). We validate this structure, and others of different geometry, using engineered intersubunit bridges. We establish an inverse relation between the efficacy of an agonist and its promiscuity to drive the LBD layer into different conformations. These results suggest that partial agonists of the AMPAR are weak activators of the receptor because they stabilize multiple non-conducting conformations, indicating that agonism is a function of both the space and time domains.

Advancing NMDA Receptor Physiology by Integrating Multiple Approaches

NMDA receptors (NMDARs) are ion channels activated by the excitatory neurotransmitter glutamate and are essential to all aspects of brain function, including learning and memory formation. Missense mutations distributed throughout NMDAR subunits have been associated with an array of neurological disorders. Recent structural, functional, and computational studies have generated many insights into the activation process connecting glutamate binding to ion-channel opening, which is central to NMDAR physiology and pathophysiology. The field appears poised for breakthroughs, including the exciting prospect of resolving the conformations and energetics of elementary steps in the activation process, and atomic-level modeling of the effects of missense mutations on receptor function. The most promising strategy going forward is through strong integration of multiple approaches.

Dynamics of the Ligand Binding Domain Layer during AMPA Receptor Activation

Ionotropic glutamate receptors are postsynaptic tetrameric ligand-gated channels whose activity mediates fast excitatory transmission. Glutamate binding to clamshell-shaped ligand binding domains (LBDs) triggers opening of the integral ion channel, but how the four LBDs orchestrate receptor activation is unknown. Here, we present a high-resolution x-ray crystal structure displaying two tetrameric LBD arrangements fully bound to glutamate. Using a series of engineered metal ion trapping mutants, we showed that the more compact of the two assemblies corresponds to an arrangement populated during activation of full-length receptors. State-dependent cross-linking of the mutants identified zinc bridges between the canonical active LBD dimers that formed when the tetramer was either fully or partially bound by glutamate. These bridges also stabilized the resting state, consistent with the recently published full-length apo structure. Our results provide insight into the activation mechanism of glutamate receptors and the complex conformational space that the LBD layer can sample.

Molecular lock regulates binding of glycine to a primitive NMDA receptor

The earliest metazoan ancestors of humans include the ctenophore Mnemiopsis leidyi The genome of this comb jelly encodes homologs of vertebrate ionotropic glutamate receptors (iGluRs) that are distantly related to glycine-activated NMDA receptors and that bind glycine with unusually high affinity. Using ligand-binding domain (LBD) mutants for electrophysiological analysis, we demonstrate that perturbing a ctenophore-specific interdomain Arg-Glu salt bridge that is notably absent from vertebrate AMPA, kainate, and NMDA iGluRs greatly increases the rate of recovery from desensitization, while biochemical analysis reveals a large decrease in affinity for glycine. X-ray crystallographic analysis details rearrangements in the binding pocket stemming from the mutations, and molecular dynamics simulations suggest that the interdomain salt bridge acts as a steric barrier regulating ligand binding and that the free energy required to access open conformations in the glycine-bound LBD is largely responsible for differences in ligand affinity among the LBD variants.

Blacks' Death Rate Due to Circulatory Diseases Is Positively Related to Whites' Explicit Racial Bias

Perceptions of racial bias have been linked to poorer circulatory health among Blacks compared with Whites. However, little is known about whether Whites' actual racial bias contributes to this racial disparity in health. We compiled racial-bias data from 1,391,632 Whites and examined whether racial bias in a given county predicted Black-White disparities in circulatory-disease risk (access to health care, diagnosis of a circulatory disease; Study 1) and circulatory-disease-related death rate (Study 2) in the same county. Results revealed that in counties where Whites reported greater racial bias, Blacks (but not Whites) reported decreased access to health care (Study 1). Furthermore, in counties where Whites reported greater racial bias, both Blacks and Whites showed increased death rates due to circulatory diseases, but this relationship was stronger for Blacks than for Whites (Study 2). These results indicate that racial disparities in risk of circulatory disease and in circulatory-disease-related death rate are more pronounced in communities where Whites harbor more explicit racial bias.

Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors

The stability of protein-protein interfaces can be essential for protein function. For ionotropic glutamate receptors, a family of ligand-gated ion channels vital for normal function of the central nervous system, such an interface exists between the extracellular ligand binding domains (LBDs). In the full-length protein, the LBDs are arranged as a dimer of dimers. Agonist binding to the LBDs opens the ion channel, and briefly after activation the receptor desensitizes. Several residues at the LBD dimer interface are known to modulate desensitization, and conformational changes around these residues are believed to be involved in the state transition. The general hypothesis is that the interface is disrupted upon desensitization, and structural evidence suggests that the disruption might be substantial. However, when cross-linking the central part of this interface, functional data suggest that the receptor can still undergo desensitization, contradicting the hypothesis of major interface disruption. Here, we illustrate how opening the dimer interface using steered molecular dynamics (SMD) simulations, and analyzing the work values required, provides a quantitative measure for interface stability. For one subtype of glutamate receptors, which is regulated by ion binding to the dimer interface, we show that opening the interface without ions bound requires less work than with ions present, suggesting that ion binding indeed stabilizes the interface. Likewise, for interface mutants with longer-lived active states, the interface is more stable, while the work required to open the interface is reduced for less active mutants. Moreover, a cross-linked mutant can still undergo initial interface opening motions similar to the native receptor and at similar energetic cost. Thus, our results support that interface opening is involved in desensitization. Furthermore, they provide reconciliation of apparently opposing data and demonstrate that SMD simulations can give relevant biological insight into longer time scale processes without the need for expensive calculations.

Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding

The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline.

Lessons from crystal structures of kainate receptors

Kainate receptors belong to the family of ionotropic glutamate receptors. These receptors assemble from five subunits (GluK1-5) into tetrameric ion channels. Kainate receptors are located at both pre- and postsynaptic membranes in the central nervous system where they contribute to excitatory synaptic transmission and modulate network excitability by regulating neurotransmitter release. Dysfunction of kainate receptors has been implicated in several neurological disorders such as epilepsy, schizophrenia and depression. Here we provide a review on the current understanding of kainate receptor structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full-length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered questions and challenges in front of us. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'.