Ligand-induced Conformation Research Articles

Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors

The interpretation of experimental observations of the dependence of membrane protein function on the properties of the lipid membrane environment calls for a consideration of the energy cost of protein-bilayer interactions, including the protein-bilayer hydrophobic mismatch. We present a novel (to our knowledge) multiscale computational approach for quantifying the hydrophobic mismatch-driven remodeling of membrane bilayers by multihelical membrane proteins. The method accounts for both the membrane remodeling energy and the energy contribution from any partial (incomplete) alleviation of the hydrophobic mismatch by membrane remodeling. Overcoming previous limitations, it allows for radially asymmetric bilayer deformations produced by multihelical proteins, and takes into account the irregular membrane-protein boundaries. The approach is illustrated by application to two G-protein coupled receptors: rhodopsin in bilayers of different thickness, and the serotonin 5-HT2A receptor bound to pharmacologically different ligands. Analysis of the results identifies the residual exposure that is not alleviated by bilayer adaptation, and its quantification at specific transmembrane segments is shown to predict favorable contact interfaces in oligomeric arrays. In addition, our results suggest how distinct ligand-induced conformations of G-protein coupled receptors may elicit different functional responses through differential effects on the membrane environment.

Kinase cascades and ligand-directed signaling at the kappa opioid receptor

The dynorphin/kappa opioid receptor (KOR) system has been implicated as a critical component of the stress response. Stress-induced activation of dynorphin-KOR is well known to produce analgesia, and more recently, it has been implicated as a mediator of stress-induced responses including anxiety, depression, and reinstatement of drug seeking. Drugs selectively targeting specific KOR signaling pathways may prove potentially useful as therapeutic treatments for mood and addiction disorders. KOR is a member of the seven transmembrane spanning (7TM) G-protein coupled receptor (GPCR) superfamily. KOR activation of pertussis toxin-sensitive G proteins leads to Galphai/o inhibition of adenylyl cyclase production of cAMP and releases Gbetagamma, which modulates the conductances of Ca(+2) and K(+) channels. In addition, KOR agonists activate kinase cascades including G-protein coupled Receptor Kinases (GRK) and members of the mitogen-activated protein kinase (MAPK) family: ERK1/2, p38 and JNK. Recent pharmacological data suggests that GPCRs exist as dynamic, multi-conformational protein complexes that can be directed by specific ligands towards distinct signaling pathways. Ligand-induced conformations of KOR that evoke beta-arrestin-dependent p38 MAPK activation result in aversion; whereas ligand-induced conformations that activate JNK without activating arrestin produce long-lasting inactivation of KOR signaling. In this review, we discuss the current status of KOR signal transduction research and the data that support two novel hypotheses: (1) KOR selective partial agonists that do not efficiently activate p38 MAPK may be useful analgesics without producing the dysphoric or hallucinogenic effects of selective, highly efficacious KOR agonists and (2) KOR antagonists that do not activate JNK may be effective short-acting drugs that may promote stress-resilience.

Label-Free Electrochemiluminescent Aptasensor with Attomolar Mass Detection Limits Based on a Ru(phen)32+-Double-Strand DNA Composite Film Electrode

Precisely known ligand-induced conformation change and complex chemical labeling of the DNA sequence with probe molecules are often needed for the signal generation in most of the previous aptasensors. Herein, a solution to the above problems was reported by the use of the Ru(phen)(3)(2+) intercalated into double strand DNA (ds-DNA) as an electrochemiluminescence (ECL) probe with thrombin as the target. After the antithrombin thiolated aptamer (27-mer) was attached to a gold electrode, ds-DNA structure was formed with its complementary 20-mer single strand DNA. Instead of the chemical modification of the aptamer or target with the probe molecule, Ru(phen)(3)(2+), as the probe, was intercalated into the ds-DNA structure. After thrombin hybridized with its aptamer, the ds-DNA dissociated and the intercalated Ru(phen)(3)(2+) released because of the higher stability of the aptamer-thrombin complex than that of the aptamer-complementary strand hybrid. The difference in ECL intensity with tripropylamine (TPA) as coreactant before and after the hybridization of thrombin and its aptamer was used to quantify thrombin. Besides the increase in the number of probe molecules over the single-site labeling, a ca. 80-fold improvement on the TPA oxidation at the ds-DNA modified electrode was found over the bare gold electrode. With the two amplification factors, the mass detection limits of 0.2 attomolar for thrombin are obtained. Because of the independence of conformational changes, the present method is readily extended to the targets whose aptamers have no specific conformational changes or other DNA-related detection without the need for chemical labeling.

Development of Androgen Receptor Antagonists with Promising Activity in Castration-Resistant Prostate Cancer

Androgen receptor (AR) continues to play a central role in prostate cancers that relapse after androgen deprivation therapy, but these tumors are refractory to available AR antagonists. In a recent issue of Science, Tran et al. describe an antagonist that prevents AR recruitment to chromatin and shows efficacy in relapsed prostate cancer.

Global gene expression profiling of progesterone receptor modulators in T47D cells provides a new classification system

Progesterone receptor modulators (PRMs) play an important role in women's health. They are widely used in oral contraception or hormone therapy, and provide an attractive treatment approach for gynecological disorders such as uterine leiomyomas, endometriosis or breast cancer. Due to the broad range of activities, various studies were conducted to assess progesterone receptor antagonists (PAs) and selective progesterone receptor modulators (SPRMs) with respect to progesterone receptor (PR) agonistic and antagonistic activities in vivo. These properties are not always adequately reflected in classical in vitro models, especially differences in the agonistic potential of SPRMs, such as asoprisnil, J1042, and J912, and mixed antagonists, such as mifepristone, are not sufficiently substantiated. The effects of PRMs upon gene expression in progesterone target tissues such as breast epithelium and uterus are poorly understood. This study compares the properties of PR ligands using mammalian two-hybrid assays and gene expression profiling. The protein–protein interaction analyses in HeLa cells provide for specific ligand-induced PR conformations, whereas Affymetrix GeneChip HG-U133Plus2.0 analyses in T47D breast cancer cells indicate the transcriptional activity on the level of target genes. The analyses comprise the pure agonist R5020, the non-steroidal PR modulator PRA-910, SPRMs (J1042, asoprisnil, J912), the mixed antagonist mifepristone, classical antagonists (onapristone, ZK 137316) and the pure antagonist lonaprisan to consider all types of ligands described before. Marginal differences were identified in coactivator interaction profiles at all, but significant differences between SPRMs and PR antagonists (PAs) were observed in recruiting the LXXLL-motif containing peptide (LX-H10), very similar to in vivo activities in endometrial transformation in the rabbit (McPhail test). Global gene expression profiles demonstrated progesterone-independent effects for all PR modulators examined and emphasised similarities of asoprisnil and J1042 compared to J912 and all types of PR antagonists. In summary, the data support the popular concept of PR modulator classification in agonists, selective progesterone receptor modulators, mixed and pure antagonists. It further refines previous classification models and accentuates unique effects for each PR modulator.

A Cellular Conformation-Based Screen for Androgen Receptor Inhibitors

The androgen receptor (AR), a member of the steroid nuclear receptor family of transcription factors, regulates a wide range of physiological processes. Androgen signaling is also associated with numerous human diseases, including prostate cancer. All current antiandrogen therapies reduce ligand access to AR, whether by competitive antagonism or inhibition of androgen production, but are limited by acquired resistance and serious side-effects. Thus, novel antiandrogens that target events subsequent to ligand binding could have important therapeutic value. We developed a high throughput assay that exploits fluorescence resonance energy transfer (FRET) to measure ligand-induced conformation change in AR. We directly compared this assay to a transcription-based assay in a screen of FDA-approved compounds and natural products. The FRET-based screen identified compounds with previously unrecognized antiandrogen activities, with equivalent sensitivity and superior specificity compared to a reporter-based screen. This approach can thus improve the identification of small molecule AR inhibitors.

Modeling and Selection of Flexible Proteins for Structure‐Based Drug Design: Backbone and Side Chain Movements in p38 MAPK

Receptor rearrangement upon ligand binding (induced fit) is a major stumbling block in docking and virtual screening. Even though numerous studies have stressed the importance of including protein flexibility in ligand docking, currently available methods provide only a partial solution to the problem. Most of these methods, being computer intensive, are often impractical to use in actual drug discovery settings. We had earlier shown that ligand-induced receptor side-chain conformational changes could be modeled statistically using data on known receptor-ligand complexes. In this paper, we show that a similar approach can be used to model more complex changes like backbone flips and loop movements. We have used p38 MAPK as a test case and have shown that a few simple structural features of ligands are sufficient to predict the induced variation in receptor conformations. Rigorous validation, both by internal resampling methods and on an external test set, corroborates this finding and demonstrates the robustness of the models. We have also compared our results with those from an earlier molecular dynamics simulation study on DFG loop conformations of p38 MAPK, and found that the results matched in the two cases. Our statistical approach enables one to predict the final ligand-induced conformation of the active site of a protein, based on a few ligand properties, prior to docking the ligand. We can do this without having to trace the step-by-step process by which this state is arrived at (as in molecular dynamics simulations), thereby drastically reducing computational effort.

The short length of the extracellular domain of ζ is crucial for T cell antigen receptor function

The T cell antigen receptor (TCR-CD3) consists of the pMHC-binding TCRαβ heterodimer and the signalling dimers CD3δɛ, CD3γɛ and ζζ. The very short length of the extracellular domain (EC) of the ζ chain is preserved through evolution, however a rational explanation for this observation has not been elucidated. Here, we show that TCR-CD3 assembly is clearly defective when the murine ζ EC domain is artificially enlarged. Under these conditions, the TCR-CD3 complex is super-competent in transducing activation signals upon engagement. Furthermore, the TCR-CD3 complexes containing enlarged ζ EC domains underwent ligand-induced conformation changes with higher efficiency than TCR-CD3 complexes with an unmodified ζ EC domain. Together these data suggest that a short ζ EC domain is needed to correctly assemble the TCR-CD3 complex. When this domain is enlarged, the resulting TCR-CD3 complex is distorted leading to a hyperactive phenotype and enhanced T cell activation.

Hypoxia alters progression of the erythroid program

Hypoxia can induce erythropoiesis through regulated increase of erythropoietin (Epo) production. We investigated the direct influence of oxygen tension (pO(2)) in the physiologic range (2-8%) on erythroid progenitor cell differentiation using cultures of adult human hematopoietic progenitor cells exposed to decreasing (20% to 2%) pO(2) and independent of variation in Epo levels. Decreases in hemoglobin (Hb)-containing cells were observed at the end of the culture period with decreasing pO(2). This is due, in part, to a reduction in cell growth and, at 2% O(2), a marked increase in cell toxicity. Analysis of the kinetics of cell differentiation showed an increase in the proportion of cells with glycophorin-A expression and Hb accumulation at physiologic pO(2). Cells were characterized by an early induction of gamma-globin expression and a delay and reduction in peak levels of beta-globin expression. Overall, fetal Hb and gamma-globin expression were increased at physiologic pO(2), but these increases were reduced at 2% O(2) as cultures become cytotoxic. At reduced pO(2), induction of Epo-receptor (Epo-R) by Epo was decreased and delayed, analogous to the delay in beta-globin induction. The oxygen-dependent reduction of Epo-R can account for the associated cytotoxicity at 2% O(2). Epo induction of erythroid transcription factors, EKLF, GATA-1, and SCL/Tal-1, was also delayed and decreased at reduced pO(2), consistent with lower levels of Epo-R and resultant Epo signaling. These changes in Epo-R and globin gene expression raise the possibility that the early increase of gamma-globin is a consequence of reduced Epo signaling and a delay in induction of erythroid transcription factors.

Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions

Essential dynamics sampling simulations of the domain conformations of unliganded Escherichia coli adenylate kinase have been performed to determine whether the ligand-induced closed-domain conformation is accessible to the open unliganded enzyme. Adenylate kinase is a three- domain protein with a central CORE domain and twoflanking domains, the LID and the NMPbind domains. The sampling simulations were applied to the CORE and NMPbind domain pair and the CORE and LID domain pair separately. One aim is to compare the results to those of a similar study on the enzyme citrate synthase to determine whether a similar domain-locking mechanism operates in adenylate kinase. Although for adenylate kinase the simulations suggest that the closed-domain conformation of the unliganded enzyme is at a slightly higher free energy than the open for both domain pairs, the results are radically different to those found for citrate synthase. In adenylate kinase the targeted domain conformations could always be achieved, whereas this was not the case in citrate synthase due to an apparent free-energy barrier between the open and closed conformations. Adenylate kinase has been classified as a protein that undergoes closure through a hinge mechanism, whereas citrate synthase has been assigned to the shear mechanism. This was quantified here in terms of the change in the number of interdomain contacting atoms upon closure which showed a considerable increase in adenylate kinase. For citrate synthase this number remained largely the same, suggesting that the domain faces slide over each other during closure. This suggests that shear and hinge mechanisms of domain closure may relate to the existence or absence of an appreciable barrier to closure for the unliganded protein, as the latter can hinge comparatively freely, whereas the former must follow a more constrained path. In general though it appears a bias toward keeping the unliganded enzyme in the open-domain conformation may be a common feature of domain enzymes.

Subtle Side-Chain Modifications of the Hop Phytoestrogen 8-Prenylnaringenin Result in Distinct Agonist/Antagonist Activity Profiles for Estrogen Receptors α and β

In search of therapeutic agents for estrogen-related pathologies, phytoestrogens are being extensively explored. In contrast to naringenin, 8-prenylnaringenin is a potent hop-derived estrogenic compound, highlighting the importance of the prenyl group for hormonal activity. We investigated the effects of substituting the prenyl group at C(8) with alkyl chains of varying lengths and branching patterns on estrogen receptor (ER) subtype ERalpha- and ERbeta-binding affinities and transcriptional activities. In addition, features of the ligand-induced receptor conformations were explored using a set of specific ER-binding peptides. The new 8-alkylnaringenins were found to span an activity spectrum ranging from full agonism to partial agonism to antagonism. Most strikingly, 8-(2,2-dimethylpropyl)naringenin exhibited full agonist character on ERalpha, but pronounced antagonist character on ERbeta. Knowledge on how ER-subtype-selective activities can be designed provides valuable information for future drug or tool compound discovery.

The Use of in Vitro Peptide Binding Profiles and in Silico Ligand-Receptor Interaction Profiles to Describe Ligand-Induced Conformations of the Retinoid X Receptor α Ligand-Binding Domain

It is hypothesized that different ligand-induced conformational changes can explain the different interactions of nuclear receptors with regulatory proteins, resulting in specific biological activities. Understanding the mechanism of how ligands regulate cofactor interaction facilitates drug design. To investigate these ligand-induced conformational changes at the surface of proteins, we performed a time-resolved fluorescence resonance energy transfer assay with 52 different cofactor peptides measuring the ligand-induced cofactor recruitment to the retinoid X receptor-alpha (RXRalpha) in the presence of 11 compounds. Simultaneously we analyzed the binding modes of these compounds by molecular docking. An automated method converted the complex three-dimensional data of ligand-protein interactions into two-dimensional fingerprints, the so-called ligand-receptor interaction profiles. For a subset of compounds the conformational changes at the surface, as measured by peptide recruitment, correlate well with the calculated binding modes, suggesting that clustering of ligand-receptor interaction profiles is a very useful tool to discriminate compounds that may induce different conformations and possibly different effects in a cellular environment. In addition, we successfully combined ligand-receptor interaction profiles and peptide recruitment data to reveal structural elements that are possibly involved in the ligand-induced conformations. Interestingly, we could predict a possible binding mode of LG100754, a homodimer antagonist that showed no effect on peptide recruitment. Finally, the extensive analysis of the peptide recruitment profiles provided novel insight in the potential cellular effect of the compound; for the first time, we showed that in addition to the induction of coactivator peptide binding, all well-known RXRalpha agonists also induce binding of corepressor peptides to RXRalpha.

Development of a coactivator displacement assay for the orphan receptor estrogen-related receptor-γ using time-resolved fluorescence resonance energy transfer

The estrogen-related receptor-γ (ERRγ) is a constitutively active orphan receptor that belongs to the nuclear receptor superfamily and is most closely related to the estrogen receptors. Although its physiological ligand is unknown, ERRγ has been shown to interact with synthetic estrogenic compounds such as 4-hydroxytamoxifen (4-OHT), tamoxifen, and diethylstilbestrol (DES). To assess how coregulator proteins interact with ERRγ in response to ligand, an in vitro interaction methodology using time-resolved fluorescence resonance energy transfer (TR–FRET) was developed using glutathione S-transferase (GST)-tagged ERRγ ligand-binding domain (LBD), a terbium-labeled anti-GST antibody, a fluorescein-labeled peptide containing sequences derived from coregulator proteins, and various ligands. An initial screen of these coregulator peptides bearing the coactivator LXXLL motif, the corepressor LXXI/HIXXXI/L motif, or other interaction motifs from natural coactivator sequences or random phage display peptides indicated that the peptides PGC1α, D22, and SRC1-4, known as class III coregulators, interacted most strongly with ERRγ in the absence of ligand. Given its assay window and biological relevance in energy metabolism and obesity, further studies were conducted with PGC1α. Fluorescein-labeled PGC1α peptide was displaced from the ERRγ LBD in the presence of increasing concentrations of 4-OHT and tamoxifen, but DES was less effective in PGC1α displacement. The statistical parameter Z′ factor that measures the robustness of the assay was greater than 0.8 for displacement of PGC1α from ERRγ LBD in the presence of saturating 4-OHT over an assay incubation time of 1–6 h, indicating an excellent assay. These findings also suggest that binding of 4-OHT, tamoxifen, or DES to ERRγ results in differential affinity of coregulators for ERRγ due to unique ligand-induced conformations.

Application of Near-Infrared and Fourier Transform Infrared Spectroscopy in the Characterization of Ligand-Induced Conformation Changes in Folate Binding Protein Purified from Bovine Milk: Influence of Buffer Type and pH

Fourier transform infrared (FT-IR) and near-infrared (NIR) spectroscopy have been applied to detect structural alterations in folate binding protein (FBP) induced by ligation in different buffer types. The amide I region pointed to a beta-sheet to alpha-helix transition upon ligation in acetate and phosphate buffers, and the formation of intermolecular beta-sheet was indicated at pH 5.0, in agreement with a dimerization of FBP taking place at this pH. The ligand-induced changes in the 2100-2300 nm NIR region were significant for FBP in acetate and phosphate buffers of pH 5.0, and the variations were interpreted as secondary structure changes, based on previous assignments of secondary structures to the combination bands in the NIR region. In the case of acetate buffer, variations in the amide combination bands agreed with the amide I analysis, but for the other buffer types some discrepancies were found and explained by side-chain contributions to the NIR, which could reflect the tertiary and quaternary structure differences. NIR spectra of FBP at pH 7.4 and 5.0 revealed contradictory effects on the side chains, reflecting different polymerization events at the two pH values, whereas the amide I region indicated similar changes at the two pH values. Therefore, we suggest that FT-IR and NIR spectroscopy may complement each other, such that the two techniques in combination may give information on all three types of protein conformational changes. While the secondary structure changes are revealed by FT-IR, the tertiary and quaternary structure changes are reflected in the NIR spectra, although the general influence of the latter changes on the NIR spectra remains to be confirmed.

Novel biosensors for the detection of estrogen receptor ligands

There exists a significant need for the detection of novel estrogen receptor (ER) ligands for pharmaceutical uses, especially for treating complications associated with menopause. We have developed fluorescence resonance energy transfer (FRET)-based biosensors that permit the direct in vitro detection of ER ligands. These biosensors contain an ER ligand-binding domain (LBD) flanked by the FRET donor fluorophore, cyan fluorescent protein (CFP), and the acceptor fluorophore, yellow fluorescent protein (YFP). The ER–LBD has been modified so that Ala 430 has been changed to Asp, which increases the magnitude of the FRET signal in response to ligand-binding by more than four-fold compared to the wild-type LBD. The binding of agonists can be distinguished from that of antagonists on the basis of the distinct ligand-induced conformations in the ER–LBD. The approach to binding equilibrium occurs within 30 min, and the FRET signal is stable over 24 h. The biosensor demonstrates a high signal-to-noise, with a Z′ value (a statistical determinant of assay quality) of 0.72. The affinity of the ER for different ligands can be determined using a modified version of the biosensor in which a truncated YFP and an enhanced CFP are used. Thus, we have developed platforms for high-throughput screens for the identification of novel estrogen receptor ligands. Moreover, we have demonstrated that this FRET technology can be applied to other nuclear receptors, such as the androgen receptor.

Glucocorticoid Ligands Specify Different Interactions with NF-κB by Allosteric Effects on the Glucocorticoid Receptor DNA Binding Domain

Glucocorticoids inhibit inflammation by acting through the glucocorticoid receptor (GR) and powerfully repressing NF-kappaB function. Ligand binding to the C-terminal of GR promotes the nuclear translocation of the receptor and binding to NF-kappaB through the GR DNA binding domain. We sought how ligand recognition influences the interaction between NF-kappaB and GR. Both dexamethasone (agonist) and RU486 (antagonist) promote efficient nuclear translocation, and we show occupancy of the same intranuclear compartment as NF-kappaB with both ligands. However, unlike dexamethasone, RU486 had negligible activity to inhibit NF-kappaB transactivation. This failure may stem from altered co-factor recruitment or altered interaction with NF-kappaB. Using both glutathione S-transferase pull-down and bioluminescence resonance energy transfer approaches, we identified a major glucocorticoid ligand effect on interaction between the GR and the p65 component of NF-kappaB, with RU486 inhibiting recruitment compared with dexamethasone. Using the bioluminescence resonance energy transfer assay, we found that RU486 efficiently recruited NCoR to the GR, unlike dexamethasone, which recruited SRC1. Therefore, RU486 promotes differential protein recruitment to both the C-terminal and DNA binding domain of the receptor. Importantly, using chromatin immunoprecipitation, we show that impaired interaction between GR and p65 with RU486 leads to reduced recruitment of the GR to the NF-kappaB-responsive region of the interleukin-8 promoter, again in contrast to dexamethasone that significantly increased GR binding. We demonstrate that ligand-induced conformation of the GR C-terminal has profound effects on the functional surface generated by the DNA binding domain of the GR. This has implications for understanding ligand-dependent interdomain communication.

Alternative farnesoid structures induce different conformational outcomes upon the Drosophila ortholog of the retinoid X receptor, ultraspiracle

In view of recent studies that the ligand-binding pocket of the Drosophila melanogaster nuclear hormone receptor, ultraspiracle (dUSP), is a necessary component of dUSP-dependent transcriptional activation by methyl epoxyfarnesoate, we have assessed qualitative differences in the effect of farnesoid and dodecanoid compounds on receptor conformation and transcriptional activation. Farnesoids possessing terminal alcohol, aldehyde, acid, ester and/or epoxide moieties induced different changes in the local environment of the ligand-binding pocket, as monitored by the change each induced in the fluorescence of the two tryptophan residues existing in dUSP (that are situated 10 residues apart on the α-helix 5 that forms one lining of ligand-binding pocket). Similarly, each compound differed in the extent that it promoted an increase in anisotropy (dimerization state) of the receptor. Dodecanoid derivatives were much weaker in causing such effects. Methyl expoxyfarnesoate (insect juvenile hormone III) exhibited the greatest biological activity to increase transcription of a DR12JHECore reporter construct in transfected Sf9 cells, even though it did not exert the most suppression of USP fluorescence nor exert the greatest increase in USP anisotropy. In a comparison of farnesoid derivatives possessing the three side branches either as all methyl groups (JH III), or one of the side branches as ethyl (JH II), or two of the side branches as ethyl (JH I), the JH III and JH I were more similar to each other in the fluorescence suppression and in vivo morphogenetic activity than either was to JH II, evidencing that dUSP does not sense JH II as a structural ‘intermediate’ between JH III and JH I. Ligand-binding domains of vertebrate retinoid X receptors respond to agonists by repositioning α-helix 12 to the edge of a hydrophobic groove, and there with the groove jointly forms a coactivator binding surface. When α-helix 12 in dUSP was mutated to place two signaling tryptophan residues its C-terminus, fluorescence signaling indicated that upon dUSP binding of methyl epoxyfarnesoate, the α-helix 12 was repositioned differently than what occurred upon binding of non-JH farnesoids. These leads on alternative ligand-induced conformations that dUSP can adopt provide a foundation for commercial development of synthetic molecules that induce specific dUSP conformations, and for identification of in vivo conditions under which endogenous molecules may exert these conformational outcomes to this receptor.

Effects of Zn(II) binding and apoprotein structural stability on the conformation change of designed antennafinger proteins.

Ligand-induced conformation change is a general strategy for controlling protein function. In this work, we demonstrate the relationships between ligand binding and conformational stability using a previously designed protein, Ant-F, which undergoes a conformation change upon Zn(II) binding. To investigate the effect of stabilization of the apo structure on the conformation change, we also created a novel protein, Ant-F-H1, into which mutations are introduced to increase its stability over that of Ant-F. The chemical denaturation experiments clarified that apo-Ant-F-H1 is more stable than apo-Ant-F (DeltaDeltaG = -1.28 kcal/mol) and that the stability of holo-Ant-F-H1 is almost the same as that of holo-Ant-F. The Zn(II) binding assay shows that the affinity of Zn(II) for Ant-F-H1 is weaker than that for Ant-F (DeltaDeltaG = 1.40 kcal/mol). A large part of the increased value of free energy in stability corresponds to the decreased value of free energy in Zn(II) binding, indicating that the stability of the apo structure directly affects the conformation change. The denaturation experiments also reveal that Zn(II) destabilizes the conformation of both proteins. From the thermodynamic linkage, Zn(II) is thought to bind to the unfolded state with high affinity. These results suggest that the binding of Zn(II) to the unfolded state is an important factor in the conformational change as well as the stability of the apo and holo structures.

Ligand-induced changes in estrogen receptor conformation as measured by site-directed spin labeling.

Site-directed spin labeling (SDSL), the site-specific incorporation of nitroxide spin-labels into a protein, has allowed us to investigate ligand-induced conformational changes in the ligand-binding domain of human estrogen receptor alpha (hERalpha-LBD). EPR (electron paramagnetic resonance) spectroscopy of the nitroxide probe attached to ER produces different spectra depending upon the identity of the bound ligand; these differences are indicative of changes in the type and degree of motional character of the spin-label induced by different ligand-induced conformations of labeled ER. Visual inspection of EPR spectra, construction of B versus C cross-correlation plots, and cross-comparison of spectral pairs using a relative squared difference (RSD) calculation allowed receptor-ligand complexes to be profiled according to their conformational character. Plotting B and C parameters allowed us to evaluate the liganded receptor according to the motional characteristics of the attached spin-label, and they were particularly illustrative for the receptor labeled at position 530, which had motion between the fast and intermediate regimes. RSD analysis allowed us to directly compare the similarity or difference between two different spectra, and these comparisons produced groupings that paralleled those seen in B versus C cross-correlation plots, again relating meaningfully with the pharmacological nature of the bound ligand. RSD analysis was also particularly useful for qualifying differences seen with the receptor labeled at position 417, which had motion between the intermediate and slow motional regimes. This work demonstrates that B and C formulas from EPR line shape theory are useful for qualitative analysis of spectra with differences subtler than those that are often analyzed by EPR spectroscopists. This work also provides evidence that the ER can exist in a range of conformations, with specific conformations resulting from preferential stabilization of ER by the bound ligand. Furthermore, it documents the complexity and uniqueness of the ligand-receptor structure, and highlights the fact that structural differences exist between the receptor bound with ligands of different pharmacological character that, nevertheless, produce similar crystal structures.

Molecular sensors of estrogen receptor conformations and dynamics.

The ligand-induced conformation of a nuclear receptor ligand-binding domain (LBD) is a principal factor leading to transcriptional activity and determining the pharmacological response. Using the estrogen receptor (ER) LBD-labeled site specifically with a fluorophore, we demonstrate that effects of ligand binding on the conformation and dynamics of this domain can be studied directly, in a quantitative and convenient fashion, by various fluorescence methods. Estrogen ligands of different pharmacological character-agonists, selective ER modulators (SERMs), and pure antagonists-each produce distinctive spectroscopic signatures, characteristic of the conformational or dynamic features of their ER-LBD complexes. We can directly follow the equilibrium of helix 12 positions through the degree of local fluorophore rotational freedom and receptor helicity near the C terminus of helix 11. We observe differences even between ligands within a specific pharmacological class, such as the SERMs raloxifene and trans-4-hydroxytamoxifen, highlighting the ability of these fluorescent receptor sensors to detect unique ER conformations induced even by closely related ligands, yet ones that produce distinctive biological activities in estrogen target cells. Fluorophore-labeled LBDs can serve as versatile molecular sensors predictive of ligand pharmacological character and should be broadly applicable to other members of the nuclear receptor superfamily.