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Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital (Y.A.E., J.H.W., B.G., L.K.B., C.A., G.B., M.A.T.), Departments of Human Genetics (Y.A.E., M.A.T.), Medicine (M.A.T., L.K.B.) and Oncology (J.H.W., G.B.), McGill University, Montreal, Quebec, Canada H3T 1E2
Address all correspondence and requests for reprints to: M. A. Trifiro, M.D., Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec, Canada H3T 1E2. E-mail: mark.trifiro{at}mcgill.ca.
| ABSTRACT |
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Molecular dynamics four-dimensional modeling clearly supports the biochemical and kinetic studies of both mutants. Such novel computational modeling may lead to a better understanding of the structure-function relationships and the molecular mechanics of ligand binding not only of the AR-LBD but also of other nuclear receptors.
| INTRODUCTION |
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AR mutations result in variable degrees of androgen insensitivity in XY individuals (3). Androgen insensitivity syndrome (AIS) ranges from complete AIS (CAIS) to mild AIS (MAIS), with a wide range of partial AIS (PAIS) in between. Phenotypically, it is a spectrum of abnormal sex differentiation ranging from XY female, in CAIS cases, to nearly normal male, in MAIS cases (3).
Most of the AR mutations reported so far are single-amino acid substitutions, and the vast majority are located in the LBD (4). Different substitutions at the same amino acid may result in receptors with different properties and thereby different degrees of AIS. Interestingly, identical substitutions at the same site may exhibit variable expressivity that results in different phenotypes not only in different families, but also within the same family (5, 6).
X-ray crystallographic studies of the AR LBD (7, 8) and other steroid receptor LBDs (9, 10, 11, 12) revealed that steroid receptors share a common LBD structure encompassing 12
-helices and a ß-turn. These
-helices undergo similar conformational changes in response to ligand binding, resulting in the formation of a hydrophobic surface by helices 3, 4, 5, and 12 that constitutes the AF-2 domain, provides binding sites for coactivators and initiates N/C-terminal interactions (13, 14).
The ligand-dependent AR N/C interactions are essential for the transactivational properties of the receptor (15). The AR N/C-terminal interactions have been shown to be direct, mediated by conserved FXXLF and WXXLF motifs located in the AR N-terminal domain and the AF-2 domain in the LBD (16, 17), or indirect, wherein members of the family of p160 coactivators interact with the AR termini and mediate their communications (18, 19). The p160 coactivators interact with the AF-2 domain through conserved LXXLL motifs (18, 20, 21); however, their interactions with the N-terminal domain are LXXLL independent (16, 19). The major structural changes that occur upon ligand binding involve a change in conformation of the C-terminal helix 12 (H12) (22). This helix is completely repositioned upon ligand binding. Further studies have shown that when bound to activating ligands, H12 adopts a conformation that promotes the binding of coactivator proteins (23). These studies suggest that H12 is significantly more mobile than the main body of the protein but shows reduced mobility upon ligand binding. Thus, the dynamic properties of H12 may be a key to the regulation of transcriptional activity.
Recent studies of proteins and nucleic acids using molecular dynamics (MD) simulations, a key computational biology technique, have generated useful insights into the structural mechanisms underlying the biological function of a number of biomacromolecules (24, 25). Further, an implicit solvation method that is based on the generalized Born model (26) has been successfully implemented for use along with molecular mechanics force fields in MD simulations (27, 28, 29) [e.g. within the AMBER package (30)]. Recently, we have investigated a pathogenic AR LBD mutation (R744C), by examining details of its altered atomic structure using MD simulations extended over a 4-nsec time period (31); these simulations have strongly supported our analysis of the mutant phenotype including its kinetic properties as well as other biochemical data.
In this study, we have identified and characterized two different substitutions at an identical position (R855H; R855C) in the LBD of the AR in two unrelated patients with MAIS and CAIS, respectively. Kinetic analysis has revealed that the alternate substitutions result in significantly different receptor abnormalities. The R855C mutant showed very low binding ability and had no transactivational activity. The R855H mutant retained normal or near-normal binding properties, but also exhibited a reduced transactivational capacity. An analysis of the R855H mutant revealed thermolability and decreased AR N/C-terminal interactions that may explain its pathogenicity. We have used MD modeling to correlate the structural alterations of these mutant receptors with the functional abnormalities that determine their very different phenotypes.
| RESULTS |
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The Effects of the Alternate Substitutions on Androgen Binding
Maximum androgen-binding capacity (Bmax), rate constant of dissociation (k), and apparent equilibrium dissociation constants (Kd) for wild-type and mutant ARs were measured in genital skin fibroblasts (GSFs) and transfected COS-1 cells with different ligands. The R855H mutant retained normal or near-normal Bmax and k but had an elevated Kd at physiological hormone concentrations both in COS-1 [for MT, k = 0.009 vs. 0.008 min1 and Kd = 0.56 vs. 0.27 nM (Fig. 1
)] and in GSFs (for MT, k = 0.014 vs. 0.012 min1 and Kd = 0.8 vs. 0.21 nM) for R855H and wild-type ARs, respectively. Similar results were obtained when mibolerone (MB) and dihydrotestosterone (DHT) were used (data not shown). In contrast, the R855C mutant receptor had negligible binding activity at normal hormone concentrations. To examine whether this was due to an absolute lack of binding or an affinity problem, cells expressing R855C receptor were incubated with 100 nM 3H-labeled hormone. At these very high hormone concentrations, the mutant receptor was indeed able to bind up to 50% compared with the wild-type receptor. Western analysis revealed that the mutant ARs were of normal size (
110 kDa) and were stable in transfected COS-1 cells incubated for 24 and 48 h with and without ligand. MB binding in GSFs expressing the R855H mutant AR was normally up-regulated, from 87198 fmol/mg protein after 2 h and overnight incubations, respectively.
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To examine the overall (H1H12) structural differences, wild-type AR-LBD and mutant R855H and R855C models were constructed from 2.54 nsec MD simulations. Relative to the structure of the wild-type, the average backbone RMSD for R855C and R855H mutants are 3.1 Å and 2.8 Å, respectively. This indicates that overall structure of R855H is more similar to that of the wild type than the R855C mutant. To visually inspect these structural abnormalities, the averaged structures for both R855H and R855C mutants were superimposed on the backbone (Fig. 8
). The average backbone RMSD between the structures of the two mutants themselves is as large as 3.7 Å. There is significantly more local structural distortion around residue 855 in the R855C mutant. Surprisingly, compared with the R855H mutant, H12 and its C-terminal extension (CTE) of the R855C mutant have adopted a significantly different position. Normally the CTE of H12 resides firmly in a pocket formed by helices 8 and 9 (33, 34). Therefore, the MD simulations have suggested that the R855C mutation, although 25 Å away from the bound R1881, repositions H12 and the CTE distinctly away from their normal position and therefore limits the receptors ability to bind ligand.
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| DISCUSSION |
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Androgen-binding analysis in the patients GSFs and transfected COS-1 cells revealed that a cysteine substitution for arginine 855 resulted in more severe binding abnormalities than the histidine substitution. Whereas the R855C mutant showed negligible binding, the R855H retained normal Bmax and k, and slightly elevated Kd with all ligands tested (DHT, MB, and MT). To ensure that the lack of androgen binding for R855C mutant was not due to protein instability and degradation, Western blot analysis was performed and showed that both mutant receptors were stable in the absence or presence of androgen.
The negligible ligand binding of the R855C mutant receptor suggested significant conformational abnormalities. A cysteine residue at this position may induce the formation and/or the replacement of a disulfide bridge, resulting in a conformation that is incompatible with ligand binding; however, no other cysteine residue appears nearby. Another possibility is that, whereas cysteine is uncharged, a positively charged residue such as arginine is required at position 855 of the AR for normal ligand binding. R855 is highly conserved in all AR-related members in the superfamily of steroid receptors (estrogen receptor, progesterone receptor, glucocorticoid receptor, mineralocorticoid receptor) as well as others not as closely related (human retinoid X receptor-
, chicken ovalbumin upstream promoter-transcription factor) (44). Thus, an arginine at position 855 seems to fulfill a strict functional requirement, most likely hydrogen bonding. This requirement may be fulfilled by the positively charged histidine, resulting in a normal ligand-binding capacity for the R855H mutant.
Recently, the availability of a three-dimensional model of the AR LBD (7) has permitted researchers to examine the possible effects that AR LBD mutations may have on the conformation and actual functioning of the ligand-binding pocket. In analyzing the x-ray crystal structure of the human AR LBD, only 18 specific residues were predicted to be in sufficiently close contact with the bound ligand (R1881) to affect ligand binding (7). Mutations at the R855 residue are particularly puzzling because they are almost 25 Å from the ligand-binding pocket, and positioned on the outside of the crystal structure, as are a significant number of the reported AR LBD mutations, again located far from the ligand-binding pocket (4).
Therefore, to elucidate how R855 mutations could possibly affect the structure of the ligand-binding pocket, and thereby explain their different effect on ligand binding, we have used MD simulations over extended periods of time (
4 nsec) to create, in effect, four-dimensional structures of the AR LBDs. Our results clearly show a significant local distortion around residue 855 at the N terminus of H10 (Figs. 7
and 8
). In the wild-type AR, residue R855 forms multiple hydrogen bonds with E803 (helix 8) and L797 (helix 7). Residue E803 is one of very few superconserved aa in the LBD present in both related and unrelated members of the steroid receptor family (44). Residue L797 is also highly conserved in the AR-related family members. In the R855H mutant, these hydrogen bonds do not exist, but a hydrogen bond between H855 and S851 is formed that could compensate for the loss of normal hydrogen bonding around residue 855. C855 does not participate in hydrogen bonding; the lack of such bonding can introduce more local flexibility, which may lead to further structural alterations.
These observations alone, however, cannot by themselves explain the kinetic abnormalities associated with both R855 mutants. Helix 12 has been widely implicated as being crucial to the ligand-binding process in the nuclear receptor family (22, 45, 46). The MD simulations clearly illustrate that whereas a significant structural distortion of H12 was caused by the R855C mutation, the R855H mutation resulted in much less H12 alteration, which would explain its near-normal ligand binding. Helix 12 appears to be the most singular flexible part of the steroid receptor LBDs and probably, because of its inherent flexibility, is most apt to adopt a favorable position such that the whole LBD can be made to accommodate specific missense mutations (23, 47) albeit at the potential risk of losing ligand-binding capability. Helix 12 appears to be fixed in its ultimate position by antiparallel ß-sheet interactions between its CTE and residues 815817 (loop 89) (7). This is obviously lacking in R855C (Fig. 8
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Although modeling offers a possible explanation for the phenotypic effects of R855C, it does not fully explain the phenotypic abnormalities associated with the R855H mutation. The main immediate difference was that R855H-androgen complexes in GSFs exhibited severe thermolability. In addition, we investigated the transactivational properties of the mutant receptors, by first testing the activation ability of the ligand-dependent AF-2 domain. The AR AF-2, unlike other steroid receptors, has very weak transcriptional activity in mammalian cells in the absence of the N-terminal domain (48); however, it is highly inducible by the coactivator TIF-2 (16). Interestingly, the R885H-AR-LBD was able to transactivate the reporter gene in a similar manner to the wild type. This indicated an intact AF-2 function and also suggested that the R855H mutation did not reduce the ability of the LBD to recruit and interact with TIF-2. However, when we tested the transactivational properties of the full-length mutant receptors, activation of the reporter gene by the R855H was 30% and 40% less than the wild type in response to MB and MT, respectively. Again, as expected for the R855C, there was no induction of the reporter gene upon ligand addition.
AR N/C-terminal interactions are essential for the transactivational activity of the receptor (49, 50). The AF-2 domain initiates AR N/C-terminal interactions and provides binding sites for the recruitment of coactivators (e.g. steroid receptor coactivator 1, TIF-2, p/CIP), which may further enhance the N/C-terminal interactions (51, 52). As we have shown previously, diminished N/C interactions may correlate with and explain the clinical phenotypes of some LBD mutants, even if their ligand-binding activities are normal (52). To characterize the N/C-terminal interactions of the R855 substitutions, we used the mammalian two-hybrid system. Our results showed no interaction for the R855C mutant, which was consistent with its lack of ligand-binding activity. The R855H mutant resulted in significantly reduced interaction compared with that of wild type, both in the absence and presence of TIF-2. The presence of TIF-2 partially rescued the defective N/C interaction of the R855H LBD, confirming the ability of the AF-2 domain of the R855H mutant to recruit and interact with TIF-2. In fact, the presence of TIF-2 resulted in a greater fold induction for the R855H N/C-terminal interactions than the wild type: 9-fold increase for R855H compared with 6-fold for the wild-type receptor. It has been suggested that the TIF2-LXXLL motif competes with the more favorable AR N-terminal-FXXLF motif for an overlapping binding site in the AF-2 domain (53). Thus, the higher fold induction for the R855H mutant may reflect increased interactions with TIF-2 due to the decreased competition of the FXXLF motifs in the N-terminal domain (i.e. decreased N/C-terminal interactions). Enhanced coactivator/AF-2 interactions may amplify the role of coactivators in the transactivational ability of the receptor and thereby their role in the variable expressivity exhibited by the R855H mutation. Enhanced TIF-2/AF-2 interaction due to reduced AR N/C-terminal interactions has been suggested as a possible mechanism for AR activation after androgen blockade in prostate cancer patients. It was proposed that, in the absence of testicular androgens, increased binding to adrenal androgens and other steroids that induce less N/C-terminal interaction result in enhanced TIF-2/AF-2 interactions and, thereby, AR transactivational ability (54).
Our results show that different phenotypes associated with alternate substitutions at the same amino acid may reflect different receptor abnormalities. Whereas the cysteine substitution that resulted in CAIS correlated with an abolished AR binding ability, the histidine substitution that resulted in PAIS reduced AR N/C-terminal interaction and the transactivational activity of the receptor without compromising its binding properties. In addition, the ability of the TIF-2 coactivator to partially rescue N/C interaction for the R855H mutation suggests an important role for coactivators in the variable expressivity exhibited by certain mutations.
The use of MD simulations strongly suggested that the lack of ligand binding of the R855C mutant is due to a local distortion that leads to the critical misplacement of H12, which is essential for ligand binding. Furthermore, it suggests how mutations in the AR that are located far away from the ligand-binding pocket can still affect ligand binding. Much more extensive MD simulations may be used to document, in a time-dependent manner, the exact series of physical changes that H12 may undergo in response to ligand binding and abnormal order of events in respect to specific missense mutations. This will be particularly important not only because of the many phenotypically significant mutations that are located at a considerable distance from the ligand-binding pocket of the AR, but also in shedding light on the role of H12 position in ligand binding.
Combined studies employing MD simulation of the mutant ARs in conjunction with the classical molecular and kinetic analysis will certainly help in establishing the widespread application of MD simulation that would be pertinent to other proteins.
| MATERIALS AND METHODS |
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Subject 9025 was a 10-wk-old 46XY infant with ambiguous genitalia, a micropenis, and hypospadia.
To identify AR mutations, DNA was extracted from the GSFs from each patient. PCR amplification and direct sequencing of exons 28 of the AR from each patient were performed as previously described (55).
Full-Length Mutant AR Plasmid Constructs
The mutations detected (R855H and R855C) were recreated in the pSVhAR.BHEX and pcDNA3-hAR expression vectors, which encode the full-length AR, by the overlap extension method. For each mutation, two overlapping fragments were amplified using the pSVhAR.BHEX as a template and the appropriate primers to incorporate each mutation into the PCR product. The internal primers used for the R855H mutation were:
9025A-(5'-TGCTCAAGACACTTCTACCAGC-3') and
9025B-(5'-TGGTAGAAGTGTCTTGAGCAGG-3'); and for the R855C mutation were
82725A-(5'-TGCTCAAGATGCTTCTACCAGC-3') and
82725B-(5'-TGGTAGAAGCATCTTGAGCAGG-3')
The substituted nucleotides are underlined. The same external primers were used for both mutations; TCFA (5'-GTCCCGGATATACAGCCAG-3') and P3' (5'-CACCAA-CCTTCTGATAGGCAGC-3'). One microliter of each of the corresponding overlapping fragments was used for the second PCR: an extension step for five cycles followed by 25 cycles with the external primers. The products of the second PCR were digested with EcoRI and BamHI and ligated into similarly digested pSVhAR.BHEX. The full-length AR mutants in pSVhAR.BHEX were then transferred into pcDNA3-hAR by NheI/BamHI double digestion and ligations. The insertion of the desired sequences was confirmed by restriction enzyme digestions and direct sequencing using the Thermo Sequenase Radiolabeled Terminator Cycle sequencing kit (United States Biochemical Corp., Cleveland, OH).
Mammalian Two-Hybrid Constructs
The wild type pM-AR(LBD) expression vector, encoding the GAL4-DNA-binding domain fused in frame with aa 628919 of the AR, the pVP16-AR(TAD20Q) plasmid, coding for the VP16 activation domain fused in frame with aa 1565 of the AR, and the pGAL4-Luc reporter vector containing GAL4-DNA-binding sites and a luciferase reporter gene were kindly provided by Dr. E. L. Yong, National University of Singapore (51). The pM-mutant AR(LBD) expression constructs were created for each mutant by a double digest of the corresponding mutant pcDNA3-hAR constructs with BstBI/XbaI and religating in frame with the similarly digested wild-type pM-AR(LBD). The pSG5-TIF-2 construct codes for the full-length transcriptional coactivator TIF-2 (51).
Cell Culture and Transfections
GSFs and COS-1 and CV-1 monkey kidney cells were maintained in Opti-MEM (Life Technologies, Inc., Gaithersburg, MD) supplemented with 5%10% fetal bovine serum, 50 U/ml of penicillin, and 50 µg/ml of streptomycin [penicillin-streptomycin solution (Life Technologies, Inc.)]. Cell transfections were performed in six and 12-well plates using LipofectAMINE 2000 (LF2000; Life Technologies, Inc.) as recommended by the manufacturer. All transfections included 12 µg pCMV-ß-galactosidase (ß-gal) as a control for transfection efficiency.
Androgen-Binding Assays
Androgen-binding studies in both GSFs and transfected COS-1 cells were performed as previously described (43). Androgens used were DHT, and the synthetic nonmetabolizable androgens MB and MT (R1881).
Thermolability of R855H-Androgen Complexes
Thermolability of R855H-MB and R855H-MT complexes was assayed in patient GSFs and a wild-type strain GSF culture plated in six-well plates. Four wells of each plate were incubated with 3 nM [3H]androgen and two with 3 nM [3H]androgen plus a 200-fold excess of androgen at 37 C. After 16 h, one plate was used to measure androgen-binding activity. The medium in the remaining plates was replaced by fresh medium supplemented with 10 µM cycloheximide before incubation at 42 C. Androgen binding was measured after 1, 2, 4, and 6 h of incubation at 42 C.
Ability to Up-Regulate and Stability of the Mutant ARs
To determine the ability of the mutant ARs to up-regulate, GSFs were plated in two six-well plates, labeled, and incubated as described above at 37 C. Androgen-binding capacity was measured after 2-h and overnight incubations. To assess the stability of mutant ARs in transfected COS-1 cells, cells were incubated with and without 10 nM MB at 37 C in the presence of 100 µM cycloheximide for 24 and 48 h. Cells were harvested and lysed in 1x Reporter Lysis buffer (Promega Corp., Madison, WI). Total protein (100 µg) was used for SDS-PAGE and Western blotting using AR 441, a mouse monoclonal antibody directed to aa 299315 of human AR (NeoMarkers, Fremont, CA) and anti-heat shock protein 70 monoclonal antibody (Stress Gen Biotechnologies Corp., Victoria, British Columbia, Canada) as a control for protein loading. Detection was performed using ECL Plus kit (Amersham Pharmacia Biotech, Inc., Piscataway, NJ).
Transactivation Assay
COS-1 cells were plated in 12-well plates at a density of 3 x 105 cells per well in 1 ml Opti-MEM per well, supplemented with 5% fetal bovine serum and without antibiotics. The following day, cells were cotransfected with 300 ng wild-type or mutant full-length AR, 1 µg of the reporter construct pMMTV-GH, and 300 ng pCMV-ß-gal complexed with 4 µl LF2000 reagent per well. Cells were incubated with 3 nM MB or MT. After 72 h, media were collected and secreted hGH was measured using an hGH-ELISA Kit (MEDICORP Inc., Montreal, Quebec, Canada). Lowry and ß-gal assays were used to determine cellular protein and transfection efficiency.
The Mammalian Two-Hybrid Assay
To assess AR N/C-terminal interactions in vivo, mammalian two-hybrid assays were performed. CV-1 cells were used for the AR N/C interaction studies due to their low background compared with COS-1 cells in our experimental settings. CV-1 cells were plated in six-well plates at a density of 5 x 105 cells per well. Transfections were performed, as described above, using 6 µl LF2000 reagent, 0.5 µg wild-type or mutant pM-AR(LBD) construct, 0.5 µg pVP16-AR(TAD20Q), 2 µg pGAL4-Luc reporter vector, and 0.5 µg pCMV-ß-gal with or without 0.5 µg pSG5-TIF-2 per well. Empty pVP16 or pM vectors were used as controls. Twenty-four hours after transfection, four wells were treated with 3 nM MB. Seventy-two hours after transfection, the cells were harvested and lysed in 1x Reporter Lysis Buffer and assayed for luciferase and ß-gal activity according to Promega protocols. Total protein content was determined using BCA Protein Assay Kit (Pierce Chemical Co., Rockford, IL).
AF-2 Domain Transactivation Potential
To assess the transactivational potential of the AF-2 domain of the mutant receptors, CV-1 cells were cotransfected as described for the two-hybrid assay, except for the pVP16-AR(TAD20Q) vector, with 0.5 µg wild-type or mutant pM-AR(LBD) construct, 2 µg pGAL4-Luc reporter vector, 0.5 µg pCMV-ß-gal, and 0.5 µg pSG5-TIF-2 per well. Empty pM vector was used as a control. Cells were incubated with 3 nM MB, harvested, and assayed for luciferase induction as described above.
Protein Modeling
The crystal structure of AR-LBD complexed with R1881 was obtained from the Protein Data Bank (PDB entry: 1e3 g), and the crystallographic waters were removed. Hydrogen atoms were added using the BIOPOLYMER module of Insight II package (Accelrys, Inc., San Diego, CA). The starting structure of the AR-LBD R855 mutants were obtained by mutating residue 855 from R to C and H in the AR-LBD crystal structure. The bound ligand, R1881, was retained in both wild-type and mutant AR-LBD.
MD Simulations
All MD simulations presented in this work were performed using the AMBER 7.0 simulation package (30) and ff99 force field (56). The detailed procedure has been described elsewhere (31). Briefly, the generalized Born solvation model instead of explicit water was used (57). Before MD simulation was initiated, the possible bad contacts resulting from amino acid substitutions were relaxed by 300 cycles of the steepest descent energy minimizations whereas the heavy atoms were restrained with a force constant of 5 kcal/mol·Å2. The MD simulations were performed at 310 K without any restraints. The average structures from a specific period of MD simulations were calculated using the PTRAJ module of AMBER package. All RMSDs were mass weighted and calculated using the CARNAL module in AMBER.
| FOOTNOTES |
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Abbreviations: aa, Amino acids; AF-2, activation function 2; AIS, androgen insensitivity syndrome; AR, androgen receptor; CAIS, complete AIS; CTE, C-terminal extension; DHT, dihydrotestosterone; ß-gal, ß-galactosidase; GSFs, genital skin fibroblasts; H12, C-terminal helix 12; LBD, ligand-binding domain; MAIS, mild AIS; MB, mibolerone; MD, molecular dynamics; MT, methyltrienolone; PAIS, partial AIS; RMSD, root mean square deviation; TIF-2, transcriptional intermediary factor 2.
Received for publication January 20, 2004. Accepted for publication April 21, 2004.
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function and stability by tamoxifen and a critical amino acid (Asp-538) in helix 12. J Biol Chem 278:76307638NURSA Molecule Pages Link:
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