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Binding Pocket Specificity and Key Amino Acids

Zach Morrow '14 and Kotiba Malek '14



I. Introduction

     The Androgen receptor (AR), is a member of the nuclear receptor superfamily. The protein activated by  binding natural and artificial androgenic hormones such as testosterone and dihydrotestosterone (DHT), both of which are naturally occuring steriods, and tetrahydrogestrinone (THG), an artifical anabolic steroid (1). After binding, the AR translocates from the cytoplasm into the nucleus and bindings to Androgen Response Elemets (ARE's) as a homodimer. ARE's typically found in the regulatory regions of genes involved in male sexual differentiation. When bound at ARE's, the AR has been found to interact directly with basal transcription facotrs, most notably, TFIIF (2).
    The AR has been exploited for years by athletes looking to gain a competitive edge. Artificial steriods have been synthesized to bind the AR, and thus increase the expression of genes which lead to increased muscle mass and strength (3). THG has been demonstrated to bind with such high affinity to the AR, that at equal concentrations, THG will displace natural hormones with 100% efficiency (1). THG was found to have the highest binding affinity, followed by DHT and then testosterone. Much research has been done to illucidate the structural features of these steriods and the binding domain of the AR that lead to such increases in binding affinity. This tutorial investigates the structural features of testosterone and THG that lead to differing binding affinities to the AR. 

II. General Structure

    The AR is composed of three functional domains: the N-Terminal Domain, the DNA binding domain, and the Ligand Binding Domain (LBD). The N-terminal domain is responsible for the recruitment of various transcription factors (2). The %nbsp is composed of two helix turn helix motifs, each belonging to one of the AR subunits of the homodimer. One alpha helix is inserted into the major groove of an ARE, and the second alpha helix, separated from the first by a variable chain and fits across the DNA phosphate backbone, thus stabilizing the binding interaction (4).
    The LBD is composed of eleven alpha helices, and four short beta sheets connected by short amino acid chains (in white). Most important to the LBD is the Ligand Binding Pocket (LBP). It is here that the interactions between the AR and different steroids occur (1). Of interest is the manner in which the LBD interacts with different ligands. When liganded, the LBP adopts a conformation typical of most nuclear receptor proteins. Three layers of alpha helices arrange in an anti-parallel manner to form a pocket that embraces the ligand (DHT shown here) . Specific interactions between residues and ligands are dependant on ligand structure. Click Here for Ligand Structures.

III. Hydrogen Bonding Interactions

   All androgens that bind the AR with high affinity possess a carbonyl oxygen at C3, and a hydroxy function at C17 The carbony oxygen at C3 has lone pairs of electrons capable of being hydrogen bond acceptors, and the hydroxy function at C17 can act as both a donor and acceptor. It is the hydrogen bonding of these functionalities to amino acid side chains that orients the ligand molecule in the proper position for other interactions to occur.
    Two amino acid side chains are capable of making h-bond interactions with the carbonyl oxygen on C3. Arg752 and Gln711 both interact with the carbonyl oxygen, but mutations in
Arg752 have been shown to cause Androgen Insensitivity Syndrom, while mutations in Gln711 have minimal effects. Arg752 and Gln711 make water mediated hydrogen bonds to the carbonyl oxygen . At the other end of the steroid molecule,  Asn705 and Thr877 make hydrogen bonds with the C17 hydroxyl group.

IV. Determinants of Binding Specificity   

    Within the LBP of the AR, a large, apolar pocket is formed, being composed of  many amino acid side chains that interact the ligand, thus creating an energetically stable environment. Loss of these interactions energetically costly and disfavored. The LBP is composed of mainly hydrophobic amino acid residues (except for those involved in h-bonding). Extensive van der Waals interactions between the ligand and LBP are made. Here, testosterone is shown in the LBP of the AR . Testosterone is composed of four carbon rings. .This general structure is consistant with most steriods that interact with the AR. The four carbon rings provide a surface for van der Waals interactions to occur. Differing numbers of van der Waals contacts are made between the ligand and LBP for different steriods. The number of hydrophobic interactions is hypothesized to be a factor leading to differing binding affinities. 
    The side chains of amino acid residues within the LBP are highly mobile. It is hypothesized that the mobility of these residues is a major factor that enables the AR to bind many different ligands. For instance, here we compare the structure of the LBP amino acid residues when the AR is complexed with testosterone, which shows low binding affinity (about 93% less), to another ligand, THG. When bound to testosterone, the distance of Met745 side chain to C4 where it is thought to make van der Waals contacts was not resolved due to its high mobility and distance from the steroid . The methyl group on C19 is thought to cause steric clash with the side chain, and thus an energetically disfavorable interaction there, influencing the spacial arrangement of this side chain. Another factor leading to high mobility of this residue when bound to testosterone is the lack of conjugated pi systems within the ligand molecule. Without conjugated pi systems, the ligand adopts many differing conformations within the LBP, thus creating an environment where Met745 must similarly adopt many conformations. This differs from Met745 in the AR complexed with THG. This ligand has considerably more conjugated pi systems, confering a higher level of rigidity, thus disfavoring the mobility of Met745 when the AR is complexed with this ligand . The distance of this side chain to THG was determined to be 3.77 angstroms, close enough to have extensive non-polar interactions. Click both buttons in the above section in sequence to observe the differing conformations of  Met745 in complex with testosterone and then THG.
    Trp741 is another amino acid that plays a role in determining binding affinity for differing ligands.  When testosterone is bound to the AR,
it has been shown that Met745 sterically clashes with Trp741 due to it's high mobility and distance from the ligand , while when THG is bound, Met745  takes a much more stable conformation near the ligand, allowing Trp741 to make apolar interactions with the face of the ligand. The observed difference in Trp741 location is a nearly 60 degree rotation about it's beta carbon.
    Further adding to the equation of binding specificity is  Met895, which  in the AR bound to testosterone,  adopts a position that is 1.2 angstroms closer to the ligand than when THG is bound. It is not well understood the effect this different conformation has on binding specificity, but the change is still noteworthy. Also of interest is Leu701 which also adopts differing conformations depending on the bound ligand.
Based upon electron density map analysis, it has been determined that testosterone makes 20 van der Waals contacts with the LBP , and THG makes 26 . An increased number of favorable contacts confers increased stability and thus a higher binding affinity as is observed. Comparison of the AR bound to both ligands shows that fewer side chains contact testosterone than THG. Possible reasons for this are steric clash of the less rigid testosterone molecule with these side chains as well as THG being slighly larger, with two ethyl groups protruding from C13 and C18, providing more surface for van der Waals interactions. Further research into the effects of the differing ligand structures and side chain conformations in the LBP of the AR will enable the determination of more factors that affect binding specificity based upon the structure of the LBD.

V. References

(1) Jesus-Tran, K. P, P. C. Cote, L. Cantin, J. Blanchet, F. Labrie, R.         Breton. “Comparison of crystal structures of human androgen         receptor ligand-binding domain complexed with various                 agonists reveals molecular determinants responsible for                 binding affinity.” Oncology and Molecular Endocrinology                 Research Center. (FEB 2006) 

(2) McEwan, I.J., J. A. Gustafsson. “Interaction of the human                     androgen receptor transactivation function with the general             transcription factor TFIIF.” Department of Biosciences. Vol. 94,         (AUG 1997):8485-8490. 

(3) Kadi, F., P. Bonnerud, A. Eriksson, L.E. Thornell. “The                         expression of androgen receptors in human neck and limb             muscles: effects of training and self-administration of                     androgenic-anabolic steroids.” Histochem Cell Biol (2000). 113:         25-29. 

(4) Shaffer, P.L., A. Jivan, D. E. Dollins, F. Claessens, D. T. Gewirth.         “Structural basis of androgen receptor binding to selective             androgen response elements.” Proc. Natl. Acad. Sci USA. Vol.         101, No. 14. (APR 2004): 4758-4763. 

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