Hydrophobic Binding Groove Research Articles

Molecule of the Month

Bad news for cancer. The Bcl-2 (B-cell lymphoma 2) family of proteins is comprised of both pro-apoptotic and anti-apoptotic members that operate through a complex series of protein-protein interactions [1-3]. The pro-apoptotic proteins are categorized into two groups based on the number of Bcl homology (BH) domains: 1) those with 3 BH domains (BH1-BH3 such as Bax and Bak) and 2) those with a single BH domain (BH-3 only such as Bad, Bik, Puma, etc...). The prosurvival (anti-apoptotic) members contain four BH domains (BH1-BH4 such as Bcl-2, Bcl-xL, etc...). Overexpression of Bcl-2 and its closely related counterpart Bcl-xL affords a mechanism by which cancer cells suppress apoptotic signaling, confer a survival advantage and provide resistance to chemotherapy [1-3]. Recognizing that inhibition of Bcl-2 family members should specifically target the abnormal cell death pathway in the overexpressing cancer cells led Elmore and co-workers at Abbott labs to launch a drug discovery campaign aimed at developing small molecule protein-protein inhibitors of the Bcl-2 family [4-6]. Initial work centered on a class of potent biarylacylsulfonamide antagonists - outside the usual α-helical mimetics - and a lead compound which bound Bcl-xL with a Ki of 800 pM [4]. Despite effective cytotoxic activity with multiple cytotoxic agents and UV irradiation, this Bcl-xL antagonist had no single agent efficacy across a large panel of human tumor cell lines. Elmore and co-workers then reasoned that since this inhibitor was developed by structure-based design aimed at Bcl-xL, it was not surprising that it exhibited much lower affinity for Bcl-2 [5,6]. Since Bcl-2 overexpression is a major hallmark of many human cancers, the team sought to broaden their inhibitor profile to target both Bcl-xL and Bcl-2; interestingly, despite only 49% homology, the three-dimensional structures of Bcl-xL and Bcl-2 are similar. The researchers focused in on the largest structural distinction between the two - a different helical fold of the α3 helix [5]. The α3 helix borders one side of the hydrophobic binding groove, and there exists a wider groove for Bcl-2 than Bcl-xL and a deeper hydrophobic pocket within the groove for Bcl-2 than Bcl-xL. Based on this key structural difference, the team designed modified inhibitors to access this deep hydrophobic pocket in the floor of the groove and thereby increasing affinity for Bcl-2. Their strategy worked! A chemical lead optimization campaign along with structure-guided design resulted in the identification of a clincal candidate, ABT-737, the first dual, subnanomolar inhibitors of Bcl- 2 and Bcl-xL (Ki < 1 nM and < 0.5 nM, respectively) and with EC50s of 8 nM and 30 nM, respectively [5]. ABT-737 showed single agent efficacy against human follicular lymphoma cell lines that overexpress Bcl-2 and efficacy in a murine tumor xenograft model of lymphoma when given as either a single agent or in combination with etoposide. ABT-737 was also efficacious in two mice small cell lung carcinoma xenograft models known to be resistant to most cytotoxic agents. For example, ABT-737 administered i.p. at 75 mg/kg/day for 21 days in a H146 model caused complete regression of established xenografts and 58 days after cessation of therapy, the tumors did not grow back in 77% of the mice [5,6]. ABT-737 represents a significant advance in the discovery and development of small molecule protein-protein inhibitors and clinical data in human patients is eagerly awaited. REFERENCES [1] Cory, S.; Adams, J.M. The Bcl2 family: regulators of the cellular life-ordeath switch. Nat. Rev. Cancer 2002, 2, 647-656. [2] Borner, C. The Bcl2 protein family: sensor and checkpoints for life-or-death decisions. Mol. Immunol. 2003, 39, 615-647. [3] van Delft, M.F.; Huang, D.S.C. How the Bcl-2 family of proteins interact to regulate apoptosis. Cell. Res. 2006, 16, 203-213. [4] Wendt, M.D.; Shen, W.; Kunzer, A.; McClellan, W.J.; Bruncko, M.; Oost, T.K.; Ding, H.; Joseph, M. K.; Zhang, H.; Nimmer, P.M.; Ng, S.-C.; Shoemaker, A.R.; Petros, A.M.; Oleksijew, A.; Marsh, K.; Bauch, J.; Oltersdorf, T.; Belli, B.A.; Martineau, D.; Fesik, S.W.; Rosenberg, S. H.; Elmore, S.W. Discovery and structure-activity relationship of antagonists of B-Cell Lymphoma 2 Family Proteins with chemopotentiation activity in vitro and in vivo. J. Med. Chem. 2006, 49, 1165-1181.

Novel FXXFF and FXXMF Motifs in Androgen Receptor Cofactors Mediate High Affinity and Specific Interactions with the Ligand-binding Domain

Upon hormone binding, a hydrophobic coactivator binding groove is induced in the androgen receptor (AR) ligand-binding domain (LBD). This groove serves as high affinity docking site for alpha-helical FXXLF motifs present in the AR N-terminal domain and in AR cofactors. Study of the amino acid requirements at position +4 of the AR FXXLF motif revealed that most amino acid substitutions strongly reduced or completely abrogated AR LBD interaction. Strong interactions were still observed following substitution of Leu+4 by Phe or Met residues. Leu+4 to Met or Phe substitutions in the FXXLF motifs of AR cofactors ARA54 and ARA70 were also compatible with strong AR LBD binding. Like the corresponding FXXLF motifs, interactions of FXXFF and FXXMF variants of AR and ARA54 motifs were AR specific, whereas variants of the less AR-selective ARA70 motif displayed increased AR specificity. A survey of currently known AR-binding proteins revealed the presence of an FXXFF motif in gelsolin and an FXXMF motif in PAK6. In vivo fluorescence resonance energy transfer and functional protein-protein interaction assays showed direct, efficient, and specific interactions of both motifs with AR LBD. Mutation of these motifs abrogated interaction of gelsolin and PAK6 proteins with AR. In conclusion, we have demonstrated strong interaction of FXXFF and FXXMF motifs to the AR coactivator binding groove, thereby mediating specific binding of a subgroup of cofactors to the AR LBD.

A Surface Groove Essential for Viral Bcl-2 Function During Chronic Infection In Vivo

Antiapoptotic Bcl-2 family proteins inhibit apoptosis in cultured cells by binding BH3 domains of proapoptotic Bcl-2 family members via a hydrophobic BH3 binding groove on the protein surface. We investigated the physiological importance of the BH3 binding groove of an antiapoptotic Bcl-2 protein in mammals in vivo by analyzing a viral Bcl-2 family protein. We show that the γ-herpesvirus 68 (γHV68) Bcl-2 family protein (γHV68 v-Bcl-2), which is known to inhibit apoptosis in cultured cells, inhibits both apoptosis in primary lymphocytes and Bax toxicity in yeast. Nuclear magnetic resonance determination of the γHV68 v-Bcl-2 structure revealed a BH3 binding groove that binds BH3 domain peptides from proapoptotic Bcl-2 family members Bax and Bak via a molecular mechanism shared with host Bcl-2 family proteins, involving a conserved arginine in the BH3 peptide binding groove. Mutations of this conserved arginine and two adjacent amino acids to alanine (SGR to AAA) within the BH3 binding groove resulted in a properly folded protein that lacked the capacity of the wild-type γHV68 v-Bcl-2 to bind Bax BH3 peptide and to block Bax toxicity in yeast. We tested the physiological importance of this v-Bcl-2 domain during viral infection by engineering viral mutants encoding a v-Bcl-2 containing the SGR to AAA mutation. This mutation resulted in a virus defective for both efficient reactivation of γHV68 from latency and efficient persistent γHV68 replication. These studies demonstrate an essential functional role for amino acids in the BH3 peptide binding groove of a viral Bcl-2 family member during chronic infection.

Solution Structure of Prosurvival Mcl-1 and Characterization of Its Binding by Proapoptotic BH3-only Ligands

The B cell lymphoma-2 (Bcl-2) homologs myeloid cell leukemia-1 (Mcl-1) and A1 are prosurvival factors that selectively bind a subset of proapoptotic Bcl homology (BH) 3-only proteins. To investigate the molecular basis of the selectivity, we determined the solution structure of the C-terminal Bcl-2-like domain of Mcl-1. This domain shares features expected of a prosurvival Bcl-2 protein, having a helical fold centered on a core hydrophobic helix and a surface-exposed hydrophobic groove for binding its cognate partners. A number of residues in the binding groove differentiate Mcl-1 from its homologs, and in contrast to other Bcl-2 homologs, Mcl-1 has a binding groove in a conformation intermediate between the open structures characterized by peptide complexes and the closed state observed in unliganded structures. Mutagenesis of potential binding site residues was used to probe the contributions of groove residues to the binding properties of Mcl-1. Although mutations in Mcl-1 had little impact on binding, a single mutation in the BH3-only ligand Bad enabled it to bind both Mcl-1 and A1 while retaining its binding to Bcl-2, Bcl-xL, and Bcl-w. Elucidating the selective action of certain BH3-only ligands is required for delineating their mode of action and will aid the search for effective BH3-mimetic drugs.

Solution Structure, Dynamics, and Hydrodynamics of the Calcium-bound Cross-reactive Birch Pollen Allergen Bet v 4 Reveal a Canonical Monomeric Two EF-Hand Assembly with a Regulatory Function

Birch pollinosis is one of the prevailing allergic diseases. In all, 5–20% of birch pollinotics mount IgE antibodies against the minor birch pollen allergen Bet v 4, a Ca 2+-binding polcalcin. Due to IgE cross-reactivity among the polcalcins these patients are polysensitized to various plant pollens. Determination of the high-resolution structure of holo Bet v 4 by heteronuclear NMR spectroscopy reveals a canonical two EF-hand assembly in the open conformation with interhelical angles closely resembling holo calmodulin. The polcalcin-specific amphipathic COOH-terminal α-helix covers only a part of the hydrophobic groove on the molecular surface. Unlike the polcalcin Phl p 7 from timothy grass, which was recently shown to form a domain-swapped dimer, the hydrodynamic parameters from NMR relaxation, NMR translational diffusion, and analytical ultracentrifugation indicate that both apo and holo Bet v 4 are predominantly monomeric, raising the question of the physiological and immunological significance of the dimeric form of these polcalcins, whose physiological function is still unknown. The reduced helicity and heat stability in the CD spectra, the poor chemical shift dispersion of the NMR spectra, and the slightly increased hydrodynamic radius of apo Bet v 4 indicate a reversible structural transition upon Ca 2+ binding, which explains the reduced IgE binding capacity of apo Bet v 4. The remarkable structural similarity of holo Bet v 4 and holo Phl p 7 in spite of different oligomerization states explains the IgE cross-reactivity and indicates that canonical monomers and domain-swapped dimers may be of similar allergenicity. Together with the close structural homology to calmodulin and the hydrophobic ligand binding groove this transition suggests a regulatory function for Bet v 4.

Direct Measurement of Antigen Binding Properties of CD1 Proteins Using Fluorescent Lipid Probes

CD1 proteins are antigen-presenting molecules that bind foreign and self-lipids and stimulate specific T cell responses. In the current study, we investigated ligand binding by CD1 proteins by developing a fluorescent probe binding approach using soluble recombinant human CD1 proteins. To increase stability and yield, soluble group 1 CD1 (CD1b and CD1c) and group 2 CD1 (CD1d) proteins were produced as single chain secreted CD1 proteins in which beta2-microglobulin was fused to the N termini of the CD1 heavy chains by a flexible peptide linker sequence. Analysis of ligand binding properties of single chain secreted CD1 proteins by using fluorescent lipid probes indicated significant differences in ligand preference and in pH dependence of binding by group 1 versus group 2 CD1 proteins. Whereas group 1 CD1 isoforms (CD1b and CD1c) show stronger binding of nitrobenzoxadiazole (NBD)-labeled dialkyl-based ligands (phosphatidylcholine, sphingomyelin, and ceramide), group 2 CD1 (CD1d) proteins were stronger binders of small hydrophobic probes such as 1-anilinonaphthalene-8-sulfonic acid and 4,4'-dianilino-1,1'-naphthyl-5,5'-disulfonic acid. Competition studies indicated that binding of fluorescent lipid probes involved association of the probe with the hydrophobic ligand binding groove of CD1 proteins. Analysis of selected alanine substitution mutants of human CD1b known to inhibit antigen presentation showed that NBD-labeled lipid probe binding could be used to distinguish mutations that interfere with ligand binding from those that affect T cell receptor docking. Our findings provide further evidence for the functional specialization of different CD1 isoforms and demonstrate the value of the fluorescent lipid probe binding method for assisting structure-based studies of CD1 function.

Induction of Flexibility through Protein-Protein Interactions

The dimerization/docking (D/D) domain of the cyclic AMP-dependent protein kinase (PKA) holoenzyme mediates important protein-protein interactions that direct the subcellular localization of the enzyme. A kinase anchoring proteins (AKAPs) provide the molecular scaffold for the localization of PKA. The recent solution structures of two D/D AKAP complexes revealed that the AKAP binds to a surface-exposed, hydrophobic groove on the D/D. In the present study, we present an analysis of the changes in hydrogen/deuterium exchange protection and internal motions of the backbone of the D/D when free and bound to the prototype anchoring protein, Ht31(pep). We observe that formation of the complex results in significant, but small, increases in H/D exchange protection factors as well as increases in backbone flexibility, throughout the D/D, and in particular, in the hydrophobic binding groove. This unusual observation of increased backbone flexibility and marginal H/D exchange protection, despite high affinity protein-ligand interactions, may be a general effect observed for the stabilization of hydrophobic ligand/hydrophobic pocket interactions.

Promiscuous Antigen Presentation by the Nonclassical MHC Ib Qa-2 Is Enabled by a Shallow, Hydrophobic Groove and Self-Stabilized Peptide Conformation

Background: Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. Results: We have determined the crystal structure, to 2.3 Å, of the Q9 gene of murine Qa-2 complexed with a self-peptide derived from the L19 ribosomal protein, which is abundant in the pool of peptides eluted from the Q9 groove. The 9 amino acid peptide is bound high in a shallow, hydrophobic binding groove of Q9, which is missing a C pocket. The peptide makes few specific contacts and exhibits extremely poor shape complementarity to the MHC groove, which facilitates the presentation of a degenerate array of sequences. The L19 peptide is in a centrally bulged conformation that is stabilized by intramolecular interactions from the invariant P7 histidine anchor residue and by a hydrophobic core of preferred secondary anchor residues that have minimal interaction with the MHC. Conclusions: Unexpectedly, the preferred secondary peptide residues that exhibit tenuous contact with Q9 contribute significantly to the overall stability of the peptide-MHC complex. The structure of this complex implies a “conformational” selection by Q9 for peptide residues that optimally stabilize the large bulge rather than making intimate contact with the MHC pockets.

Solution structure of the antiapoptotic protein bcl-2.

The structures of two isoforms of Bcl-2 that differ by two amino acids have been determined by NMR spectroscopy. Because wild-type Bcl-2 behaved poorly in solution, the structures were determined by using Bcl-2/Bcl-x(L) chimeras in which part of the putative unstructured loop of Bcl-2 was replaced with a shortened loop from Bcl-x(L). These chimeric proteins have a low pI compared with the wild-type protein and are soluble. The structures of the two Bcl-2 isoforms consist of 6 alpha-helices with a hydrophobic groove on the surface similar to that observed for the homologous protein, Bcl-x(L). Comparison of the Bcl-2 structures to that of Bcl-x(L) shows that although the overall fold is the same, there are differences in the structural topology and electrostatic potential of the binding groove. Although the structures of the two isoforms of Bcl-2 are virtually identical, differences were observed in the ability of the proteins to bind to a 25-residue peptide from the proapoptotic Bad protein and a 16-residue peptide from the proapoptotic Bak protein. These results suggest that there are subtle differences in the hydrophobic binding groove in Bcl-2 that may translate into differences in antiapoptotic activity for the two isoforms.

Three-dimensional structure of H-2D d complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120

The crystal structure of the mouse major histocompatibility complex (MHC) class I molecule H-2D dwith an immunodominant peptide, designated P18-I10 (RGPGRAFVTI), from human immunodeficiency virus envelope glycoprotein 120 was determined at 3.2 Å resolution. A novel orientation of the α3 domain of D drelative to the α1/α2 domains results in significantly fewer contacts between α3 and β 2-microglobulin compared with other MHC class I proteins. Four out of ten peptide residues (P2 Gly, P3 Pro, P5 Arg and P10 Ile) are nearly completely buried in the D dbinding groove. This is consistent with previous findings that D dexploits a four-residue binding motif comprising a glycine at P2, a proline at P3, a positively charged residue at P5, and a C-terminal hydrophobic residue at P9 or P10. The side-chain of P5 Arg is directed toward the floor of the predominantly hydrophobic binding groove where it forms two salt bridges and one hydrogen bond with D dresidue Asp77. The selection of glycine at P2 appears to be due to a narrowing of the B pocket, relative to that of other class I molecules, caused by Arg66 whose side-chain folds down into the binding cleft. Residue P3 Pro of P18-I10 occupies part of pocket D, which in D dis partially split by a prominent hydrophobic ridge in the floor of the binding groove formed by Trp97 and Trp114. Residues P6 through P9 form a solvent-exposed bulge, with P7 Phe protruding the most from the binding groove and thereby probably constituting a major site of interaction with T cell receptors. A comparison of H-2D d/P18-I10 with other MHC class I/peptide complexes of known structure provides insights into the possible basis for the specificity of the natural killer cell receptor Ly-49A for several related class I molecules.

Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove.

CD1 represents a third lineage of antigen-presenting molecules that are distantly related to major histocompatibility complex (MHC) molecules in the immune system. The crystal structure of mouse CD1d1, corresponding to human CD1d, at 2.8 resolution shows that CD1 adopts an MHC fold that is more closely related to that of MHC class I than to that of MHC class II. The binding groove, although significantly narrower, is substantially larger because of increased depth and it has only two major pockets that are almost completely hydrophobic. The extreme hydrophobicity and shape of the binding site are consistent with observations that human CD1b and CD1c can present mycobacterial cell wall antigens, such as mycolic acid and lipoarabinomannans. However, mouse CD1d1 can present very hydrophobic peptides, but must do so in a very different way from MHC class Ia and class II molecules.

Structure of angiotensin II-binding site probed with diaminoalkanes

The nature of the hormone-binding site of detergent-solubilized angiotensin II receptor from the bovine adrenal cortex has been characterized using diaminoalkanes. Their affinity for the hormone-binding site showed a dramatic alteration depending on their chain length; at the hexamethylene stage, a maximum and competitive inhibition was observed. These results indicate that the angiotensin II receptors have a definite hydrophobic binding groove limbed with diagonally located two negative charges, and those hydrophobic and electrostatic forces may play an important role in the proper register between the receptor and hormone.