Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental parameters the 13 C ␣ , 13 C ␤ , 13 C , 15 N, 1 H ␣ and 1 H N NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7-1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination. molecular fragment replacement ͉ protein structure prediction ͉ ROSETTA ͉ structural genomics

Estrogen receptor alpha (ER␣), a key driver of growth in the majority of breast cancers, contains an unstructured transactivation domain (AF1) in its N terminus that is a convergence point for growth factor and hormonal activation. This domain is controlled by phosphorylation, but how phosphorylation impacts AF1 structure and function is unclear. We found that serine 118 (S118) phosphorylation of the ER␣ AF1 region in response to estrogen (agonist), tamoxifen (antagonist), and growth factors results in recruitment of the peptidyl prolyl cis/trans isomerase Pin1. Phosphorylation of S118 is critical for Pin1 binding, and mutation of S118 to alanine prevents this association. Importantly, Pin1 isomerizes the serine118-proline119 bond from a cis to trans isomer, with a concomitant increase in AF1 transcriptional activity. Pin1 overexpression promotes ligand-independent and tamoxifeninducible activity of ER␣ and growth of tamoxifen-resistant breast cancer cells. Pin1 expression correlates with proliferation in ER␣-positive rat mammary tumors. These results establish phosphorylation-coupled proline isomerization as a mechanism modulating AF1 functional activity and provide insight into the role of a conformational switch in the functional regulation of the intrinsically disordered transactivation domain of ER␣.E strogen receptor alpha (ER␣), a member of the nuclear receptor superfamily of transcription factors, mediates the actions of estrogen in normal physiology and disease (17). ER␣ is expressed in the normal mammary gland and in 70% of human breast cancers and is a key driver of breast cell proliferation (16,26,83). Directed overexpression of ER␣ in the mammary gland is sufficient to induce hyperplasia, and blockade of ER␣ activity by hormonal therapies (aromatase inhibitors, tamoxifen, and fulvestrant) reduces recurrence and improves clinical outcomes of ER␣-positive breast cancer patients (19,22). Two activation functions mediate the transcriptional activity of ER␣, a C-terminal liganddependent AF2 and an N-terminal ligand-independent AF1 (89). Regulation of ER␣ activity via the C-terminal AF2 has been wellcharacterized through biochemical and crystallographic studies and forms the basis for our understanding of hormonal therapy for breast cancer (10,34,84). In the canonical activation pathway, ligand binding initiates C-terminal structural rearrangements that facilitate downstream events, including dimerization, DNA binding, and coregulator interactions, ultimately engaging the basal transcriptional machinery to regulate gene expression. However, ER␣ can also be activated by growth factors and kinases, which phosphorylate the receptor N terminus and other domains to regulate transcription in the absence of direct ligand engagement (for reviews, see references 27, 47, 75, 94, and 95). In contrast to the C-terminal AF2 domain, biochemical and structural mechanisms that control N-terminal AF1 remain poorly understood (48,91).Multiple challenges have hindered molecular dissection of AF1 regulation. First, AF1 resid...

Vitamin D receptor (VDR) is a member of the nuclear hormone receptor superfamily. When bound to a variety of vitamin D analogs, VDR manifests a wide diversity of physiological actions. The molecular mechanism by which different vitamin D analogs cause specific responses is not understood. The published crystallographic structures of the ligand binding domain of VDR (VDR-LBD) complexed with ligands that have differential biological activities have exhibited identical protein conformations. Here we report that rat VDR-LBD (rVDR-LBD) in solution exhibits differential chemical shifts when bound to three ligands that cause diverse responses: the natural hormone, 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], a potent agonist analog, 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 [2MD], and an antagonist, 2-methylene-(22E)-(24R)-25-carbobutoxy-26,27-cyclo-22-dehydro-1α,24-dihydroxy-19-norvitamin D3 [OU-72]. Ligand-specific chemical shifts mapped not only to residues at or near the binding pocket but also to residues remote from the ligand binding site. The complexes of rVDR-LBD with native hormone and the potent agonist 2MD exhibited chemical shift differences in signals from helix-12, which is part of the AF2 transactivation domain that appears to play a role in the selective recruitment of co-activators. By contrast, formation of the complex of rVDR-LBD with the antagonist OU-72 led to disappearance of signals from residues in helices-11 and 12. We present evidence that disorder in this region of the receptor in the antagonist complex prevents the attachment of co-activators.

This article describes an associating system that integrates the specificity of multiple hydrogen bonding and the strength of dynamic covalent interactions. Linear oligoamides that sequence-specifically pair into H-bonded duplexes in nonpolar solvents were modified with S-trityl groups, allowing the reversible formation of disulfide bonds. The disulfide-crosslinking reactions of oligoamides capable of pairing via two, four, and six intermolecular H-bonds, along with several control strands, were examined using ESI, MALDI-TOF, reverse phase HPLC, and two-dimensional NMR. Results from these studies demonstrate that this system possesses both the high fidelity of multiply H-bonded assemblies and the high stability of covalent interaction, leading to the sequence-specific crosslinking of complementary oligoamides in not only nonpolar (methylene chloride) solutions but also highly competitive (aqueous) media. Experiments were designed to systematically probe the mechanism behind the specific formation of the sequence-matched products, which revealed a thermodymically controlled process. Multiple pairs in the same solution were crosslinked in a sequence-specific fashion. In addition, a length-dependent selectivity was also observed. Thus, oligoamides with different lengths or sequences did not crosslink into mismatched products. As few as two H-bonds is sufficient to bias the specific formation of the crosslinked product in aqueous media, suggesting that associating units with tunable sizes, high stability, and high specificity can be conveniently designed. The combination of H-bonding and dynamic covalent interactions represents a new, generalizable strategy for developing highly specific molecular associating units that are stable in a wide variety of media. These associating units will greatly facilitate the construction of various structures with many applications.

Background: ToxB is a proteinaceous toxin but its homolog toxb has no toxic activity. Results: Both adopt a ␤-sandwich fold stabilized by two disulfide bonds but differ in the dynamics of one sandwich half. Conclusion: Toxicity is correlated with decreased compactness, increased flexibility, and polymorphism in an active site loop. Significance: ToxB activity depends on interplay between internal dynamics and interactions with putative targets.