[Show abstract][Hide abstract] ABSTRACT: The molecular chaperone Hsp90 undergoes an ATP-driven cycle of conformational changes in which large structural rearrangements precede ATP hydrolysis. Well-established small-molecule inhibitors of Hsp90 compete with ATP-binding. We wondered whether compounds exist that can accelerate the conformational cycle. In a FRET-based screen reporting on conformational rearrangements in Hsp90 we identified compounds. We elucidated their mode of action and showed that they can overcome the intrinsic inhibition in Hsp90 which prevents these rearrangements. The mode of action is similar to that of the co-chaperone Aha1 which accelerates the Hsp90 ATPase. However, while the two identified compounds influence conformational changes, they target different aspects of the structural transitions. Also, the binding site determined by NMR spectroscopy is distinct. This study demonstrates that small molecules are capable of triggering specific rate-limiting transitions in Hsp90 by mechanisms similar to those in protein cofactors.
Angewandte Chemie International Edition 09/2014; · 11.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Der Reaktionszyklus des molekularen Chaperons Hsp90 ist durch ATP-getriebene Konformationsänderungen charakterisiert, die der ATP-Hydrolyse vorgeschaltet sind. Es gibt bereits niedermolekulare Inhibitoren von Hsp90, die mit der ATP-Bindung konkurrieren. Wir fragten uns, ob Verbindungen existieren, die den konformationellen Zyklus beschleunigen können. In einem FRET-basierten Screen, der Konformationsänderungen in Hsp90 detektiert, identifizierten wir zwei Verbindungen und analysierten ihre Wirkungsweise. Wir können zeigen, dass die intrinsische Inhibition von Hsp90, welche konformationelle Umlagerungen verhindert, durch diese Substanzen überwunden wird. Diese Wirkungsweise ähnelt der des Cochaperons Aha1 von Hsp90, das die ATPase-Aktivität beschleunigt. Während beide Verbindungen Konformationsänderungen beeinflussen, so steuern sie jeweils verschiedene Aspekte der Strukturübergänge. Zudem unterscheiden sich ihre durch NMR-Spektroskopie bestimmten Bindestellen. Unsere Studie zeigt, dass kleine Moleküle in der Lage sind, spezifische geschwindigkeitsbestimmende Übergänge in Hsp90 in ähnlicher Weise zu beschleunigen wie dies durch Protein-Cofaktoren geschieht.
[Show abstract][Hide abstract] ABSTRACT: Genetic equality between males and females is established by chromosome-wide dosage-compensation mechanisms. In the fruitfly Drosophila melanogaster, the dosage-compensation complex promotes twofold hypertranscription of the single male X-chromosome and is silenced in females by inhibition of the translation of msl2, which codes for the limiting component of the dosage-compensation complex1, 2. The female-specific protein Sex-lethal (Sxl) recruits Upstream-of-N-ras (Unr) to the 3′ untranslated region of msl2 messenger RNA, preventing the engagement of the small ribosomal subunit3. Here we report the 2.8 Å crystal structure, NMR and small-angle X-ray and neutron scattering data of the ternary Sxl–Unr–msl2 ribonucleoprotein complex featuring unprecedented intertwined interactions of two Sxl RNA recognition motifs, a Unr cold-shock domain and RNA. Cooperative complex formation is associated with a 1,000-fold increase of RNA binding affinity for the Unr cold-shock domain and involves novel ternary interactions, as well as non-canonical RNA contacts by the α1 helix of Sxl RNA recognition motif 1. Our results suggest that repression of dosage compensation, necessary for female viability, is triggered by specific, cooperative molecular interactions that lock a ribonucleoprotein switch to regulate translation. The structure serves as a paradigm for how a combination of general and widespread RNA binding domains expands the code for specific single-stranded RNA recognition in the regulation of gene expression.
[Show abstract][Hide abstract] ABSTRACT: The REtention and Splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and to promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total eighteen residues of Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp232 in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that the Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RNA recognition motif (RRM)-protein interactions, analogous to the one seen in for nucleic acid interactions.
[Show abstract][Hide abstract] ABSTRACT: Roquin function in T cells is essential for the prevention of autoimmune disease. Roquin interacts with the 3' untranslated regions (UTRs) of co-stimulatory receptors and controls T-cell activation and differentiation. Here we show that the N-terminal ROQ domain from mouse roquin adopts an extended winged-helix (WH) fold, which is sufficient for binding to the constitutive decay element (CDE) in the Tnf 3' UTR. The crystal structure of the ROQ domain in complex with a prototypical CDE RNA stem-loop reveals tight recognition of the RNA stem and its triloop. Surprisingly, roquin uses mainly non-sequence-specific contacts to the RNA, thus suggesting a relaxed CDE consensus and implicating a broader spectrum of target mRNAs than previously anticipated. Consistently with this, NMR and binding experiments with CDE-like stem-loops together with cell-based assays confirm roquin-dependent regulation of relaxed CDE consensus motifs in natural 3' UTRs.
[Show abstract][Hide abstract] ABSTRACT: NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
Progress in Nuclear Magnetic Resonance Spectroscopy 07/2014; 80C:26-63. · 6.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that rely on antibodies as part of their adaptive immune system. They produce the immunoglobulin new antigen receptor (IgNAR), a homodimeric heavy chain-only antibody, as a major part of their humoral adaptive immune response. Here, we report the atomic resolution structure of the IgNAR constant domains and a structural model of this heavy chain-only antibody. We find that despite low sequence conservation, the basic Ig fold of modern antibodies is already present in the evolutionary ancient shark IgNAR domains, highlighting key structural determinants of the ubiquitous Ig fold. In contrast, structural differences between human and shark antibody domains explain the high stability of several IgNAR domains and allowed us to engineer human antibodies for increased stability and secretion efficiency. We identified two constant domains, C1 and C3, that act as dimerization modules within IgNAR. Together with the individual domain structures and small-angle X-ray scattering, this allowed us to develop a structural model of the complete IgNAR molecule. Its constant region exhibits an elongated shape with flexibility and a characteristic kink in the middle. Despite the lack of a canonical hinge region, the variable domains are spaced appropriately wide for binding to multiple antigens. Thus, the shark IgNAR domains already display the well-known Ig fold, but apart from that, this heavy chain-only antibody employs unique ways for dimerization and positioning of functional modules.
Proceedings of the National Academy of Sciences 05/2014; · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Ultra-high-field NMR spectroscopy requires an increased bandwidth for heteronuclear decoupling, especially in biomolecular NMR applications. Composite pulse decoupling cannot provide sufficient bandwidth at practical power levels, and adiabatic pulse decoupling with sufficient bandwidth is compromised by sideband artifacts. A novel low-power, broadband heteronuclear decoupling pulse is presented that generates minimal, ultra-low sidebands. The pulse was derived using optimal control theory and represents a new generation of decoupling pulses free from the constraints of periodic and cyclic sequences. In comparison to currently available state-of-the-art methods this novel pulse provides greatly improved decoupling performance that satisfies the demands of high-field biomolecular NMR spectroscopy.
Angewandte Chemie International Edition in English 04/2014; · 13.45 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Multi-domain proteins containing intrinsically disordered linkers exhibit large-scale dynamic modes that play key roles in a multitude of molecular recognition and signaling processes. Here we determine the conformational space sampled by the multi-domain splicing factor U2AF65 using complementary nuclear magnetic resonance spectroscopy and small angle scattering data. Available degrees of conformational freedom are initially stochastically sampled and experimental data then used to delineate the potential energy landscape in terms of statistical probability. The spatial distribution of U2AF65 conformations is found to be highly anisotropic, comprising significantly populated inter-domain contacts that appear to be electrostatic in origin. This hypothesis is supported by the reduction of signature PREs reporting on this interface with increasing salt concentration. The described spatial distribution reveals the complete spectrum of the unbound forms of U2AF65 that co-exist with the small percentage of a pre-formed RNA-bound domain arrangement required for polypyrimidine-tract recognition by conformational selection. The presence of a range of dynamically interconverting conformers may imply beneficial conformational entropy for unbound U2AF65. More generally, the proposed approach to describing conformational equilibria of multi-domain proteins can be further combined with other experimental data that are sensitive to domain dynamics.
Journal of the American Chemical Society 04/2014; · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multi-disciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is on well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue-resolution, but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography and small angle scattering is thus very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, small angle scattering provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography and small angle scattering data to characterize protein complexes in solution.
[Show abstract][Hide abstract] ABSTRACT: Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5' splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2-RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs.
Nucleic Acids Research 03/2014; · 8.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Hsp90 is the most abundant molecular chaperone in the eukaryotic cell. One of the most stringent clients is the glucocorticoid receptor (GR), whose in vivo function strictly depends on the interaction with the Hsp90 machinery. However, the molecular mechanism of this interaction has been elusive. Here we have reconstituted the interaction of Hsp90 with hormone-bound GR using purified components. Our biochemical and structural analyses define the binding site for GR on Hsp90 and reveal that binding of GR modulates the conformational cycle of Hsp90. FRET experiments demonstrate that a partially closed form of the Hsp90 dimer is the preferred conformation for interaction. Consistent with this, the conformational cycle of Hsp90 is decelerated, and its ATPase activity decreases. Hsp90 cochaperones differentially affect formation of the Hsp90-GR complex, serving as control elements for cycle progression and revealing an intricate interplay of client and cochaperones as molecular modulators of the Hsp90 machine.
[Show abstract][Hide abstract] ABSTRACT: Protein import into peroxisomes relies on the import receptor Pex5, which recognizes proteins with a peroxisomal targeting signal 1 (PTS1) in the cytosol and directs them to a docking complex at the peroxisomal membrane. Receptor-cargo docking occurs at the membrane-associated protein Pex14. In human cells, this interaction is mediated by seven conserved diaromatic pentapeptide motifs (WxxxF/Y-motifs) in the N-terminal half of Pex5 and the N-terminal domain (NTD) of Pex14. A systematic screening of a Pex5-peptide library by ligand blot analysis revealed a novel Pex5-Pex14 interaction site of Pex5. The novel motif comprises the sequence LVAEF with the evolutionary conserved consensus sequence LVxEF. Replacement of the amino acids LVAEF sequence by alanines strongly affects matrix protein import into peroxisomes in vivo. The NMR structure of a complex of Pex5-(57-71) with Pex14-NTD showed that the novel motif binds in a similar α-helical orientation as the WxxxF/Y motif but that the tryptophan pocket is now occupied by a leucine residue. Surface plasmon resonance analyses revealed 33-times faster dissociation rates for the LVxEF ligand when compared to a WxxxF/Y motif. Surprisingly, substitution of the novel motif with the higher affinity WxxxF/Y motif impairs protein import into peroxisomes. These data indicate that the distinct kinetic properties of the novel Pex14-binding site in Pex5 are important for processing of the PTS1 receptor at the peroxisomal membrane. The novel Pex14 binding site may represent the initial tethering site of Pex5 from which the cargo-loaded receptor is further processed in a sequential manner.
Journal of Biological Chemistry 01/2014; 289(1):437-448. · 4.65 Impact Factor