Least-squares analysis of experimental data from the analytical ultracentrifuge is discussed in detail, with particular attention to the use of interference optics in studying nonideal self-associating macromolecular systems. Several samples are given that describe the application of the technique, the expected precision of the results, and some of its limitations. A FORTRAN IV computer program is available from the authors.

The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5′-AGGG(TTAGGG)3] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na+ solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K+ revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K+ solutions. Sedimentation coefficients were determined experimentally in both Na+ and K+ solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na+ solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K+ solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K+ yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K+ solutions, but not in Na+ solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K+ quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K+ solution is not the one determined in the published crystalline state.

IRF-3, a member of the interferon regulatory factor (IRF) family of transcription factors, functions as a molecular switch for antiviral activity. IRF-3 uses an autoinhibitory mechanism to suppress its transactivation potential in uninfected cells, and virus infection induces phosphorylation and activation of IRF-3 to initiate the antiviral responses. The crystal structure of the IRF-3 transactivation domain reveals a unique autoinhibitory mechanism, whereby the IRF association domain and the flanking autoinhibitory elements condense to form a hydrophobic core. The structure suggests that phosphorylation reorganizes the autoinhibitory elements, leading to unmasking of a hydrophobic active site and realignment of the DNA binding domain for transcriptional activation. IRF-3 exhibits marked structural and surface electrostatic potential similarity to the MH2 domain of the Smad protein family and the FHA domain, suggesting a common molecular mechanism of action among this superfamily of signaling mediators.

Smad3 transduces the signals of TGF-βs, coupling transmembrane receptor kinase activation to transcriptional control. The membrane-associated molecule SARA (Smad Anchor for Receptor Activation) recruits Smad3 for phosphorylation by the receptor kinase. Upon phosphorylation, Smad3 dissociates from SARA and enters the nucleus, in which its transcriptional activity can be repressed by Ski. Here, we show that SARA and Ski recognize specifically the monomeric and trimeric forms of Smad3, respectively. Thus, trimerization of Smad3, induced by phosphorylation, simultaneously activates the TGF-β signal by driving Smad3 dissociation from SARA and sets up the negative feedback mechanism by Ski. Structural models of the Smad3/SARA/receptor kinase complex and Smad3/Ski complex provide insights into the molecular basis of regulation.

Vinca alkaloids are antimitotic drugs that inhibit microtubule assembly and induce tubulin self-association into coiled spiral aggregates. Previous sedimentation velocity results with vinblastine have been interpreted by a mechanism involving isodesmic ligand-mediated or ligand-mediated plus ligand-facilitated self-association [Lobert et al. (1995) Biochemistry 34, 8050-8060]. In this study, we compare the vincristine- or vinorelbine-induced self-association of porcine brain tubulin with our prior vinblastine studies in the presence of 50 microM GDP or 50 microM GTP. Vincristine demonstrates the highest overall affinity for tubulin, K1K2, and vinorelbine the lowest (vincristine > vinblastine > vinorelbine). These and the first quantitative studies comparing the interaction of a new vinca alkaloid derivative, vinorelbine (Navelbine), with other vinca alkaloids. The relative binding affinities reported here correlate with the weekly drug doses used clinically in cancer chemotherapy, where vincristine is used at the lowest dosages and vinorelbine at the highest. Surprisingly, K1, the affinity of drug for tubulin heterodimers, is identical for all three drugs. When data are fit with the ligand-mediated model, the differences in overall affinity are due to effects on K2, the affinity of liganded heterodimers for spiral polymers. When data are fit with the ligand-mediated plus-facilitated model, affinity differences are also reflected in K3, the binding of the drug to unliganded polymers. We find that GDP enhances self-association in the presence of all three drugs 3-5-fold over GTP. The enhancement is manifested in K2 and K3 and amounts to an average of 0.90 +/= 0.17 kcal/mol. Thus, nucleotide enhancement is linked to the self-association step. Data collected at 5, 25, and 36 degrees C for all three drugs show increased maximum s-20,w values with increasing temperature and are consistent with an entropically driven reaction for the overall process. To investigate these results further, stopped-flow light scattering experiments have been conducted. Relaxation times are longest for the largest vincristine polymers and shortest for the smallest vinorelbine polymers, consistent with a cascade of events corresponding to successive dissociation events from spiral polymers, the larger the polymers the longer the relaxation time. Relaxation times for any single drug decrease with increasing tubulin concentration, consistent with the occurrence of oligomer annealing in addition to the association of liganded heterodimers to the ends of the growing spirals. Relaxation times were used to estimate on and off rates for liganded heterodimer association with spirals, and their ratio gives affinity constants (Kapp) that are independently consistent with K2 estimates from sedimentation velocity results for vinblastine and vinorelbine. For vincristine-induced tubulin polymers, a two-step process is observed with a second relaxation time more than 20-fold longer than times observed for vinblastine or vinorelbine. Sedimentation velocity ...

The Spire protein, together with the formin Cappuccino and profilin, plays an important role in actin-based processes that establish oocyte polarity. Spire contains a cluster of four actin-binding WH2 domains. It has been shown to nucleate actin filaments and was proposed to remain bound to their pointed ends. Here we show that the multifunctional character of the WH2 domains allows Spire to sequester four G-actin subunits binding cooperatively in a tight SA(4) complex and to nucleate, sever, and cap filaments at their barbed ends. Binding of Spire to barbed ends does not affect the thermodynamics of actin assembly at barbed ends but blocks barbed end growth from profilin-actin. The resulting Spire-induced increase in profilin-actin concentration enhances processive filament assembly by formin. The synergy between Spire and formin is reconstituted in an in vitro motility assay, which provides a functional basis for the genetic interplay between Spire, formin, and profilin in oogenesis.

Interferon regulatory factors (IRFs) are essential in the innate immune response and other physiological processes. Activation of these proteins in the cytoplasm is triggered by phosphorylation of Ser/Thr residues in a C-terminal autoinhibitory region, which stimulates dimerization, transport into the nucleus, assembly with the coactivator CBP/p300 and initiation of transcription. The novel crystal structure of the transactivation domain of pseudophosphorylated human IRF5 reveals a striking dimer in which the bulk of intersubunit interactions involve a highly extended C-terminal region. The corresponding region has previously been shown to block CBP/p300 binding to unphosphorylated IRF3. Mutation of key interface residues supports the observed dimer as the physiologically activated state of IRF5 and IRF3. Thus phosphorylation likely activates IRF5 and other family members by triggering remarkable conformational rearrangements that switch the C-terminal segment from an autoinihibitory to a dimerization role.

Eg5 is a slow, plus-end-directed microtubule-based motor of the BimC kinesin family that is essential for bipolar spindle formation during eukaryotic cell division. We have analyzed two human Eg5/KSP motors, Eg5-367 and Eg5-437, and both are monomeric based on results from sedimentation velocity and sedimentation equilibrium centrifugation as well as analytical gel filtration. The steady-state parameters were: for Eg5-367: Eukaryotic cell division requires proper assembly and maintenance of the bipolar spindle, an intricate protein complex composed of a dynamic array of microtubules and microtubulebased motor proteins (reviewed in Refs.