StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies

Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.     

On the Generality of Assuming that a Family of Continuous Functions Separates Points

For an algebra ${\mathcal{A}}$ of complex-valued, continuous functions on a compact Hausdorff space (X, τ), it is standard practice to assume that ${\mathcal{A}}$ separates points in the sense that for each distinct pair ${x, y \in X}$ , there exists an ${f \in \mathcal{A}}$ such that ${f(x) \neq f(y)}$ . If ${\mathcal{A}}$ does not separate points, it is known that there exists an algebra ${\widehat{\mathcal{A}}}$ on a compact Hausdorff space ${(\widehat{X}, \widehat{\tau})}$ that does separate points such that the map ${\mathcal{A} \mapsto \widehat{\mathcal{A}}}$ is a uniform norm isometric algebra isomorphism. So it is, to a degree, without loss of generality that we assume ${\mathcal{A}}$ separates points. The construction of ${{\widehat{\mathcal{A}}}}$ and ${(\widehat{X}, \widehat{\tau})}$ does not require that ${\mathcal{A}}$ has any algebraic structure nor that ${(X, \tau)}$ has any properties, other than being a topological space. In this work we develop a framework for determining the degree to which separation of points may be assumed without loss of generality for any family ${\mathcal{A}}$ of bounded, complex-valued, continuous functions on any topological space ${(X, \tau)}$ . We also demonstrate that further structures may be preserved by the mapping ${\mathcal{A} \mapsto \widehat{\mathcal{A}}}$ , such as boundaries of weak peak points, the Lipschitz constant when the functions are Lipschitz on a compact metric space, and the involutive structure of real function algebras on compact Hausdorff spaces.     

Directing stem cell fate by controlling the affinity and density of ligand-receptor interactions at the biomaterials interface

Sticky situation: the differentiation of mesenchymal stem cells can be influenced by the affinity and density of an immobilized ligand for the integrin receptors. Cells adherent to monolayers that present the high-affinity, cyclic-RGD peptide (left) show increased expression of osteogenic markers, while cells on monolayers presenting the lower-affinity, linear-RGD peptide (right) express early markers of myogenesis at a high density and neurogenesis at a low density of the ligand.     

Metrics with nonnegative curvature on {S^2 \times \mathbb{R}^4}

We study nonnegatively curved metrics on S²×\mathbbR⁴{S^2\times\mathbb{R}^4}. First, we prove rigidity theorems for connection metrics; for example, the holonomy group of the normal bundle of the soul must lie in a maximal torus of SO(4). Next, we prove that Wilking’s almost-positively curved metric on S ² × S ³ extends to a nonnegatively curved metric on S²×\mathbbR⁴{S^2\times\mathbb{R}^4} (so that Wilking’s space becomes the distance sphere of radius 1 about the soul). We describe in detail the geometry of this extended metric.     

Ultrahigh-field NMR spectroscopy of quadrupolar transition metals: 55Mn NMR of several solid manganese carbonyls

55Mn NMR spectra acquired at 21.14 T (nu(L)(55Mn) = 223.1 MHz) are presented and demonstrate the advantages of using ultrahigh magnetic fields for characterizing the chemical shift tensors of several manganese carbonyls: eta5-CpMn(CO)3, Mn2(CO)10, and (CO)5MnMPh3 (M = Ge, Sn, Pb). For the compounds investigated, the anisotropies of the manganese chemical shift tensors are less than 250 ppm except for eta5-CpMn(CO)3, which has an anisotropy of 920 ppm. At 21.14 T, one can excite the entire m(I) = 1/2 <--> m(I) = -1/2 central transition of eta5-CpMn(CO)3, which has a breadth of approximately 700 kHz. The breadth arises from second-order quadrupolar broadening due to the 55Mn quadrupolar coupling constant of 64.3 MHz, as well as the anisotropic shielding. Subtle variations in the electric field gradient tensors at the manganese are observed for crystallographically unique sites in two of the solid pentacarbonyls, resulting in measurably different C(Q) values. MQMAS experiments are able to distinguish four magnetically unique Mn sites in (CO)(5)MnPbPh3, each with slightly different values of delta(iso), C(Q), and eta(Q).     

Obstruction to Positive Curvature on Homogeneous Bundles

Examples of almost-positively and quasi-positively curved spaces of the form M = H\((G, h) × F) were discovered recently [J. Differential Geom. 65:273–287, 2003; Invent. Math. 148:117–141, 2002]. Here h is a left-invariant metric on a compact Lie group G, F is a compact Riemannian manifold on which the subgroup acts isometrically on the left, and M is the orbit space of the diagonal left action of H on (G, h) × F with the induced Riemannian submersion metric. We prove that no new examples of strictly positive sectional curvature exist in this class of metrics. This result generalizes the case F = {point} proven by Geroch [Proc. Amer. Math. Soc. 66(2):321–326, 1977].Supported in part by NSF grant DMS–0303326.     

Synthesis and structures of acyclic monoanionic tetradentate aza beta-diketiminate complexes of magnesium, zinc, and cadmium

An acyclic monoanionic tetradentate nitrogen ligand was prepared through the condensation of 2-(4-tolyl)-malondialdehyde and 8-aminoquinoline to give (BDI(QQ))H where (BDI(QQ))H = (8-quinolyl)-NCHC(4-tolyl)CHNH-(8-quinolyl). Metal complexes, (BDI(QQ))MX, were prepared where MX = MgBr 2, ZnCl 3, and CdOAc 4. The spectroscopic and crystallographic properties of compounds 2, 3, and 4 were explored. Structures of complexes 2, 3, 4, and the tridentate ligand, (BDI(Q))OH, 5, are reported.     

Solid-state Ru-99 NMR spectroscopy: a useful tool for characterizing prototypal diamagnetic ruthenium compounds

The feasibility of (99)Ru NMR spectroscopy as a tool to characterize solid compounds is demonstrated. Results of the first solid-state (99)Ru NMR investigation of diamagnetic compounds are presented for Ru(NH(3))(6)Cl(2), K(4)Ru(CN)(6). xH(2)O (x = 0, 3), LaKRu(CN)(6), and Ru(3)(CO)(12). The sensitivity of the ruthenium magnetic shielding tensor to subtle changes in the local structure about the ruthenium nucleus is highlighted by comparing the (99)Ru isotropic chemical shift of Ru(NH(3))(6)Cl(2) in aqueous solutions and in the solid state. The narrow isotropic (99)Ru NMR peak observed for solid Ru(NH(3))(6)Cl(2) indicates that this compound is an ideal secondary reference sample for solid-state (99)Ru NMR studies. The isotropic (99)Ru chemical shift, (99)Ru nuclear quadrupolar coupling constant, C(Q), and quadrupolar asymmetry parameter of K(4)Ru(CN)(6). xH(2)O (x = 0, 3) are shown to be sensitive to x. For Ru(3)(CO)(12), the magnetic shielding tensors of each of the three nonequivalent Ru nuclei have spans of 1300-1400 ppm, and the (99)Ru C(Q) values are also similar, 1.36-1.85 MHz, and are surprisingly small given that (99)Ru has a moderate nuclear quadrupole moment. Information about the relative orientation of the Ru magnetic shielding and electric field gradient tensors has been determined for Ru(3)(CO)(12) from experimental (99)Ru NMR spectra as well as quantum chemical calculations.     

Characterization of porosity in organic and metal-organic macrocycles by hyperpolarized 129Xe NMR spectroscopy

Hyperpolarized (129)Xe NMR spectroscopy is used to establish the solid-state porosity of shape-persistent macrocycles with either an organic or metal-organic framework. These studies show that even upon removal of cocrystallized solvent molecules, the macrocycles maintain a porous or channeled structure. The technique can provide valuable information about systems for which X-ray crystallographic analysis is not feasible. [structure: see text]     

Aligned single‐wall carbon nanotube polymer composites using an electric field

While high shear alignment has been shown to improve the mechanical properties of single‐wall carbon nanotube (SWNT)‐polymer composites, this method does not allow for control over the electrical and dielectric properties of the composite and often results in degradation of these properties. Here, we report a novel method to actively align SWNTs in a polymer matrix, which permits control over the degree of alignment of the SWNTs without the side effects of shear alignment. In this process, SWNTs were aligned via AC field‐induced dipolar interactions among the nanotubes in a liquid matrix followed by immobilization by photopolymerization under continued application of the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy, and the morphology of the aligned nanocomposites was investigated by high‐resolution scanning electron microscopy. The structure of the field induced aligned SWNTs was intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field parameters. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1751–1762, 2006