Design and Application of a Data-Independent Precursor and Product Ion Repository

The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.     

Synthesis and characterization of iron complexes with monoanionic and dianionic N,N',N' '-trialkylguanidinate ligands

Trisubstitued N,N',N' '-tri(alkyl)guanidinate anions have been used in the synthesis of a family of Fe(II) and Fe(III) complexes. Complexes FeCl[((i)PrN)(2)C(HN(i)Pr)](2) (1), [Fe[micro-((i)PrN)(2)C(HN(i)Pr)][((i)PrN)(2)C(HN(i)Pr)]](2) (2), and [Fe[mgr;-(CyN)(2)C(HNCy)][(CyN)(2)C(HNCy)]](2) (3) were prepared from the reaction of the appropriate lithium tri(alkyl)guanidinate and FeCl(3) or FeBr(2). The complex [FeBr[micro-(CyN)(2)C(HNCy)]](2) (4), an apparent intermediate in the formation of 3, has also been isolated and characterized. Complexes 1 and 2 react with alkyllithium reagents to yield products that depend on the identity of the reagent as well as the reaction stoichiometry. Reaction of 2 with MeLi (1:2 ratio) produces Li(2)[Fe[micro-((i)PrN)(2)C=N(i)Pr][((i)PrN)(2)C(HN(i)Pr)]](2) (5). Reaction of 1 with an equimolar amount of LiCH(2)SiMe(3) results in reduction to Fe(II) and generation of 2 while reaction with 4 LiCH(2)SiMe(3) proceeds by a combination of reduction, substitution, and deprotonation of guandinate to yield Li(4)(THF)(2)[Fe[((i)PrN)(2)CN(i)Pr](CH(2)SiMe(3))(2)](2) (7). Both complexes 5 and 7 posssess dianionic guanidinate ligands. The reaction of 2 with 1 equiv of LiCH(2)SiMe(3) generated Fe(2)[micro-((i)PrNCN(i)Pr)(2)(N(i)Pr)][((i)PrN)(2)C(HN(i)Pr)](2) (6). Compound 6 has a dianionic biguanidinate ligand derived from the coupling of the two bridging guanidinate ligands of 2.     

Polypeptide-templated synthesis of hexagonal silica platelets

Several studies have demonstrated the use of biomimetic approaches in the synthesis of a variety of inorganic materials. Poly-L-lysine (PLL) promotes the precipitation of silica from a silicic acid solution within minutes. The molecular weight of PLL was found to affect the morphology of the resulting silica precipitate. Larger-molecular weight PLL produced hexagonal silica platelets, whereas spherical silica particles were obtained using low-molecular weight PLL. Here we report on the polypeptide secondary-structure transition that occurs during the silicification reaction. The formation of the hexagonal silica platelets is attributed to the PLL helical chains that are formed in the presence of monosilicic acid and phosphate ions. Hexagonal PLL crystals can also serve as templates in directing the growth of the silica in a manner that generates a largely mesoporous silica phase that is oriented with respect to the protein crystal template.     

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

A series of high-order surface element discretization schemes for variational boundary element methods are introduced. The surface elements are chosen in accord with angular quadrature rules for integration of spherical harmonics. Surface element interactions are modeled by Coulomb integrals between spherical Gaussian functions with exponents chosen to reproduce the exact variational energy and Gauss's law for a point charge in a spherical cavity. The present work allows high-order surface element expansions to be made for variational methods such as the conductorlike screening model for solvation and the variational electrostatic projection method for generalized solvent boundary potentials in molecular simulations.     

A procedure to calculate torsion¶of elliptic curves over ℚ

We present an algorithm which uses the analytic parameterization of elliptic curves to rapidly calculate torsion subgroups, and calculate its running time. This algorithm is much faster than the “traditional” Lutz–Nagell algorithm used by most computer algebra systems to calculate torsion subgroups. Received: 7 August 1997 / Revised version: 28 November 1997     

Single-molecule magnet behavior with a single metal center enhanced through peripheral ligand modifications

Bis(imino)pyridine pincer ligands in conjunction with two isothiocyanate ligands have been used to prepare two mononuclear Co(II) complexes. Both complexes have a distorted square-pyramidal geometry with the Co(II) centers lying above the basal plane. This leads to significant spin-orbit coupling for the d(7) Co(II) ions and consequently to slow relaxation of the magnetization that is characteristic of Single-Molecule Magnet (SMM) behavior.     

Dependence of Self-Assembled Peptide Hydrogel Network Structure on Local Fibril Nanostructure

Physically cross-linked, fibrillar hydrogel networks are formed by the self-assembly of β-hairpin peptide molecules with varying degrees of strand asymmetry. The peptide registry in the self-assembled state can be used as a design element to generate fibrils with twisting, nontwisting, or laminated morphology. The mass density of the networks varies significantly, and can be directly related to the local fibrillar morphology as evidenced by small angle neutron scattering (SANS) and in situ substantiation using cryogenic transmission electron microscopy (cryo-TEM) under identical concentrations and conditions. Similarly, the density of the network is dependent on changes in the peptide concentration. Bulk rheological properties of the hydrogels can be correlated to the fibrillar nanostructure, with the stiffer, laminated fibrils forming networks with a higher G' as compared to the flexible, singular fibrillar networks.     

On Dynamics Related to a Class of Numeration Systems

 In this paper, we investigate the class of numeration systems and we study the associated dynamical systems, called odometers. It is shown that these odometers are measure-theoretically isomorphic to rank one transformations on the unit interval, constructed by a cutting-stacking method. Furthermore, a symbolic coding leads to isomorphic shift systems arising from substitutions. Some skew products of the odometers by cocycles related to the sum of digits are shown to be ergodic.     

A decomposition theorem for frames and the Feichtinger Conjecture

In this paper we study the Feichtinger Conjecture in frame theory, which was recently shown to be equivalent to the 1959 Kadison-Singer Problem in -Algebras. We will show that every bounded Bessel sequence can be decomposed into two subsets each of which is an arbitrarily small perturbation of a sequence with a finite orthogonal decomposition. This construction is then used to answer two open problems concerning the Feichtinger Conjecture: 1. The Feichtinger Conjecture is equivalent to the conjecture that every unit norm Bessel sequence is a finite union of frame sequences. 2. Every unit norm Bessel sequence is a finite union of sets each of which is -independent for -sequences.