Shedding light on biomolecule conformational dynamics using fluorescence measurements of trapped ions

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.     

A dialectical framework for problem structuring and information technology

This paper proposes that problem structuring is characterized by dialectical processes, and that different problem situations call for differing emphasis on the organizing versus disorganizing potential of information technologies. The term ‘dialectical’ emphasizes the conflicting forces of structuring and unstructuring in processes of problem solving. A case study of an enterprise software conversion project examines four processes: structuring, unstructuring, groping, and adjusting. Applying the dialectic perspective to the classic Gorry and Scott-Morton framework yields propositions as to which of these four processes should be emphasized by information systems addressing different types of problems. Implications for the design of decision support systems and for future research are discussed.     

A method for automatic identification of water and fat images from a symmetrically sampled dual-echo Dixon technique

Sampling water and fat signals symmetrically (i.e., at 0° and 180° relative phase angles) in a dual-echo Dixon technique offers high intrinsic tolerance to phase fluctuations in postprocessing and maximum signal-to-noise performance for the separated water and fat images. However, identification of which image is water and which image is fat after their separation is not possible based on the phase information alone. In this work, we proposed a semiempirical automatic image identification method that is based on the intrinsic asymmetry between the water and fat chemical shift spectra. Specifically, the approximately bimodal feature of the fat spectra and the observation that most in vivo tissues are either predominantly water or predominantly fat are used to construct a spectrum-based algorithm. Additional refinement is accomplished by considering the spatial distribution of the tissues that may have a coexistence of water and fat. The final improved algorithm was tested on a total of 131 three-dimensional patient datasets collected from different scanners and found to yield correct water and fat identification in all datasets.     

Stages in tropoelastin coalescence during synthetic elastin hydrogel formation

Synthetic human tropoelastin was chemically cross-linked to form elastic hydrogel-like structures in vitro. Discrete stages were identified during elastic hydrogel formation by cross-linking tropoelastin with bis(sulfosuccinimidyl) suberate at a range of protein concentrations during this process. In the early stages of this process, particles with the same dimensions as tropoelastin were seen. As hydrogel formation progressed, monomer width fibres were also observed. Overall, four distinct stages were identified: (1) tropoelastin monomers form discrete particles in the order of 200 nm diameter, (2) these particles merge to form larger spheres, (3) spheres coalesce into open linked networks, (4) coalesced spheres consolidate to form a porous structure to give synthetic elastin hydrogels.     

Hamel’s Formalism for Classical Field Theories

This paper introduces Hamel’s formalism for classical field theories with the goal of analyzing the dynamics of continuum mechanical systems with velocity constraints. The developed formalism is utilized to prove the existence and uniqueness of motions of an infinite-dimensional generalization of the Chaplygin sleigh, a canonical example of nonholonomic dynamics. The formalism is very flexible and, for mechanical field theories, includes the Eulerian and Lagrangian representations of continuum mechanics as special cases. It also provides a useful approach to analyzing symmetry reduction.

     

Fixed point property for Banach algebras associated to locally compact groups

In this paper we investigate when various Banach algebras associated to a locally compact group G have the weak or weak^∗ fixed point property for left reversible semigroups. We proved, for example, that if G is a separable locally compact group with a compact neighborhood of the identity invariant under inner automorphisms, then the Fourier-Stieltjes algebra of G has the weak^∗ fixed point property for left reversible semigroups if and only if G is compact. This generalizes a classical result of T.C. Lim for the case when G is the circle group T.     

Simple ℤ<Subscript>2</Subscript>-actions twisted by aperiodic automorphisms

We construct a simple transformation whose centralizer is isomorphic to (?)² ? _A ?, where A is an aperiodic automorphism of ?². As a corollary we obtain an example of a ?²-action \({({T_g})_{g \in {Z^2}}}\) with minimal self-joinings which is conjugate to the (twisted by A) action \({({T_{Ag}})_{g \in {Z^2}}}\). This answers a question of E. Glasner.     

Categorical geometric skew Howe duality

We categorify the R-matrix isomorphism between tensor products of minuscule representations of U_q(\mathfraksl_n)U_{q}({\mathfrak{sl}}_{n}) by constructing an equivalence between the derived categories of coherent sheaves on the corresponding convolution products in the affine Grassmannian. The main step in the construction is a categorification of representations of U_q(\mathfraksl₂)U_{q}({\mathfrak{sl}}_{2}) which are related to representations of U_q(\mathfraksl_n)U_{q}({\mathfrak{sl}}_{n}) by quantum skew Howe duality. The resulting equivalence is part of the program of algebro-geometric categorification of Reshitikhin-Turaev tangle invariants developed by the first two authors.