Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.     

Desynchronization by phase slip patterns in networks of pulse-coupled oscillators with delays

Coupling delays may cause drastic changes in the dynamics of oscillatory networks. In the present paper we investigate how coupling delays alter synchronization processes in networks of all-to-all coupled pulse oscillators. We derive an analytic criterion for the stability of synchrony and study the synchronization areas in the space of the delay and coupling strength. Specific attention is paid to the scenario of destabilization on the borders of the synchronization area. We show that in bifurcation points the system possesses homoclinic loops, which give rise to complex long- or quasi-periodic solutions. These newly born solutions are characterized by a synchronous group, from which an oscillator periodically escapes, laps one period, and rejoins. We call such a dynamical regime “phase slip patterns”.     

Formation and manipulation of discrete supramolecular azobenzene assemblies

Azobenzene derivatives were deposited onto a Au(111) surface and studied by scanning tunneling microscopy. The symmetry of the parent azobenzene was broken by introducing tert-butyl groups which are known to decouple the molecular core from the substrate, on the one end, and carboxylic acid groups which direct and stabilize the supramolecular assembly structure on the surface by intermolecular hydrogen bonding, on the other end. As a consequence of the interacting COOH groups, the molecules assemble on the surface either in extended, polymeric chains and/or in discrete, hexameric rosettes. The high stability of the rosette structure is proven experimentally by controlled lateral displacement on the surface without breaking the non-covalent interactions. Although switching attempts were not successful, the approach herein should facilitate the construction of well-defined multi-switch arrays. Electronic Supplementary Material  The online version of this article () contains supplementary material, which is available to authorized users.     

Multiphase Jet Flow in Abrasive Water Jet Cutting

A numerical model for ultra-high velocity abrasive water jets (AWJ) is developed and jet dynamic characteristics are calculated under steady-state, turbulent, compressible, multi-phase flow conditions. The model is tested by comparison with analytical solutions for related theoretical problems, generally with very good agreement. Simulations of more realistic flows produce the expected values and behavior. (© 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Stability of compact upwind‐biased finite‐difference schemes forfeedback‐coupled advection equations

A fifth‐order compact upwind‐biased finite‐difference scheme has been developed which is asymptotically stable when applied to linear 2 × 2 systems. This scheme was optimised with respect to wave propagation through the boundaries. In order to achieve asymptotic stability for such systems a sufficient stability condition, based on the Nyquist criterion of linear system theory, was included in the optimisation as additional constraint. The evaluation of the stability condition was done numerically. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Diophantine approximation and parametric geometry of numbers

Dirichlet’s Theorem on simultaneous approximation involves a parameter Q. It can be derived from Minkowski’s geometry of numbers involving a symmetric convex body depending on Q. Therefore it is natural to study parametric Geometry of Numbers. In turn, this will shed new light on diophantine approximation.