Collision-induced dissociation of lys-lys intramolecular crosslinked peptides

The use of chemical crosslinking is an attractive tool that presents many advantages in the application of mass spectrometry to structural biology. The correct assignment of crosslinked peptides, however, is still a challenge because of the lack of detailed fragmentation studies on resultant species. In this work, the fragmentation patterns of intramolecular crosslinked peptides with disuccinimidyl suberate (DSS) has been devised by using a set of versatile, model peptides that resemble species found in crosslinking experiments with proteins. These peptides contain an acetylated N-terminus followed by a random sequence of residues containing two lysine residues separated by an arginine. After the crosslinking reaction, controlled trypsin digestion yields both intra- and intermolecular crosslinked peptides. In the present study we analyzed the fragmentation of matrix-assisted laser desorption/ionization-generated peptides crosslinked with DSS in which both lysines are found in the same peptide. Fragmentation starts in the linear moiety of the peptide, yielding regular b and y ions. Once it reaches the cyclic portion of the molecule, fragmentation was observed to occur either at the following peptide bond or at the peptide crosslinker amide bond. If the peptide crosslinker bond is cleaved, it fragments as a regular modified peptide, in which the DSS backbone remains attached to the first lysine. This fragmentation pattern resembles the fragmentation of modified peptides and may be identified by common automated search engines using DSS as a modification. If, on the other hand, fragmentation happens at the peptide bond itself, rearrangement of the last crosslinked lysine is observed and a product ion containing the crosslinker backbone and lysine (m/z 222) is formed. The detailed identification of fragment ions can help the development of softwares devoted to the MS/MS data analysis of crosslinked peptides.     

The cages, dynamics, and structuring of incipient methane clathrate hydrates

Interest in describing clathrate hydrate formation mechanisms spans multiple fields of science and technical applications. Here, we report findings from multiple molecular dynamics simulations of spontaneous methane clathrate hydrate nucleation and growth from fully demixed and disordered two-phase fluid systems of methane and water. Across a range of thermodynamic conditions and simulation geometries and sizes, a set of seven cage types comprises approximately 95% of all cages formed in the nucleated solids. This set includes the ubiquitous 5(12) cage, the 5(12)6(n) subset (where n ranges from 2-4), and the 4(1)5(10)6(n) subset (where n also ranges from 2-4). Transformations among these cages occur via water pair insertions/removals and rotations, and may elucidate the mechanisms of solid-solid structural rearrangements observed experimentally. Some consistency is observed in the relative abundance of cages among all nucleation trajectories. 5(12) cages are always among the two most abundant cage types in the nucleated solids and are usually the most abundant cage type. In all simulations, the 5(12)6(n) cages outnumber their 4(1)5(10)6(n) counterparts with the same number of water molecules. Within these consistent features, some stochasticity is observed in certain cage ratios and in the long-range ordering of the nucleated solids. Even when comparing simulations performed at the same conditions, some trajectories yield swaths of multiple adjacent sI unit cells and long-range order over 5 nm, while others yield only isolated sI unit cells and little long-range order. The nucleated solids containing long-range order have higher 5(12)6(2)/5(12) and 5(12)6(3)/4(1)5(10)6(2) cage ratios when compared to systems that nucleate with little long-range order. The formation of multiple adjacent unit cells of sI hydrate at high driving forces suggests an alternative or addition to the prevailing hydrate nucleation hypotheses which involve formation through amorphous intermediates.     

Rapid hydrogen hydrate growth from non-stoichiometric tuning mixtures during liquid nitrogen quenching

In this study the rapid growth of sII H(2) hydrate within 20 min of post formation quenching towards liquid nitrogen (LN(2)) temperature is presented. Initially at 72 MPa and 258 K, hydrate samples would cool to the conditions of ~60 MPa and ~90 K after quenching. Although within the stability region for H(2) hydrate, new hydrate growth only occurred under LN(2) quenching of the samples when preformed hydrate "seeds" of THF + H(2) were in the presence of unconverted ice. The characterization of hydrate seeds and the post-quenched samples was performed with confocal Raman spectroscopy. These results suggest that quenching to LN(2) temperature, a common preservation technique for ex situ hydrate analysis, can lead to rapid unintended hydrate growth. Specifically, guest such as H(2) that may otherwise need sufficiently long induction periods to nucleate, may still experience rapid growth through an increased kinetic effect from a preformed hydrate template.     

Orbits of unbounded energy in quasi-periodic perturbations of geodesic flows

We show that certain mechanical systems, including a geodesic flow in any dimension plus a quasi-periodic perturbation by a potential, have orbits of unbounded energy.The assumptions we make in the case of geodesic flows are:

(a)

The metric and the external perturbation are smooth enough.

(b)

The geodesic flow has a hyperbolic periodic orbit such that its stable and unstable manifolds have a tranverse homoclinic intersection.

(c)

The frequency of the external perturbation is Diophantine.

(d)

The external potential satisfies a generic condition depending on the periodic orbit considered in (b).

The assumptions on the metric are C² open and are known to be dense on many manifolds. The assumptions on the potential fail only in infinite codimension spaces of potentials.The proof is based on geometric considerations of invariant manifolds and their intersections. The main tools include the scattering map of normally hyperbolic invariant manifolds, as well as standard perturbation theories (averaging, KAM and Melnikov techniques).We do not need to assume that the metric is Riemannian and we obtain results for Finsler or Lorentz metrics. Indeed, there is a formulation for Hamiltonian systems satisfying scaling hypotheses. We do not need to make assumptions on the global topology of the manifold nor on its dimension.     

Synthesis and preliminary antifungal evaluation of a library of phytosphingolipid analogues

A library of 64 phytosphingolipid analogues resulting from the systematic variation of the C1, C3, C4, and the N-acyl moiety of phytosphingosine (PHS) has been prepared from common scaffolds derived from the chiral pool and Sharpless asymmetric dihydroxylation reactions. Library members have been evaluated as growth inhibitors of the yeast Saccaromyces cerevisiae. In addition, 1-amino-N-pivaloyl PHS analogues were also tested as IPC synthase inhibitors, in comparison with the natural product khafrefungin.