Doubly charged protonated a ions derived from small peptides

Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.     

Asymmetric synthesis of phosphonotrifluoroalanine and its derivatives using N-tert-butanesulfinyl imine derived from fluoral

Addition of dialkyl phosphites to (S)-N-tert-butanesulfinyl imine derived from fluoral afforded, under mild conditions, the corresponding N-tert-butanesulfinyl α-aminophosphonates in moderate to high yields and diastereoselectivity. The major diastereomers of N-tert-butanesulfinyl α-aminophosphonates of (S_S,S) configuration were isolated, and after partial or complete deprotection, converted into enantiomerically pure phosphonotrifluoroalanine and its dialkyl esters.     

The extent and effects of peptide sequence scrambling via formation of macrocyclic <Emphasis Type="Italic">b</Emphasis> ions in model proteins

The extent and effects of sequence scrambling in peptide ions during tandem mass spectrometry (MS/MS) have been examined using tryptic peptides from model proteins. Sequencescrambled b ions appeared in about 35% of 43 tryptic peptides examined under MS/MS conditions. In general, these ions had relatively low abundances with averages of 8% and 16%, depending on the instrumentation used. A few tryptic peptides gave abundant scrambled b ions in MS/MS. However, peptide and protein identifications under proteomic conditions with Mascot were not affected, even for these peptides wherein scrambling was prominent. From the 43 tryptic peptides that have been investigated, the conclusion is that sequence scrambling is unlikely to impact negatively on the accuracy of automated peptide and protein identifications in proteomics.     

Bilipschitz maps of boundaries of certain negatively curved homogeneous spaces

In this paper we study certain groups of bilipschitz maps of the boundary minus a point of a negatively curved space of the form \mathbbR \ltimes_M \mathbbRⁿ{\mathbb{R} \ltimes_{M} \mathbb{R}^{n}}, where M is a matrix whose eigenvalues all lie outside of the unit circle. The case where M is diagonal was previously studied by Dymarz (Geom Funct Anal (GAFA) 19:1650–1687, 2009). As an application, combined with work of Eskin-Fisher-Whyte and Peng, we provide the last steps in the proof of quasi-isometric rigidity for a class of lattices in solvable Lie groups.     

Infrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexes

Collision-induced charge disproportionation limits the stability of triply charged metal ion complexes and has thus far prevented successful acquisition of their gas-phase IR spectra. This has curtailed our understanding of the structures of triply charged metal complexes in the gas phase and in biological environments. Herein we report the first gas-phase IR spectra of triply charged La(III) complexes with a derivative of tryptophan (N-acetyl tryptophan methyl ester), and an unusual dissociation product, a lanthanum amidate. These spectra are compared with those predicted using density functional theory. The best structures are those of the lowest energies that differ by details in the π-interaction between La(3+) and the indole rings. Other binding sites on the tryptophan derivative are the carbonyl oxygens. In the lanthanum amidate, La(3+) replaces an H(+) in the amide bond of the tryptophan derivative.     

14N Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy of the Cation Radical P840+, the Primary Electron Donor of the Chlorobium limicola Reaction Center

The electronic structure of the oxidized primary chlorophyll electron donor, P840^+., of the green sulfur bacterium Chlorobium limicola has been investigated using electron spin echo envelope modulation (ESEEM) spectroscopy. This ESEEM investigation of the electron spin density distribution in the radical cation P840^+. in membranes isolated from C. limicola confirms that the electron spin is shared eqully between the two bacteriochlorophyll a molecules. Observation of the small hyperfine couplings to the ring nitrogens by ESEEM gives results that are in agreement with those obtained from ENDOR measurements (S. E. J. Rigby, R. Thapar, M. C. W. Evans and P. Heathcote, FEBS Lett. 350,24–28, 1994) of the large hyperfine couplings to the methyl group protons. These results in combination with the Raman spectroscopy of P840 (U. Feiler, D. Albouy, B. Robert and T. A. Mattioli, Biochemistry 34,11099–11105, 1995) all indicate that the reaction center of green sulfur photosynthetic bacteria is functionally a protein homodimer providing a symmetrical protein environment for the primary electron donor.     

Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

Phase-sensitive nuclear Overhauser enhancement spectroscopy (NOESY) experiments, (3)J couplings and computational molecular modeling (MM2* and MMFF force fields) were employed to examine the conformational properties of verrucarin A in chloroform solutions. The MMFF force field calculations resulted in a family of 12 low-energy structures along with their populations, the latter being determined by the NMR analysis of molecular flexibility in solution(NAMFIS) deconvolution analysis. The concluded model was capable of reproducing successfully the experimental NOESY cross-peak volumes and the proton-coupling constants. Among the 12 conformers, the one which was similar to the structure of verrucarin A in the solid state was the predominant accounting for 75% of the total relative population, although other low-energy conformations contributed to a lesser degree in order to explain the experimental data.     

Large Scale Geometry of Nilpotent-By-Cyclic Groups

We show quasi-isometric rigidity for a class of finitely generated, non-polycyclic nilpotent-by-cyclic groups. Specifically, let Γ₁, Γ₂ be ascending HNN extensions of finitely generated nilpotent groups N ₁ and N ₂, such that Γ₁ is irreducible (see Definition 1.1). If Γ₁ and Γ₂ are quasi-isometric to each other then N ₁ and N ₂ are virtual lattices in a common simply connected nilpotent Lie group [(N)\tilde]{\tilde{N}}. As a consequence, we show the class of irreducible ascending HNN extensions of finitely generated nilpotent groups is quasi-isometrically rigid.