A hydration study of (1-->4) and (1-->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR

The hydration behavior of two model disaccharides, methyl-alpha-D-maltoside (1) and methyl-alpha-D-isomaltoside (2), has been investigated by a comparative 10 ns molecular dynamics study. The detailed hydration of the two disaccharides was described using three force fields especially developed for modeling of carbohydrates in explicit solvent. To validate the theoretical results the two compounds were synthesized and subjected to 500 MHz NMR spectroscopy, including pulsed field gradient diffusion measurements (1: 4.0. 10(-6) cm(2). s(-1); 2: 4.2. 10(-6) cm(2). s(-1)). In short, the older CHARMM-based force field exhibited a more structured carbohydrate-water interaction leading to better agreement with the diffusional properties of the two compounds, whereas especially the alpha-(1-->6) linkage and the primary hydroxyl groups were inaccurately modeled. In contrast, the new generation of the CHARMM-based force field (CSFF) and the most recent version of the AMBER-based force field (GLYCAM-2000a) exhibited less structured carbohydrate-water interactions with the result that the diffusional properties of the two disaccharides were underestimated, whereas the simulations of the alpha-(1-->6) linkage and the primary hydroxyl groups were significantly improved and in excellent agreement with homo- and heteronuclear coupling constants. The difference between the two classes of force field (more structured and less structured carbohydrate-water interaction) was underlined by calculation of the isotropic hydration as calculated by radial pair distributions. At one extreme, the radial O em leader O pair distribution function yielded a peak density of 2.3 times the bulk density in the first hydration shell when using the older CHARMM force field, whereas the maximum density observed in the GLYCAM force field was calculated to be 1.0, at the other extreme.     

Effects of glycosylation on peptide conformation: a synergistic experimental and computational study

Asparagine-linked glycosylation, the co-translational covalent attachment of carbohydrates to asparagine side chains, has a major effect on the folding, stability, and function of many proteins. The carbohydrate composition in mature glycoproteins is heterogeneous due to modification of the initial oligosaccharide by glycosidases and glycosyltransferases during the glycoprotein passage through the endoplasmic reticulum and Golgi apparatus. Despite the diversity of carbohydrate structures, the core beta-D-(GlcNAc)(2) remains conserved in all N-linked glycoproteins. Previously, results from our laboratory showed that the molecular composition of the core disaccharide has a critical and unique conformational effect on the peptide backbone. Herein, we employ a synergistic experimental and computational approach to study the effect of the stereochemistry of the carbohydrate--peptide linkage on glycopeptide structure. A glycopeptide derived from a hemagglutinin protein fragment was synthesized, with the carbohydrate attached to the peptide with an alpha-linked stereochemistry. Computational and biophysical analyses reveal that the conformations of the peptide and alpha- and beta-linked glycopeptides are uniquely influenced by the attached saccharide. The value of computational approaches for probing the influence of attached saccharides on polypeptide conformation is highlighted.     

Crystal structure,physical and photophysical properties of a platinum(II) complex coordinated to the biphenyl dianion and cyclooctadiene

The complex, Pt(bph)(COD), where bph is the biphenyl dianion and COD is 1,5-cyclooctadiene, crystallizes in the orthorhombic space groupPbca witha=12.178(4) Å,b=9.693(3) Å andc=25.344(9) Å andZ=8. The Pt–C distances to the olefinic carbon atoms that result from the electron donation of the COD ligand are in the range 2.20(3)–2.27(3) Å and the Pt–C distances to the bonded bph ligand are shorter at 2.01(3)–2.03(2) Å. The lowest energy absorption of the complex is at 383 nm (=1.2×10³). The emission spectrum is structured in fluid solution at room temperature with the emission energy maximum at 537 nm, _cm, and =1.93 s. Temperature dependent emission lifetime measurements result in ak _o value of 2.69×10⁴, a preexponential factor of 2.47×10⁶ and a E₁ value of 324 cm^–1.     

Ferrichrome: Surprising stability of a cyclic peptide-FeIII complex revealed by mass spectrometry

Ferrichrome, a fungal siderophore that is also utilized by some bacterial species, was studied with liquid secondary ion mass spectrometry (LSIMS) and matrix-assisted laser desorption ionixation (MALDI) mass spectrometry. A strong ionic signal corresponding to a Fe^III complex was observed with LSIMS in the positive ion mode. Switching the polarity of the mass spectrometer did not necessarily result in reduction of ferric ion, although certain conditions led to appearance of a Fe^II complex signal as well. The results of the structural studies of the metal ion-cyclic peptide complex with collisionally induced dissociation allowed unambiguous identification of the chelation sites. The action of the siderophore on Fe^III was studied by in vitro chelation of ferric ion (from ferric citrate) by the iron-free ferrichrome. Effective chelation of ferric ion was compared to actions of the iron-free ferrichrome on other metal ions. Unlike LSIMS, desorption with MALDI did not form selectively molecular ions of intact ferrichrome: the spectra contained abundant peaks corresponding to the cyclic peptide itself and its nonspecific association with alkali metal ions.     

Inhibition of [FeFe]-hydrogenase by formaldehyde: proposed mechanism and reactivity of FeFe alkyl complexes

The mechanism for inhibition of [FeFe]-hydrogenases by formaldehyde is examined with model complexes. Key findings: (i) CH₂ donated by formaldehyde covalently link Fe and the amine cofactor, blocking the active site and (ii) the resulting Fe-alkyl is a versatile electrophilic alkylating agent. Solutions of Fe₂[(μ-SCH₂)₂NH](CO)₄(PMe₃)₂ (1) react with a mixture of HBF₄ and CH₂O to give three isomers of [Fe₂[(μ-SCH₂)₂NCH₂](CO)₄(PMe₃)₂]⁺ ([2]⁺). X-ray crystallography verified the NCH₂Fe linkage to an octahedral Fe(ii) site. Although [2]⁺ is stereochemically rigid on the NMR timescale, spin-saturation transfer experiments implicate reversible dissociation of the Fe–CH₂ bond, allowing interchange of all three diastereoisomers. Using ¹³CH₂O, the methylenation begins with formation of [Fe₂[(μ-SCH₂)₂N¹³CH₂OH](CO)₄(PMe₃)₂]⁺. Protonation converts this hydroxymethyl derivative to [2]⁺, concomitant with ¹³C-labelling of all three methylene groups. The Fe–CH₂N bond in [2]⁺ is electrophilic: PPh₃, hydroxide, and hydride give, respectively, the phosphonium [Fe₂[(μ-SCH₂)₂NCH₂PPh₃](CO)₄(PMe₃)₂]⁺, 1, and the methylamine Fe₂[(μ-SCH₂)₂NCH₃](CO)₄(PMe₃)₂. The reaction of [Fe₂[(μ-SCH₂)₂NH](CN)₂(CO)₄]²⁻ with CH₂O/HBF₄ gave [Fe₂[(μ-SCH₂)₂NCH₂CN](CN)(CO)₅]⁻ ([4]⁻), the result of reductive elimination from [Fe₂[(μ-SCH₂)₂NCH₂](CN)₂(CO)₄]⁻. The phosphine derivative [Fe₂[(μ-SCH₂)₂NCH₂CN](CN)(CO)₄(PPh₃)]⁻ ([5]⁻) was characterized crystallographically.

The mechanism for inhibition of [FeFe]-hydrogenases by formaldehyde is examined with model complexes.     

Spatiotemporal dynamics of damped propagation in excitable cardiac tissue

Compared to steadily propagating waves (SPW), damped waves (DW), another solution to the nonlinear wave equation, are seldom studied. In cardiac tissue after electrical stimulation in an SPW wake, we observe DW with diminished amplitude and velocity that either gradually decrease as the DW dies, or exhibit a sharp amplitude increase after a delay to become an SPW. The cardiac DW-SPW transition is a key link in understanding defibrillation and stimulation close to the refractory period, and is ideal for a general study of DW dynamics.     

Continuum approach to car-following models

A continuum version of the car-following Bando model is developed using a series expansion of the headway in terms of the density. This continuum model obeys the same stability criterion as its discrete counterpart. To compare both models we show that traveling wave solutions of the Bando model are very similar to those of the continuum model in the limit of small changes of headway. As the change of headway across the wave increases the solutions gradually diverge. Our transformation relating headway to density enables predictions of the global impact and characteristics of any car-following model using the analogous continuum model. In contrast, we show that the conventional continuum models which account for effects of pressure and dispersion predict behavior which is distinct from the global behavior of discrete models.