Directing the secondary structure of polypeptides at will: from helices to amyloids and back again?

An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation.     

EARLY BIOCHEMICAL RESPONSES TO PHOTODYNAMIC THERAPY MONITORED BY NMR SPECTROSCOPY

Abstract Studies directed at determining the biochemical events that lead to tumor cytotoxicity following photodynamic therapy, a promising new approach for treatment of neoplasia, have demonstrated that exposure of R3230AC mammary tumors to hematoporphyrin derivative or Photofrin II plus visible light caused marked impairment of mitochondrial enzymes functioning in oxidative phosphorylation and electron transport. ³¹P-NMR spectroscopy has now demonstrated that a rapid and striking decrease in NTP (ATP) levels, concomitant with a marked increase in P_;, occurs in tumors shortly after photodynamic therapy. These effects appear to be fluence related. Possible changes in tumor vascularity, as detected by ²H-NMR measurements of the uptake of D₂0, were not observed under the conditions studied. Taken together with our earlier results, we conclude that the reduction in tumor ATP levels in situ , probably via inhibition of mitochondrial function, is a direct and early response of neoplastic tissue to porphyrin-induced photosensitization.     

Membrane binding and structure of de novo designed alpha-helical cationic coiled-coil-forming peptides.

We introduce a de novo designed peptide model system that enables the systematic study of 1) the role of a membrane environment in coiled-coil peptide folding, 2) the impact of different domains of an alpha-helical coiled-coil heptad repeat on the interaction with membranes, and 3) the dynamics of coiled-coil peptide-membrane interactions depending on environmental conditions. Starting from an ideal alpha-helical coiled-coil peptide sequence, several positively charged analogues were designed that exhibit a high propensity toward negatively charged lipid membranes. Furthermore, these peptides differ in their ability to form a stable alpha-helical coiled-coil structure. The influence of a membrane environment on peptide folding is studied. All positively charged peptides show strong interactions with negatively charged membranes. This interaction induces an alpha-helical structure of the former random-coil peptides, as revealed by circular dichroism measurements. Furthermore, vesicle aggregation is induced by a coiled-coil interaction of vesicle-bound peptides. Dynamic light scattering experiments show that the strength of vesicle aggregation increases with the peptide's intrinsic ability to form a stable alpha-helical coiled coil. Thus, the peptide variant equipped with the strongest inter- and intra-helical coiled-coil interactions shows the strongest effect on vesicle aggregation. The secondary structure of this peptide in the membrane-bound state was studied as well as its effect on the phospholipids. Peptide conformation within the peptide-lipid aggregates was analyzed by (13)C cross-polarization magic-angle spinning NMR experiments. A uniformly (13)C- and (15)N-labeled Leu residue was introduced at position 12 of the peptide chain. The (13)C chemical shift and torsion angle measurements support the finding of an alpha-helical structure of the peptide in its membrane-bound state. Neither membrane leakage nor fusion was observed upon peptide binding, which is unusual for amphiphatic peptide structures. Our results lay the foundation for a systematic study of the influence of the alpha-helical coiled-coil folding motif in membrane-active events on a molecular level.     

Measure Density and Extension of Besov and Triebel–Lizorkin Functions

We show that a domain is an extension domain for a Haj?asz–Besov or for a Haj?asz–Triebel–Lizorkin space if and only if it satisfies a measure density condition. We use a modification of the Whitney extension where integral averages are replaced by median values, which allows us to handle also the case \(0<p<1\). The necessity of the measure density condition is derived from embedding theorems; in the case of Haj?asz–Besov spaces we apply an optimal Lorentz-type Sobolev embedding theorem which we prove using a new interpolation result. This interpolation theorem says that Haj?asz–Besov spaces are intermediate spaces between \(L^p\) and Haj?asz–Sobolev spaces. Our results are proved in the setting of a metric measure space, but most of them are new even in the Euclidean setting, for instance, we obtain a characterization of extension domains for classical Besov spaces \(B^s_{p,q}\), \(0<s<1\), \(0<p<\infty \), \(0<q\le \infty \), defined via the \(L^p\)-modulus of smoothness of a function.     

Chemotaxis in microfluidic devices--a study of flow effects

The use of microfluidic devices has become increasingly popular in the study of chemotaxis due to the exceptional control of flow properties and concentration profiles on the length scale of individual cells. In these applications, it is often neglected that cells, attached to the inner surfaces of the microfluidic chamber, are three-dimensional objects that perturb and distort the flow field in their vicinity. Depending on the interplay of flow speed and geometry with the diffusive time scale of the chemoattractant in the flow, the concentration distribution across the cell membrane may differ strongly from the optimal gradient in a perfectly smooth channel. We analyze the underlying physics in a two-dimensional approximation and perform systematic numerical finite element simulations to characterize the three-dimensional case and to identify optimal flow conditions.     

Fast and Tunable Phosphorescence from Organic Ionic Crystals

Crystalline diphosphonium iodides [MeR₂P-spacer-R₂Me]I with phenylene ( 1 , 2 ), naphthalene ( 3 , 4 ), biphenyl ( 5 ) and anthracene ( 6 ) as aromatic spacers, are photoemissive under ambient conditions. The emission colors (λ_em values from 550 to 880 nm) and intensities (Φ_em reaching 0.75) are defined by the composition and substitution geometry of the central conjugated chromophore motif, and the anion-π interactions. Time-resolved and variable-temperature luminescence studies suggest phosphorescence for all the titled compounds, which demonstrate observed lifetimes of 0.46–92.23 μs at 297 K. Radiative rate constants k_r as high as 2.8×10⁵ s⁻¹ deduced for salts 1 – 3 were assigned to strong spin-orbit coupling enhanced by an external heavy atom effect arising from the anion-π charge-transfer character of the triplet excited state. These rates of anomalously fast metal-free phosphorescence are comparable to those of transition metal complexes and organic luminophores that utilize triplet excitons via a thermally activated delayed fluorescence mechanism, making such ionic luminophores a new paradigm for the design of photofunctional and responsive molecular materials.     

Implementation of a cohesive zone model for crack closure analysis of rotors

The presence of a crack in a rotor introduces a local flexibility which affects its dynamic response. Moreover, the crack may open and close during the vibration period. The crack status is a function of time and also depends on the rotational speed and the vibration amplitude of the rotor. This nonlinear case is still a challenging research topic especially in the field of closing crack in the rotating shaft. A cohesive zone model is developed in order to analyze the stiffness of a crack in a rotating shaft. The proposed expression will be compared to three different crack models, namely, a breathing crack model, a switching crack model and an open crack model. Moreover, a cohesive law to predict and to analyse the stress at the crack tip is presented. The numerical model is implemented using a finite element formulation. (© 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine N‐Oxide Complexes

A study of the strong N?X???^?O?N⁺ (X=I, Br) halogen bonding interactions reports 2×27 donor×acceptor complexes of N‐halosaccharins and pyridine N‐oxides (PyNO). DFT calculations were used to investigate the X???O halogen bond (XB) interaction energies in 54 complexes. A simplified computationally fast electrostatic model was developed for predicting the X???O XBs. The XB interaction energies vary from ?47.5 to ?120.3 kJ mol^?1; the strongest N?I???^?O?N⁺ XBs approaching those of 3‐center‐4‐electron [N?I?N]⁺ halogen‐bonded systems (ca. 160 kJ mol^?1). ¹H NMR association constants (K_XB) determined in CDCl₃ and [D₆]acetone vary from 2.0×10⁰ to >10⁸ m ^?1 and correlate well with the calculated donor×acceptor complexation enthalpies found between ?38.4 and ?77.5 kJ mol^?1. In X‐ray crystal structures, the N‐iodosaccharin‐PyNO complexes manifest short interaction ratios (R_XB) between 0.65–0.67 for the N?I???^?O?N⁺ halogen bond.     

Modulation of Metallophilic and π–π Interactions in Platinum Cyclometalated Luminophores with Halogen Bonding

Luminescent cyclometalated complexes [M(C^N^N)CN] (M=Pt, Pd; HC^N^N=pyridinyl- (M=Pt 1 , Pd 5 ), benzyltriazolyl- (M=Pt 2 ), indazolyl- (M=Pt 3 , Pd 6 ), pyrazolyl-phenylpyridine (M=Pt 4 )) decorated with cyanide ligand, have been explored as nucleophilic building blocks for the construction of halogen-bonded (XB) adducts using IC₆F₅ as an XB donor. The negative electrostatic potential of the CN group afforded CN⋅⋅⋅I noncovalent interactions for platinum complexes 1 – 3 ; the energies of XB contacts are comparable to those of metallophilic bonding according to QTAIM analysis. Embedding the chromophore units into XB adducts 1 – 3 ⋅⋅⋅IC₆F₅ has little effect on the charge distribution, but strongly affects Pt⋅⋅⋅Pt bonding and π-stacking, which lead to excited states of MMLCT (metal–metal-to-ligand charge transfer) origin. The energies of these states and the photoemissive properties of the crystalline materials are primarily determined by the degree of aggregation of the luminophores via metal–metal interactions. The adduct formation depends on the nature of the metal and the structure of the metalated ligand, the variation of which can yield dynamic XB-supported systems, exemplified by thermally regulated transition 3 ↔ 3 ⋅⋅⋅IC₆F₅.