An alternative approach to amyloid fibrils morphology: CdSe/ZnS quantum dots labelled beta-amyloid peptide fragments Abeta (31-35), Abeta (1-40) and Abeta (1-42)

Aβ (31–35) peptide and control peptides as well as full length Aβ (1–40) and Aβ (1–42) peptides were labelled with luminescent CdSe/ZnS quantum dots (QDs) to observe the morphology of amyloid fibers. A comparison was made between QDs and an organic dye, namely Dansyl group, which showed that the QDs present a much better contrast for imaging than the organic dye.     

Structure inducing ionic liquids-enhancement of alpha helicity in the Abeta(1-40) peptide from Alzheimer's disease

We have studied the impact of ionic liquid solvents on the structure of the Abeta(1-40) peptide from Alzheimer's disease and found that ionic liquid solvents were able to induce a conformational change in the structure of the Abeta(1-40) peptide. This conformational change impacts the self-assembly of the peptide into amyloid fibrils.     

Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations

We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Abeta(21-30) peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer's disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants ((3)J(H(N)H(alpha))), chemical-shift values, (13)C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Abeta(21-30). We find robust prediction of the (13)C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Abeta(21-30) peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Abeta(21-30) conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Abeta(21-30) peptide involves a majority population (approximately 60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a beta-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Abeta(1-40) and Abeta(1-42), for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.     

Switching from bonding to nonbonding: temperature-dependent metal coordination in a zinc(II) sulfadiazine complex

The metal coordination in the mononuclear complex diamminebis(sulfadiazine)zinc shows a unique temperature dependence: High-resolution diffraction data prove that the coordination is almost tetrahedral at 100 K, whereas a fifth longer interaction becomes relevant at 200 K. The change in the geometry is fully reversible and is also reflected in the charge density of the compound.     

Conformational control of the Q(A) to Q(B) electron transfer in bacterial reaction centers: evidence for a frozen conformational landscape below -25 degrees C

The competition between the P(+)Q(A)(-) --> PQ(A) charge recombination (P, bacteriochlorophyll pair acting as primary photochemical electron donor) and the electron transfer to the secondary quinone acceptor Q(A)(-)Q(B) --> Q(A)Q(B)(-) (Q(A) and Q(B), primary and secondary electron accepting quinones) was investigated in chromatophores of Rb. capsulatus, varying the temperature down to -65 degrees C. The analysis of the flash-induced pattern for the formation of P(+)Q(A)Q(B)(-) shows that the diminished yield, when lowering the temperature, is not due to a homogeneous slowing of the rate constant k(AB) of the Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron transfer but to a distribution of conformations that modulate the electron transfer rate over more than 3 orders of magnitude. This distribution appears "frozen", as no dynamic redistribution was observed over time ranges > 10 s (below -25 degrees C). The kinetic pattern was analyzed to estimate the shape of the distribution of k(AB), showing a bell-shaped band on the high rate side and a fraction of "blocked" reaction centers (RCs) with very slow k(AB). When the temperature is lowered, the high rate band moves to slower rate regions and the fraction of blocked RCs increases at the expense of the high rate band. The RCs that recombine from the P(+)Q(A)Q(B)(-) state appear temporarily converted to a state with rapid k(AB), indicating that the stabilized state described by Kleinfeld et al. (Biochemistry 1984, 23, 5780-5786) is still accessible at -60 degrees C.     

2-(4-Sulfophenylsulfonyl)ethoxycarbonyl group: a new water-soluble N-protecting group and its application to solid phase peptide synthesis in water

Solid phase peptide synthesis is carried out in organic solvents, creating environmental problems after disposal. To avoid this problem, we aimed to perform solid phase peptide synthesis in water. A new water-soluble N-protecting group, 2-(4-sulfophenylsulfonyl)ethoxycarbonyl (Sps) group, was designed and Sps-amino acids were prepared. To evaluate the utility of this technique, Leu-enkephalin amide was prepared by solid phase synthesis using Sps-amino acids in water.     

STM/STS observation of polyoxoanions on HOPG surfaces: the wheel-shaped [Cu20Cl(OH)24(H2O)12(P8W48O184)]25- and the ball-shaped [{Sn(CH3)2(H2O)}24{Sn(CH3)2}12(A-PW9O34)12]36-

A combination of scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) techniques have been performed on the wheel-shaped [Cu20Cl(OH)24(H2O)12(P8W48O184)]25- and the ball-shaped [{Sn(CH3)2(H2O)}24{Sn(CH3)2}12(A-PW9O34)12]36- deposited on highly oriented pyrolytic graphite surfaces. Small, regular molecule clusters, as well as separated single molecules, were observed. The size of the molecules is in agreement with the data determined by X-ray crystallography. In STS measurements, we found a rather large contrast at the expected location of the Cu metal centers in our molecules, i.e., the location of the individual Cu ions in their organic matrix is directly addressable by STS.     

Novel (E)- and (Z)-3(5)-(2-hydroxyphenyl)-4-styrylpyrazoles from (E)- and (Z)-3-styrylchromones: the unexpected case of (E)-3(5)-(2-hydroxyphenyl)-4-(4-nitrostyryl)pyrazoles

An efficient synthetic method for the preparation of (E)- and (Z)-3(5)-(2-hydroxyphenyl)-4-styrylpyrazoles has been developed. The reaction of (E)- and (Z)-3-styrylchromones with hydrazine hydrate afforded the corresponding (E)- and (Z)-4-styrylpyrazoles, respectively, saved 4′-nitro-derivatives where both (E)- and (Z)-4′-nitro-3-styrylchromones afforded (E)-3(5)-(2-hydroxyphenyl)-4-(4-nitrostyryl)pyrazoles. The reaction mechanism for these transformations was discussed and the stereochemistry of all products was assigned by NMR experiments.     

Channel activity of a viral transmembrane peptide in micro-BLMs: Vpu(1-32) from HIV-1

We report for the first time on pore-suspending lipid bilayers, which we call micro-black lipid membranes (micro-BLMs), based on a highly ordered macroporous silicon array. Micro-BLMs were established by first functionalizing the backside porous silicon surface with gold and then chemisorbing 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol followed by spreading 1,2-diphytanoyl-sn-glycero-3-phosphocholine dissolved in n-decane. Impedance spectroscopy revealed the formation of single lipid bilayers confirmed by a mean specific capacitance of 0.6 +/- 0.2 microF/cm2. Membrane resistances were in the G omega-regime and beyond. The potential of the system for single channel recordings was demonstrated by inserting the transmembrane domain of the HIV-1 accessory peptide Vpu(1-32), which forms helix bundles with characteristic opening states. We elucidated different amilorides as potential drugs to inhibit channel activity of Vpu.     

{(Mo)Mo5O21(H2O)3(SO4)}12(VO)30(H2O)20]36-: a molecular quantum spin icosidodecahedron

Self-assembly of aqueous solutions of molybdate and vanadate under reducing, mildly acidic conditions results in a polyoxomolybdate-based {Mo72V30} cluster compound Na8K16(VO)(H2O)5[K10 subset{(Mo)Mo5O21(H2O)3(SO4)}12(VO)30(H2O)20].150H2O, 1, a quantum spin-based Keplerate structure.     

Relative strength of cation-pi vs salt-bridge interactions: the Gtalpha(340-350) peptide/rhodopsin system

Interactions between cationic and aromatic side chains of amino acid residues, the so-called cation-pi interaction, are thought to contribute to the overall stability of the folded structure of peptides and proteins. The transferred NOE NMR structure of the G(t)alpha(340-350) peptide bound to photoactivated rhodopsin (R*) geometrically suggests a cation-pi interaction stabilizing the structure between the epsilon-amine of Lys341 and the aromatic ring of the C-terminal residue, Phe350. This interaction has been explored by varying substituents on the phenyl ring to alter the electron density of the aromatic ring of Phe350 and observing the impact on binding of the peptide to R*. The results suggest that while a cation-pi interaction geometrically exists in the G(t)alpha(340-350) peptide when bound to R*, its energetic contribution to the stability of the receptor-bound structure is relatively insignificant, as it was not observed experimentally. The presence of an adjacent and competing salt-bridge interaction between the epsilon-amine of Lys341 and the C-terminal carboxylate of Phe350 effectively shields the charge of the ammonium group. Experimental data supporting a significant cation-pi interaction can be regained through a series of Phe350 analogues where the C-terminal carboxyl has been converted to the neutral carboxamide, thus eliminating the shielding salt-bridge. TrNOE NMR experiments confirmed the existence of the cation-pi interaction in the carboxamide analogues. Various literature estimates of the strength of cation-pi interactions, including some that estimate strengths in excess of salt-bridges, are compromised by omission of the relevant anion in the calculations.     

Hydrogen-bond transition from the vibration mode of ordinary water to the (H,Na)I hydration states: Molecular interactions and solution viscosity

With the aid of differential phonon spectrometrics (DPS) and surface stress detection, we show that HI and NaI solvation transforms different fractions of the HO stretching phonons from the mode of ordinary water centred at ∼3200 to the mode of hydration shell at ∼3500 cm⁻¹. Observations suggest that an addition of the H ↔ H anti-hydrogen-bond to the Zundel notion, [H(H₂O)₂]⁺, would be necessary as the HO bond due H₃O⁺ has a 4.0 eV energy, and the H ↔ H fragilization disrupts the solution network and the surface stress. The I⁻ and Na⁺ ions form each a charge centre that aligns, stretches, and polarize the O:HO bond, resulting in shortening the HO bond and its phonon blue shift in the hydration shell or at the solute-solvent interface. The solute capabilities of bond-number-fraction transition follow: f_H = 0, f_Na ∝ C, and f_I ∝ 1 − exp(−C/C₀) toward saturation, with C being the solute molar concentration and C₀ the decay constant. The f_H = 0 evidences the non-polarizability of the H⁺ because of the H ↔ H formation. The linear f_Na(C) suggests the invariance of the Na⁺ hydration shell size because of the fully-screened cationic potential by the H₂O dipoles in the hydration shell but the nonlinear f_I(C) fingerprints the I⁻ ↔ I⁻ interactions at higher concentrations. Concentration trend consistency between Jones–Dole’s viscosity and the f_NaI(C) coefficient may evidence the same polarization origin of the solution viscosity and surface stress.     

The phase transfer mechanism of 12- and 18-molybdophosphate anions (Keggin- and Dawson-type structures) across the water/nitrobenzene interface

The electrolytic transfer of 12- and 18-molybdophosphate anions across the water/nitrobenzene interface has been investigated by cyclic voltammetry (CV) and chronopotentiometry with cyclic linear current-scanning (CLC). The transfer behavior is very complicated due to the coupled chemical reactions occurring in the system. The transfer processes of heteropoly anions with a negative charge of 3 or 4 are determined by a set of rather obscure equilibria of dissociation and disproportionation, etc., and depend on pH as well as on the composition of the heteropoly anions. The stable forms and pH ranges of heteropoly anions can be confirmed directly through their voltammetric behavior. The experimental results show that an electrochemical study at the water/organic phase interface is very useful for monitoring the states of the heteropoly acids or salts in solution.     

Down to the quantum limit at the neutral-to-ionic phase transition of (BEDT-TTF)-(ClMe-TCNQ): symmetry analysis and phase diagram

We report on the neutral-to-ionic (N-I) phase transition in the one-dimensional organic complex (BEDT-TTF)-(ClMeTCNQ). The X-ray studies at room temperature show that the neutral phase of (BEDT-TTF)-(ClMeTCNQ) is already characterized by a polar long-range ordering, at variance with other charge-transfer compounds comprising noncentrosymmetric molecules. From a detailed neutron diffraction study of this complex under high pressure, we present the phase diagram of the N-I transition down to the quantum limit. We discuss the symmetry breaking associated with the transition and the evolution of its first-order character under pressure.     

Probing the kinetic landscape of transient peptide-protein interactions by use of peptide (15)n NMR relaxation dispersion spectroscopy: binding of an antithrombin peptide to human prothrombin

Protein-ligand interactions may lead to the formation of multiple molecular complexes in dynamic exchange, affecting the kinetic and thermodynamic characteristics of the binding equilibrium. We followed the dissociation kinetics of the transient and specific complex of an antithrombotic peptide N-acetyl-Asp(55)-Phe-Glu-Glu-Ile-Pro(60)-Glu-Glu-Tyr-Leu-Gln(65) with human prothrombin by use of (15)N NMR relaxation dispersion spectroscopy of the peptide. Every one of the five (15)N-labeled adjacent residues of the peptide exhibited apparently different kinetic exchange and relaxation behaviors, which were especially evident at different concentrations of prothrombin. Binding-induced (15)N relaxation dispersion of residues Phe(56), Glu(57), Glu(58), and Ile(59) can be fitted phenomenologically to a two-site on-and-off exchange mechanism with physically feasible relaxation and kinetic parameters obtained for residues Phe(56), Glu(58), and Ile(59), independent of the prothrombin concentration. The apparent kinetic parameters of Glu(57) show some dependence on the concentration of prothrombin and the extracted transverse relaxation rate for Glu(57) in the bound state was severalfold higher than that expected for a protein-peptide complex with a size of approximately 72 kDa. In addition, the equilibrium population of the bound peptide obtained for Glu(57) was inconsistent with those for Phe(56), Glu(58), and Ile(59) and with the prothrombin/peptide ratios used in the experiments. These discrepancies can be explained by the presence of two conformations for the peptide-protein complex exchanging at a rate of approximately 100 s(-)(1). In all, our study shows that fast dissociation of protein-peptide complexes can be studied quantitatively using peptide (15)N NMR relaxation dispersion measurements without a precise knowledge of the peptide and protein concentrations. In addition, protein titration was found to improve the accuracy of quantitative analysis and may make it possible to determine the rate of conformational changes within the protein-peptide complex.     

A cassette ligation strategy with thioether replacement of three Gly-Gly peptide bonds: total chemical synthesis of the 101 residue protein early pregnancy factor [psi(CH(2)S)28-29,56-57,76-77

The 101 residue protein "early pregnancy factor" (EPF), also known as human chaperonin 10, was synthesized from four functionalized, but unprotected, peptide segments by a sequential thioether ligation strategy. The approach exploits the differential reactivity of a peptide-NHCH(2)CH(2)SH thiolate with XCH(2)CO-peptides, where X = Cl or I/Br. Initial model studies with short functionalized (but unprotected) peptides showed a significantly faster reaction of a peptide-NHCH(2)CH(2)SH thiolate with a BrCH(2)CO-peptide than with a ClCH(2)CO-peptide, where thiolate displacement of the halide leads to chemoselective formation of a thioether surrogate for the Gly-Gly peptide bond. This rate difference was used as the basis of a novel sequential ligation approach to the synthesis of large polypeptide chains. Thus, ligation of a model bifunctional N(alpha)-chloroacetyl, C-terminal thiolated peptide with a second N(alpha)-bromoacetyl peptide demonstrated chemoselective bromide displacement by the thiol group. Further investigations showed that the relatively unreactive N(alpha)-chloroacetyl peptides could be "activated" by halide exchange using saturated KI solutions to yield the highly reactive N(alpha)-iodoacetyl peptides. These findings were used to formulate a sequential thioether ligation strategy for the synthesis of EPF, a 101 amino acid protein containing three Gly-Gly sites approximately equidistantly spaced within the peptide chain. Four peptide segments or "cassettes" comprising the EPF protein sequence (BrAc-[EPF 78-101] 12, ClAc-[EPF 58-75]-[NHCH(2)CH(2)SH] 13, ClAc-[EPF 30-55]-[NHCH(2)CH(2)SH] 14, and Ac-[EPF 1-27]-[NHCH(2)CH(2)SH] 15) of EPF were synthesized in high yield and purity using Boc SPPS chemistry. In the stepwise sequential ligation strategy, reaction of peptides 12 and 13 was followed by conversion of the N-terminal chloroacetyl functional group to an iodoacetyl, thus activating the product peptide for further ligation with peptide 14. The process of ligation followed by iodoacetyl activation was repeated to yield an analogue of EPF (EPF psi(CH(2)S)(28)(-)(29,56)(-)(57,76)(-)(77)) 19 in 19% overall yield.     

"Squaring the clusters": a Mn(III)4Ni(II)4 molecular square from nickel(II)-induced structural transformation of a Mn(II/III/IV)12 cage

A Mn(III)(4)Ni(II)(4) molecular square exhibiting slow magnetization relaxation has been prepared from the reaction of a Mn(II)(4)Mn(III)(6)Mn(IV)(2) cluster and a simple Ni(II) source.     

Solid-phase peptide synthesis of analogues of the N-terminus A-ring fragment of the lantibiotic nisin: Replacements for the dehydroalanine (Dha) residue at position 5 and the first incorporation of a thioamide residue

A number of A-ring analogues of the lantibiotic nisin, containing replacements for the Dha residue at position 5, have been successfully prepared by solid-phase peptide synthesis. The Dha replacements include glycine, alanine, phenylalanine, serine and 1-aminocyclopropyl carboxylic acid (ACCa). The incorporation of a thioamide-isoleucine residue at position 4 is also described and represents the first reported preparation of a lantibiotic ring fragment containing a thioamide link.     

Solid-phase peptide synthesis in water. Part 3: A water-soluble N-protecting group, 2-[phenyl(methyl)sulfonio]ethoxycarbonyl tetrafluoroborate, and its application to solid phase peptide synthesis in water

Chemical synthesis of peptides has been performed in various organic solvents, but the safe disposal of organic solvents is now an important environmental issue. Our aim is to be able to perform solid-phase peptide synthesis in water. For this, we have designed a new water-soluble N-protecting group, 2-[phenyl(methyl)sulfonio]ethoxycarbonyl (Pms), and have studied its introduction onto amino acids. Pms-amino acids were prepared by treating 2-(phenylthio)ethoxycarbonyl amino acids with methyl iodide in the presence of silver tetrafluoroborate. Because sulfur-containing amino acids, such as Met and Cys, were modified by the reaction, we designed a new reagent, 2-[phenyl(methyl)sulfonio]ethyl-4-nitrophenyl carbonate, to introduce the Pms group on amino acids. This reagent is a stable crystalline material and its introduction onto amino acids (including sulfur-containing amino acids) was successful. The solid-phase synthesis of Leu- and Met-enkephalin amides using Pms-protected amino acids was successfully achieved in water.