Single molecule force spectroscopy using polyproteins

In recent years single molecule force spectroscopy has emerged as a powerful new tool to explore the mechanical stability and folding pathways of individual proteins. This technique is used to apply a stretching force between two points of a protein, unfolding the protein to an extended state. By measuring the unfolding and folding trajectories of individual proteins, insight can be gained into the physical mechanisms of protein folding. In this tutorial review we introduce the reader to single molecule force spectroscopy using the atomic force microscope (AFM), and explain the two main modes of operation of the AFM for force spectroscopy: force-extension and force-clamp. We introduce the approach of using polyproteins to obtain a clear mechanical fingerprint for monitoring the response of proteins to an applied mechanical force. In addition, we provide an informative and representative review of recent research on proteins using single molecule force spectroscopy. We focus on areas which have made a significant contribution to the single molecule protein folding field and highlight emerging areas of research which have wider implications for the general scientific community.     

Electronic states of 1,4-bis(phenylethynyl)benzene: A synchrotron radiation linear dichroism investigation

The electronic transitions of 1,4-bis(phenylethynyl)benzene (BPEB) were investigated by UV synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 25,000-58,000 cm⁻¹ (400-170 nm) on molecular samples aligned in stretched polyethylene. The investigation was supported by variable temperature spectroscopy and by quantum chemical calculations in the LCOAO and TD-DFT models. The molecular alignment of BPEB in stretched polyethylene was found to be remarkably efficient, leading to an orientation factor equal to 0.95 for the long molecular axis. The observed band shape depended strongly on the degree of stretching and on temperature. The combined experimental and theoretical evidence leads to the characterization of several previously unobserved transitions and supports the assumption that BPEB adopts a nearly planar conformation in stretched polyethylene.     

Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.     

Structural rearrangements and magic numbers in reactions between pyridine-containing water clusters and ammonia

Molecular cluster ions H(+)(H(2)O)(n), H(+)(pyridine)(H(2)O)(n), H(+)(pyridine)(2)(H(2)O)(n), and H(+)(NH(3))(pyridine)(H(2)O)(n) (n = 16-27) and their reactions with ammonia have been studied experimentally using a quadrupole-time-of-flight mass spectrometer. Abundance spectra, evaporation spectra, and reaction branching ratios display magic numbers for H(+)(NH(3))(pyridine)(H(2)O)(n) and H(+)(NH(3))(pyridine)(2)(H(2)O)(n) at n = 18, 20, and 27. The reactions between H(+)(pyridine)(m)(H(2)O)(n) and ammonia all seem to involve intracluster proton transfer to ammonia, thus giving clusters of high stability as evident from the loss of several water molecules from the reacting cluster. The pattern of the observed magic numbers suggest that H(+)(NH(3))(pyridine)(H(2)O)(n) have structures consisting of a NH(4)(+)(H(2)O)(n) core with the pyridine molecule hydrogen-bonded to the surface of the core. This is consistent with the results of high-level ab initio calculations of small protonated pyridine/ammonia/water clusters.     

Preussianone, a new flavanone-chromone biflavonoid from Garcinia preussii Engl

A new flavanone-chromone biflavonoid, preussianone (1), has been isolated from the leaves of Garcinia preussii, along with four known biflavonoids. The absolute stereostructures were elucidated by chemical, spectroscopic, and chiroptical methods. The biological properties of the new biflavonoid against several bacterial strains were evaluated.     

Inclusion complexes between cyclic siloxanes and cyclodextrins: synthesis and characterization

Molecular inclusion complexes between cyclodextrins and cyclic siloxanes were prepared and characterized via a combination of liquid and solid state NMR, FT-IR, TGA, powder X-ray diffraction, SEM–EDS and elemental analyses. The crystalline complexes adopted the channel-type conformation. Depending from the size of both the cyclic sugar cavity and the silicon guest, various yields (between 0 and 41%) and host–guest molar ratios (between 1:1 and 4:1) were obtained. α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were observed to form crystalline inclusion complexes only with D₃ (cyclic dimethyltrisiloxane) due to steric effects, whereas the larger γ-cyclodextrin (γ-CD) formed inclusion complexes both with D₃, D₄ (cyclic dimethyltetrasiloxane) and D₅ (cyclic dimethylpentasiloxane). This study is believed to be the first step towards the selective removal of cyclic siloxanes impurities from commercial PDMS preparations.     

Aromatic capping surprisingly stabilizes furan moieties in peptides against acidic degradation

We herein describe the synthesis of furan containing peptides for further post-synthetic derivatisation in solution through our recently developed furan-oxidation-labeling technology. Previously, it was reported by others that during acidic cleavage of furan-modified peptides, furan moieties can suffer from degradation. We demonstrate here that this degradation is position dependent and can be fully suppressed through introduction of proximate aromatic residues. Versatile introduction of 2-furylalanine at internal, C-terminal as well as the sensitive N-terminal positions has now been proven possible.