Unbinding Molecular Recognition Force Maps of Localized Single Receptor Molecules by Atomic Force Microscopy

Atomic force microscopy is a technique capable to study biological recognition processes at the single‐molecule level. In this work we operate the AFM in a force‐scan based mode, the jumping mode, where simultaneous topographic and tip–sample adhesion maps are acquired. This approach obtains the unbinding force between a well‐defined receptor molecule and a ligand attached to the AFM tip. The method is applied to the avidin–biotin system. In contrast with previous data, we obtain laterally resolved adhesion maps of avidin–biotin unbinding forces highly correlated with single avidin molecules in the corresponding topographic map. The scanning rate 250 pixel s^?1 (2 min for a 128×128 image) is limited by the hydrodynamic drag force. We are able to build a rupture‐force distribution histogram that corresponds to a single defined molecule. Furthermore, we find that due to the motility of the polymer used as spacer to anchor the ligand to the tip, its direction at rupture does not generally coincide with the normal to the tip–sample, this introduces an appreciable error in the measured force.     

Highly Coherent Spectroscopy of Ultracold Atoms and Molecules in Optical Lattices

Cooling and trapping of neutral atoms using laser techniques has enabled extensive progress in precise, coherent spectroscopy. In particular, trapping ultracold atoms in optical lattices in a tight confinement regime allows us to perform high‐resolution spectroscopy unaffected by atomic motion. We report on the recent developments of optical lattice atomic clocks that have led to optical spectroscopy coherent at the one second timescale. The lattice clock techniques also open a promising pathway toward trapped ultracold molecules and the possible precision measurement opportunities such molecules offer.     

Determination of volatile and non-volatile nickel and vanadium compounds in crude oil using electrothermal atomic absorption spectrometry after oil fractionation into saturates, aromatics, resins and asphaltenes

In recent work, it has been shown that electrothermal atomic absorption spectrometry (ET AAS) can be used to differentiate between volatile and non-volatile nickel and vanadium compounds in crude oil. In the present work, the distribution of these two groups of compounds over different fractions of crude oil was investigated. For this purpose two crude oil samples were separated in two steps: firstly, the asphaltenes were precipitated with n-heptane, and secondly, the maltenes were loaded on a silica column and eluted with solvents of increasing polarity. The four fractions of maltenes eluted from silica column were: F1, saturated and light aromatics; F2, polyaromatics; F3, resins; and F4, polar compounds. Fractions F1 and F2 were further investigated using gas chromatography, and all fractions were characterized by CHN analysis, confirming the increase of aromatics in the fractions 2, 3, 4 and asphaltenes. For the determination of Ni and V by ET AAS, oil-in-water emulsions were prepared. The speciation analysis was carried out measuring without chemical modifier (stable compounds) and with 20 μg palladium (total Ni and V) and the volatile fraction was calculated by difference. The limits of detection were 0.02 μg g⁻¹ and 0.06 μg g⁻¹, for Ni and V, respectively, based on an emulsion of 2 g of oil in 10 mL. The volatile species of Ni and V were associated with fractions F3 and F4, while only thermally stable Ni and V was precipitated in part together with the asphaltenes.     

The use of microemulsion for determination of sodium and potassium in biodiesel by flame atomic absorption spectrometry

A new method for F AAS determination of sodium and potassium in biodiesel using water-in-oil microemulsion as sample preparation is proposed. The method was investigated for biodiesel produced from different sources, as soybean, castor and sunflower oil and animal fat and was also applied for vegetable oils. The optimized condition for microemulsion formation was 57.6% (w/w) of n-pentanol, 20% (w/w) of biodiesel or vegetable oil, 14.4% (w/w) of Triton X-100 and 8% (w/w) of water (aqueous standard of KCl or NaCl in/or diluted HNO₃). The optimized instrumental parameters were: aspiration rate of 2 mL min⁻¹ and the flame composition of 0.131 of C₂H₂/air ratio. For comparison purpose, the determination of sodium and potassium were also carried out according to European norms (EN 14108 and EN 14109, respectively). These norms are applied for determination of sodium and potassium in fatty acid methylic ester samples and consist in the sample dilution using organic solvent and determination by F AAS. The stability of microemulsified aqueous standards and samples was investigated and it was found to be stable for at least 3 days while the organic standard diluted with xylene showed a decrease around of 15% in the analytical signal in 1 h. The limits of detection were 0.1 μg g⁻¹ and 0.06 μg g⁻¹ and the obtained characteristic concentrations were 25 μg L⁻¹ and 28 μg L⁻¹ for sodium and potassium, respectively. The proposed method presented two times better limits of detection and better precision (0.4–1.0%) when compared with the dilution technique (1.5–4.5%). The accuracy of the method was evaluated through recovery tests and comparison with the results obtained by dilution technique. The recoveries ranged from 95% to 115% for biodiesel and 90% to 115% for vegetable oil samples. Comparison between the results obtained for biodiesel by both methods showed no significant differences at the 95% confidence level according to a Student's t-test. This study shows that the proposed method based on microemulsion as sample preparation can be applied as an efficient alternative for sodium and potassium determination in biodiesel samples.     

Bovine serum albumin adsorption onto 316L stainless steel and alumina: a comparative study using depletion,protein radiolabeling,quartz crystal microbalance and atomic force microscopy

The importance of protein adsorption on biomaterials is widely recognized, but the dependence of the adsorption results on the chosen technique has not been much addressed. The objective of this work is to compare adsorption data obtained using several techniques under experimental conditions as closely as possible. Two case studies were investigated: adsorption of bovine serum albumin (BSA) onto 316L stainless steel (SS) and onto alumina. Both materials were used as powders and plates, whose characterization was done through zeta potential (ZP) measurements. The experimental techniques were depletion, protein radiolabeling, quartz crystal microbalance with dissipation (QCM‐D) and atomic force microscopy (AFM). The adsorption isotherms obtained with depletion and QCM‐D techniques, although quantitatively different, present some similarities in shape. Both techniques suggest the existence of a compact end‐on monolayer of protein on the SS surface, while on the alumina surface a less dense side‐on monolayer is formed at lower BSA concentration, followed by a second layer at higher concentration. AFM topographical characterization of the protein films adsorbed on both materials confirms those findings. Further use of AFM in determining the thickness of the film adsorbed on SS yielded values in good agreement with the QDM‐D results. Different surface charges measured on powders and plates do not seem to affect adsorption. Protein radiolabeling seems to be the least reliable technique because it yields, for both materials, adsorption values higher than those from the other techniques. In the case of SS, the difference amounts to one order of magnitude. Copyright © 2008 John Wiley & Sons, Ltd.     

Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory

The polarizable continuum model (PCM) for describing the solvent effect was combined with the fragment molecular orbital-based time-dependent density functional theory (TDDFT). Several levels of the many-body expansion were implemented, and the importance of the many-body contributions to the singlet-excited states was discussed. To calibrate the accuracy, we performed a number of the model calculations using our method and the regular TDDFT in solution, applying them to phenol and polypeptides at the long-range corrected BLYP/6-31G* level. It was found that for systems up to 192 atoms the largest error in the excitation energy was 0.006 eV (vs. the regular TDDFT/PCM of the full system). The solvent shifts and the conformer effects were discussed, and the scaling was found to be nearly linear. Finally, we applied our method to the lowest singlet excitation of the photoactive yellow protein (PYP) in aqueous solution and determined the excitation energy to be in reasonable agreement with experiment. The excitation energy analysis provided the contributions of individual residues, and the main factors as well as their solvent shifts were determined.     

CH/pi hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: an ab initio fragment molecular orbital study

The CH/pi hydrogen bond is a weak molecular force occurring between CH groups (soft acids) and pi-systems (soft bases), and has been recognized to be important in the interaction of proteins with their specific ligands. For instance, it is well known that Src homology-2 protein (SH2) recognizes its specific pTyr peptide in two key regions, pTyr-binding region and specificity-determining region, by the use of attractive molecular forces, including the CH/pi hydrogen bond. We hypothesized that the CH/pi hydrogen bond plays a key role in determining the selectivity of SH2 proteins, and studied this issue by the ab initio fragment molecular orbital (FMO) method. The FMO calculations were carried out, at the HF/6-31G* and MP2/6-31G* level, for SH2 domains of Src, Grb2, P85alpha(N), Syk, and SAP, in complex with corresponding pTyr peptides. CH/pi hydrogen bonds have in fact been found to be important in stabilizing the structure of the complexes. We conclude that the CH/pi hydrogen bond plays an indispensable role in the recognition of SH2 domains with their specific pTyr peptides, thus playing a vital role in the signal transduction system.