Genome-based proteomics

Protein-protein interactions play crucial roles in various biological pathways and functions. Therefore, the characterization of protein levels and also the network of interactions within an organism would contribute considerably to the understanding of life. The availability of the human genome sequence has created a range of new possibilities for biomedical research. A crucial challenge is to utilize the genetic information for better understanding of protein distribution and function in normal as well as in pathological biological processes. In this review, we have focused on different platforms used for systematic genome-based proteome analyses. These technologies are in many ways complementary and should be seen as various ways to elucidate different functions of the proteome.     

Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides

Ultraviolet photoelectron spectroscopy in an ion beam was used to investigate the electronic properties of isolated DNA oligonucleotides [dA(5)-4H](4-) and [dT(5)-4H](4-), carrying four excess negative charges. We find the fourth adiabatic electron affinity to be slightly negative for [dA(5)-4H](4-), while it is positive for [dT(5)-4H](4-). This implies a significant influence of the base composition on energetics, which is in turn relevant for analytic applications and also for charge transport properties.     

Two types of intramolecular addition of an Al-N multiple-bonded monomer LAlNAr' arising from the reaction of LAl with N3Ar' (L = HC[(CMe)(NAr)]2, Ar' = 2,6-Ar2C6H3, Ar = 2,6-iPr2C6H3)

The reaction of beta-diketiminated aluminum(I) monomer LAl with a large bulky azide N3Ar' (L = HC(CMeNAr)2, Ar' = 2,6-Ar2C6H3, Ar = 2,6-iPr2C6H3) in the temperature range from -78 degrees C to room temperature affords two different isomers 2 and 3, which have been characterized by spectroscopic and X-ray structural analyses, as well as elemental analysis. The variable-temperature 1H NMR kinetic studies of this reaction indicate the existence of the monomer LAlNAr' (1) at low temperature and the thermal stability of the compounds increases in the order of 1 < 2 < 3.     

Structure Elucidation of the Diagnostic Product Ion at <Emphasis Type="Italic">m/z</Emphasis> 97 Derived from Androst-4-en-3-One-Based Steroids by ESI-CID and IRMPD Spectroscopy

Structure elucidation of steroids by mass spectrometry has been of great importance to various analytical arenas and numerous studies were conducted to provide evidence for the composition and origin of (tandem) mass spectrometry-derived product ions used to characterize and identify steroidal substances. The common product ion at m/z 97 generated from androst-4-ene-3-one analogs has been subject of various studies, including stable isotope-labeling and (high resolution/high accuracy) tandem mass spectrometry, but its gas-phase structure has never been confirmed. Using high resolution/high accuracy mass spectrometry and low resolution tandem mass spectrometry, density functional theory (DFT) calculation, and infrared multiple photon dissociation (IRMPD) spectroscopy employing a free electron laser, the structure of m/z 97 derived from testosterone was assigned to protonated 3-methyl-2-cyclopenten-1-one. This ion was identified in a set of six cyclic C₆H₉O⁺ isomers as computed at the B3LYP/6-311++G(2d,2p) level of theory (protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one and 2-cyclohexen-1-one). Product ions of m/z 97 obtained from MS² and MS³ experiments of protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one, 2-cyclohexen-1-one, and testosterone corroborated the suggested gas-phase ion structure, which was eventually substantiated by IRMPD spectroscopy yielding a spectrum that convincingly matched the predicted counterpart. Finally, the dissociation pathway of the protonated molecule of testosterone to m/z 97 was revisited and an alternative pathway was suggested that considers the exclusion of C-10 along with the inclusion of C-5, which was experimentally demonstrated with stable isotope labeling.     

Polychloride monoanions from [Cl3]- to [Cl9]- : a Raman spectroscopic and quantum chemical investigation

Polychloride monoanions stabilized by quaternary ammonium salts are investigated using Raman spectroscopy and state-of-the-art quantum-chemical calculations. A regular V-shaped pentachloride is characterized for the [N(Me)(4)][Cl(5)] salt, whereas a hockey-stick-like structure is tentatively assigned for [N(Et)(4)][Cl(2)???Cl(3)(-)]. Increasing the size of the cation to the quaternary ammonium salts [NPr(4)](+) and [NBu(4)](+) leads to the formation of the [Cl(3)](-) anion. The latter is found to be a pale yellow liquid at about 40 °C, whereas all the other compounds exist as powders. Further to these observations, the novel [Cl(9)](-) anion is characterized by low-temperature Raman spectroscopy in conjunction with quantum-chemical calculations.     

Self-assembly of class II hydrophobins on polar surfaces

Hydrophobins are structural proteins produced by filamentous fungi that are amphiphilic and function through self-assembling into structures such as membranes. They have diverse roles in the growth and development of fungi, for example in adhesion to substrates, for reducing surface tension to allow aerial growth, in forming protective coatings on spores and other structures. Hydrophobin membranes at the air-water interface and on hydrophobic solids are well studied, but understanding how hydrophobins can bind to a polar surface to make it more hydrophobic has remained unresolved. Here we have studied different class II hydrophobins for their ability to bind to polar surfaces that were immersed in buffer solution. We show here that the binding under some conditions results in a significant increase of water contact angle (WCA) on some surfaces. The highest contact angles were obtained on cationic surfaces where the hydrophobin HFBI has an average WCA of 62.6° at pH 9.0, HFBII an average of 69.0° at pH 8.0, and HFBIII had an average WCA of 61.9° at pH 8.0. The binding of the hydrophobins to the positively charged surface was shown to depend on both pH and ionic strength. The results are significant for understanding the mechanism for formation of structures such as the surface of mycelia or fungal spore coatings as well as for possible technical applications.     

Bio serves nano: biological light-harvesting complex as energy donor for semiconductor quantum dots

Light-harvesting complex (LHCII) of the photosynthetic apparatus in plants is attached to type-II core-shell CdTe/CdSe/ZnS nanocrystals (quantum dots, QD) exhibiting an absorption band at 710 nm and carrying a dihydrolipoic acid coating for water solubility. LHCII stays functional upon binding to the QD surface and enhances the light utilization of the QDs significantly, similar to its light-harvesting function in photosynthesis. Electronic excitation energy transfer of about 50% efficiency is shown by donor (LHCII) fluorescence quenching as well as sensitized acceptor (QD) emission and corroborated by time-resolved fluorescence measurements. The energy transfer efficiency is commensurable with the expected efficiency calculated according to F?rster theory on the basis of the estimated donor-acceptor separation. Light harvesting is particularly efficient in the red spectral domain where QD absorption is relatively low. Excitation over the entire visible spectrum is further improved by complementing the biological pigments in LHCII with a dye attached to the apoprotein; the dye has been chosen to absorb in the "green gap" of the LHCII absorption spectrum and transfers its excitation energy ultimately to QD. This is the first report of a biological light-harvesting complex serving an inorganic semiconductor nanocrystal. Due to the charge separation between the core and the shell in type-II QDs the presented LHCII-QD hybrid complexes are potentially interesting for sensitized charge-transfer and photovoltaic applications.     

Synthesis of silver nanoparticle necklaces without explicit addition of reducing or templating agents

Here we report that silver nanoparticle necklaces can be readily formed by treatment of colloidal silica with ammoniacal silver complex solution followed by washing, deposition and ageing. We investigate the morphology of the produced materials and elucidate the key variables that influence this promising new approach to one-dimensional nanostructuring.     

Magnetically activated micromixers for separation membranes

Presented here is a radically novel approach to reduce concentration polarization and, potentially, also fouling by colloids present in aqueous feeds: magnetically responsive micromixing membranes. Hydrophilic polymer chains, poly(2-hydroxyethyl methacrylate) (PHEMA), were grafted via controlled surface-initiated atom transfer radical polymerization (SI-ATRP) on the surface of polyamide composite nanofiltration (NF) membranes and then end-capped with superparamagnetic iron oxide magnetite (Fe(3)O(4)) nanoparticles. The results of all functionalization steps, that is, bromide ATRP initiator immobilization, SI-ATRP, conversion of PHEMA end groups from bromide to amine, and carboxyl-functional Fe(3)O(4) nanoparticle immobilization via peptide coupling, have been confirmed by X-ray photoelectron spectroscopy (XPS) and field emission scanning electron microscopy (FESEM). These nanoparticles experience a magnetic force as well as a torque under an oscillating external magnetic field. It has been shown, using particle image velocimetry (PIV), that the resulting movement of the polymer brushes at certain magnetic field frequencies induces mixing directly above the membrane surface. Furthermore, it was demonstrated that with such membranes the NF performance could significantly be improved (increase of flux and salt rejection) by an oscillating magnetic field, which can be explained by a reduced concentration polarization in the boundary layer. However, the proof-of-concept presented here for the active alteration of macroscopic flow via surface-anchored micromixers based on polymer-nanoparticle conjugates has much broader implications.