Examination of segmental average mass spectra from liquid chromatography–tandem mass spectrometric (LC–MS/MS) data enables screening of multiple types of protein modifications

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1–3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra (^saMS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography–mass spectrometric (LC–MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC–MS map, we have implemented a set of computer programs, or the ^saMS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC–MS/MS data.     

Singlet oxygen production by Peptide-coated quantum dot-photosensitizer conjugates

Peptide-coated quantum dot-photosensitizer conjugates were developed using novel covalent conjugation strategies on peptides which overcoat quantum dots (QDs). Rose bengal and chlorin e6, photosensitizers (PSs) that generate singlet oxygen in high yield, were covalently attached to phytochelatin-related peptides. The photosensitizer-peptide conjugates were subsequently used to overcoat green- and red-emitting CdSe/CdS/ZnS nanocrystals. Generation of singlet oxygen could be achieved via indirect excitation through F?rster (fluorescence) resonance energy transfer (FRET) from the nanocrystals to PSs, or by direct excitation of the PSs. In the latter case, by using two color excitations, the conjugate could be simultaneously used for fluorescence imaging and singlet oxygen generation. Singlet oxygen quantum yields as high as 0.31 were achieved using 532-nm excitation wavelengths.     

Novel butterfly tungsten-osmium carbido cluster Complexes from the reaction of Os3(CO)10(NCME)2 CPW(CO)3(CH2SMe)

Condensation of be triosmium acetonitrile complex Os₃(CO)₁₀(NCMe)₂ with the sulfido complex CpW(CO)₃(CH₂SMe) in refluxing THF solution produced three sulfur-containing compounds Os₃(C0)₁₀)(µ-H)(µ-SMe) (1), Os₃(CO)₁₁ [S(Me)CH₂W(CO)₃Cp] (2) and CpWOs₃(CO)₁₂(µ-CH₂)(µ-SMe) (3). Clusters 2 and 3 were products involving a 1:1 combination of starting materials and were characterized by X-ray diffraction studies. Crystals of 2 belongs to monoclinic space group P 2₁ /c witha=8.418(2),b = 11.912(2),c = 28.288 Å,=97.64(2)°,Z=4;R _F=0.044,R _W,=0.044. Crystal dara far 3: space group P 2₁/e,a 18.156(4).b=9.255(6),c = 15.347(4) Å. = 103.49(2)°,Z = 4;R _F -=0.047,R _W = 0.045. Upon thermolysis in toluene, the methylene cluster 3 released CO and induced C-H bond activation to afford two tetrametallic carbido clusters with formula CPWOS₃(CO)₉(µ₄-C)(µ-H)₂(µ-SMe) (4) and CPWOs₃(CO)₁₁(µ₄-C)(µ-SMe) (5) as the principle products. The first complex possesses a butterfly framework encapsulating a µ₄-C ligmd and a µ-SMe ligand linking a W-Os edge, whereas the second product adopts a puckered, cyclic arrangement of WOs₃ metal atoms with µ-SMe ligand located on a nonbonding Os-Os vector. Complex4 crystallizes in monoclinic space group P 2₁ /c witha=15.633(4) Å,b = 8.699 (3) Å,c=15.422(4) Å,=93.12(2)=°, Z=4,R=0.036,R _W =0.034 for 2780 observed reflections. Crystal data for5: space groupP nma,a=14.542(3),b=13.710(6),c=11.758(3) Å.Z=4,R _F =0.038,R _W = 0.037 for 1826 observed reflections. A variable temperature¹H NMR study was also presented to demonstrate the solution fluxionality of5.     

Protein aggregation containing beta-amyloid,alpha-synuclein and hyperphosphorylated tau in cultured cells of hippocampus,substantia nigra and locus coeruleus after rotenone exposure

Background  

Protein aggregates containing alpha-synuclein, beta-amyloid and hyperphosphorylated tau are commonly found during neurodegenerative processes which is often accompanied by the impairment of mitochondrial complex I respiratory chain and dysfunction of cellular systems of protein degradation. In view of this, we aimed to develop an in vitro model to study protein aggregation associated to neurodegenerative diseases using cultured cells from hippocampus, locus coeruleus and substantia nigra of newborn Lewis rats exposed to 0.5, 1, 10 and 25 nM of rotenone, which is an agricultural pesticide, for 48 hours.     

Rotational and translational diffusion of peptide-coated CdSe/CdS/ZnS nanorods studied by fluorescence correlation spectroscopy

CdSe/CdS/ZnS nanorods (NRs) of three aspect ratios were coated with phytochelatin-related peptides and studied using fluorescence correlation spectroscopy (FCS). Theoretical predictions of the NRs' rotational diffusion contribution to the correlation curves were experimentally confirmed. We monitored rotational and translational diffusion of NRs and extracted hydrodynamic radii from the extracted diffusion constants. Translational and rotational diffusion constants (D(trans) and D(rot)) for NRs were in good agreement with Tirado and Garcia de la Torre's as well as with Broersma's theories when accounting for the ligand dimensions. NRs fall in the size range where rotational diffusion can be monitored with higher sensitivity than translational diffusion due to a steeper length dependence, D(rot) approximately L(-)(3) versus D(trans) approximately L(-)(1). By titrating peptide-coated NRs with bovine serum albumin, we monitored (nonspecific) binding through rotational diffusion and showed that D(rot) is an advantageous observable for monitoring binding. Monitoring rotational diffusion of bioconjugated NRs using FCS might prove to be useful for observing binding and conformational dynamics in biological systems.     

Continuous multi-element (Cu, Mn, Ni, Se) monitoring in saline and cell suspension using on-line microdialysis coupled with simultaneous electrothermal atomic absorption spectrometry

We have developed a microdialysis sampling technique coupled on-line with simultaneous electrothermal atomic absorption spectrometry (SIMAAS) for the continuous monitoring of copper (Cu), manganese (Mn), nickel (Ni), and selenium (Se) in saline solutions and in cell suspensions. These trace elements are considered to be those associated most significantly with oxidative stress in biological systems. We employed ultrapure saline (0.9% NaCl) as the perfusate and, thus, the dialysate samples contained a high concentration of salt in the matrix. The use of modifiers [Pd coupled with Mg(NO₃)₂] prevented the target elements from undergoing evaporation at a pyrolysis temperature of 1200 °C, a process that effectively eliminated interference from NaCl. The excellent linearity, detection limits, and precision of the SIMAAS technique allowed the Cu, Mn, Ni, and Se concentrations to be determined in saline. For the on-line microdialysis-SIMAAS system, the ultrapure saline was perfused at a flow rate of 1 μL/min. The probe recoveries of Cu, Mn, Ni, and Se in saline were 57.9, 65.0, 65.5, and 67.9%, respectively. A standard saline solution was measured continuously by the on-line system to ensure long-term stability; each measurement fell within a range of two standard deviations. We determined the on-line spiked recoveries of Cu, Mn, Ni, and Se (101.3, 88.8, 91.3, and 98.5%, respectively) by adding a spiking standard into the stirred saline. The spiked recoveries (Cu, 37.5%; Mn, 3.8%; Ni, 71.1%; Se, 33.8%) were also determined through on-line spiking of a standard into the stirred cell suspension; these values demonstrate that Cu, Mn, and Se were depleted in the cell suspension, but Ni was not. The use of this on-line microdialysis-SIMAAS system permitted the in situ, dynamic, and continuous monitoring of Cu, Mn, Ni, and Se in cell suspensions at a temporal resolution of 20 min.     

Chalcogenide glass waveguides integrated with quantum cascade lasers for on-chip mid-IR photonic circuits

We demonstrate on-chip hybrid integration of chalcogenide glass waveguides and quantum cascade lasers (QCLs). Integration is achieved using an additive solution-casting and molding method to directly form As(2)S(3) strip waveguides on an existing QCL chip. Integrated As(2)S(3) strip waveguides constructed in this manner display strong optical confinement and guiding around 90° bends, with a NA of 0.24 and bend loss of 12.9dB at a 1mm radius (λ=4.8μm).