Painting Proteins with Covalent Labels: What's In the Picture?

Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein—ligand complexes. Highlighted here are five different mass spectrometry—based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution.     

New method for prefractionation of plasma for proteomic analysis

The depth of proteome analysis is severely limited in complex samples with a wide dynamic range of protein abundance such as plasma. Removal of high‐abundance proteins should reveal the signal of lower abundance plasma proteins. However, smaller proteins may be part of larger protein complexes and hence the removal of proteins involved in complexes with high‐abundance proteins such as albumin may inhibit the search for disease biomarkers. Prefractionation of a sample divides it into fractions of reduced complexity, allowing improved detection of lower abundance proteins. Using a prefractionation device, which employs Gradiflow? technology, we were able to separate small volume plasma samples into multiple fractions based on the molecular weight and/or charge. The resulting samples of reduced complexity were directly compatible with 2‐DE. The use of this prefractionation machine may therefore be useful in the hunt for disease biomarkers.     

Experimental observation of spin delocalisation onto the aryl-alkynyl ligand in the complexes [Mo(C≡CAr)(Ph2PCH2CH2PPh2)(η-C7H7)]+ (Ar = C6H5, C6H4-4-F; C7H7 = cycloheptatrienyl): an EPR and ENDOR investigation

The paramagnetic aryl-alkynyl complexes [Mo(C≡CAr)(dppe)(η-C(7)H(7))](+) (dppe = Ph(2)PCH(2)CH(2)PPh(2); Ar = C(6)H(5), [1](+); C(6)D(5), [2](+); C(6)H(4)-4-F, [3](+); C(6)H(4)-4-Me, [5](+)) and [Mo(C≡CBu(t))(dppe)(η-C(7)H(7))](+) [4](+), have been investigated in a combined EPR and ENDOR study. Direct experimental evidence for the delocalisation of unpaired spin density over the framework of an aryl-alkynyl ligand has been obtained. The X-band solution EPR spectrum of the 4-fluoro derivative, [3](+), exhibits resolved hyperfine coupling to the remote para position of the aryl group [a(iso)((19)F) = 4.5 MHz, (1.6 G)] in addition to couplings attributable to (95/97)Mo, (31)P and (1)H of the C(7)H(7) ring. A full analysis of the (1)H ENDOR spectra is restricted by the low g anisotropy of the system which prevents the use of orientation selection. However, inter-comparison of the (1)H cw-ENDOR frozen solution spectra of [1](+), [2](+), [4](+) and [5](+), combined with spectral simulation informed by calculated values derived from DFT investigations, has facilitated estimation of the experimental a(iso)((1)H) hyperfine couplings of [1](+) including the ortho, ±3.7 MHz (±1.3 G) and para, ±3.9 MHz (±1.4 G) positions of the C(6)H(5) substituent of the aryl-alkynyl ligand.     

Chloro and hydroxo forms of a boron(III) subtriazaporphyrin macrocycle

cis-3,4-Dicyano-3-hexene undergoes cyclotrimerization with BCl3 to form the new subtriazaporphyrin chloro[hexaethylsubtriazaporphyrinato]boron(III). The hydroxo derivative of this macrocycle has also been made, and the X-ray crystal structure of the hydroxy form was determined. Electronic absorption and magnetic circular dichroism spectra of the hydroxo monomer species were interpreted using time-dependent density functional theory calculations.     

Mercury determination by cold vapor atomic absorption spectrometry utilizing UV photoreduction

A method for the determination of mercury via UV photoreduction has been investigated. Mercury vapor was generated by the reduction of mercury species in an acetic acid solution using UV radiation. Detection of the volatile mercury was accomplished by atomic absorption spectrometry. An optimized system was found to provide a detection limit (defined as the concentration giving a signal equal to three times the standard deviation of the blank) of 2.1 μg L⁻¹ with a precision of 2.9% relative standard deviation (n = 8) for a 500 μg L⁻¹ mercury standard. The effect of various metal ions on the mercury signal was investigated and the method validated with a NRCC certified dogfish liver material (DOLT-3) using the method of standard additions. A reaction pathway is hypothesized for UV photoreduction.     

Is the hypothiocyanite anion (OSCN)- the major product in the peroxidase catalyzed oxidation of the thiocyanate anion (SCN)-? A joint experimental and theoretical study

The hypothiocyanate anion (OSCN)(-) is reported to be a major product of the lactoperoxidase/H(2)O(2)/(SCN)(-) system, and this anion is proposed to have significant antimicrobial properties. The collision induced (CID) negative ion mass spectrum of "(OSCN)(-)" has been reported: there is a pronounced parent anion at m/z 74, together with fragment anions at m/z 58 (SCN)(-) and 26 (CN)(-). These fragment anions are consistent with structure (OSCN)(-). However there is also a lesser peak at m/z 42 (OCN(-) or CNO(-)) in this spectrum which is either formed by rearrangement of (OSCN)(-) or from an isomer of this anion. The current theoretical investigation of (OSCN)(-) and related isomers, together with the study of possible rearrangements of these anions, indicates that ground-state singlet (OSCN)(-) is a stable species and that isomerization is unlikely. The three anions (OSCN)(-), (SCNO)(-), and (SNCO)(-) have been synthesized (in the ion source of a mass spectrometer) by unequivocal routes, and their structures have been confirmed by a consideration of their collision induced (negative ion) and charge reversal (positive ion) mass spectra. The CID mass spectrum of (SCNO)(-) shows formation of m/z 42 (CNO(-)), but the corresponding spectra of (OSCN)(-) or (SNCO)(-) lack peaks at m/z 42. Combined theoretical and experimental data support earlier evidence that the hypothiocyanite anion is a major oxidation product of the H(2)O(2)/(SCN)(-) system. However, the formation of m/z 42 in the reported CID spectrum of "(OSCN)(-)" does not originate from (OSCN)(-) but from another isomer, possibly (SCNO)(-).     

Highly degenerate quadratic forms over

Let K be a finite extension of F₂. We consider quadratic forms written as the trace of xR(x), where R(x) is a linearized polynomial. We determine the K and R(x) where the form has a radical of codimension 2. This is applied to constructing maximal Artin–Schreier curves.     

Projective Modules Over Frobenius Algebras and Hopf Comodule Algebras

This note presents some results on projective modules and the Grothendieck groups K ₀ and G ₀ for Frobenius algebras and for certain Hopf Galois extensions. Our principal technical tools are the Higman trace for Frobenius algebras and a product formula for Hattori-Stallings ranks of projectives over Hopf Galois extensions.