Conformations of biopolymers in the gas phase: a new mass spectrometric method

A method is developed for measuring collision cross sections of gas-phase biomolecules using a slightly modified commercial triple quadrupole instrument. The modifications allow accurate stopping potentials to be measured for ions exiting the collision region of the instrument. A simple model allows these curves to be converted to cross sections. In order to account for certain poorly defined experimental parameters (exact ion energy, absolute pressure in the collision cell, etc.) variable parameters are included in the model. These parameters are determined on a case by case basis by normalizing the results to the well known cross section of singly charged bradykinin, Two relatively large systems were studied (cytochrome c and myoglobin) so comparisons could be made to literature values. A number of new peptide systems were then studied in the 9 -14 residue range. These included singly and doubly charged ions of luteinizing hormone releasing hormone (LHRH) substance P, and bombesin in addition to bradykinin. The experimental cross sections were in very good agreement with predictions from extensive molecular dynamics modeling. One interesting result was the experimental observation that the cross section of the doubly charged ions of LHRH, substance P, and bombesin were all smaller than those of the corresponding singly charged ions. Molecular dynamics did not reproduce this result, predicting doubly charged cross sections of the same magnitude or slightly larger than for the singly charged species. The experimental results appear to be correct, however. Possible shortcomings in the modeling procedure for multiply charged ions were suggested that might account for the discrepancy

Far-Ultraviolet Emission from Elliptical Galaxies at z=0.33

We present far-ultraviolet (far-UV) images of the rich galaxy cluster ZwCl1358.1+6245, taken with the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope (HST). When combined with archival HST observations, our data provide a measurement of the UV-to-optical flux ratio in 8 early-type galaxies at z=0.33. Because the UV flux originates in a population of evolved, hot, horizontal branch (HB) stars, this ratio is potentially one of the most sensitive tracers of age in old populations -- it is expected to fade rapidly with lookback time. We find that the UV emission in these galaxies, at a lookback time of 3.9 Gyr, is significantly weaker than it is in the current epoch, yet similar to that in galaxies at a lookback time of 5.6 Gyr. Taken at face value, these measurements imply different formation epochs for the massive ellipticals in these clusters, but an alternative explanation is a "floor" in the UV emission due to a dispersion in the parameters that govern HB morphology.Comment: 4 pages, Latex. 2 figures. Uses corrected version of emulateapj.sty and apjfonts.sty (included). Accepted for publication in ApJ Letter

Recommendations for reporting ion mobility Mass Spectrometry measurements

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method‐dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc

A Century of Grading Research: Meaning and Value in the Most Common Educational Measure

Grading refers to the symbols assigned to individual pieces of student work or to composite measures of student performance on report cards. This review of over 100 years of research on grading considers five types of studies: (a) early studies of the reliability of grades, (b) quantitative studies of the composition of K-12 report card grades, (c) survey and interview studies of teachers’ perceptions of grades, (d) studies of standards-based grading, and (e) grading in higher education. Early 20th century studies generally condemned teachers’ grades as unreliable. More recent studies of the relationships of grades to tested achievement and survey studies of teachers’ grading practices and beliefs suggest that grades assess a multidimensional construct containing both cognitive and non-cognitive factors reflecting what teachers value in student work. Implications for future research and for grading practices are discussed

3-Dimensional structural characterization of cationized polyhedral oligomeric silsesquioxanes (POSS) with styryl and phenylethyl capping agents

The 3-dimensional gas-phase conformations of polyhedral oligomeric silsesquioxanes (POSS), R 8 Si 8 O 12 , capped with styryl and phenylethyl substituents (R) and cationized by sodium were examined. MALDI was used to generate sodiated styryl-POSS (Na + Sty 8 T 8 ) and phenylethyl-POSS (Na + PhEt 8 T 8 ) ions and their collision cross-sections in helium were measured using ion mobility-based methods. Five distinct conformers with different collision cross-sections were experimentally observed for Na + Sty 8 T 8 while only one conformer was detected for Na + PhEt 8 T 8 . Theoretical modeling of Na + Sty 8 T 8 , using molecular mechanics/dynamics calculations, predicts three low-energy conformations. In each conformer, the Na + ion binds to four oxygens on one side of the Si-O cage and the styryl groups extend away from the cage. However, different numbers of styryl groups "pair" together (forming 2, 3 or 4 pairs), yielding three different conformations. The calculated cross-sections of these conformers match the largest three cross-sections obtained from the ion mobility experiments (â\u88¼2% error). If, however, one or two of the styryl groups are rotated so that the phenyl groups are "cis" with respect to the Si atom on the cage (i.e., the Si-C=C-C dihedral angle changes from 180 to 0 â\u80¢ ) two smaller conformers are predicted by theory whose cross-sections match the smallest two values obtained from the ion mobility experiments (1-2% error). Theoretical modeling of Na + PhEt 8 T 8 yields one low-energy conformation in which the Na + ion binds to one oxygen on the Si-O cage and is sandwiched between two phenyl groups. The remaining phenylethyl groups fold toward the Si-O cage, yielding a significantly more compact structure than Na + Sty 8 T 8 (â\u88¼20% smaller cross-section). The calculated cross-section of the predicted Na + PhEt 8 T 8 structure agrees very well with the experimental cross-section obtained from the ion mobility experiments (â\u88¼1% error)

Phage Orf family recombinases:conservation of activities and involvement of the central channel in DNA binding

Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination

Spermine Binding to Parkinson’s Protein α-Synuclein and Its Disease-Related A30P and A53T Mutants

Aggregation of α-synuclein (α-syn), a protein implicated in Parkinson’s disease (PD), is believed to progress through formation of a partially folded intermediate. Using nanoelectrospray ionization (nano-ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for α-syn and its disease-related A53T mutant with net charges of −6, −7, and −8. For the other early onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of −6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of −10 to a net charge of −6. This charge reduction is accompanied by a dramatic size reduction of about a factor of 2 (cross section of 2600 Å^2 (−10 charge state) down to 1430 Å^2 (−6 charge state)). We conclude that spermine increases the aggregation rate of α-syn by inducing a collapsed conformation, which then proceeds to form aggregates

Normal systems over ANR's, rigid embeddings and nonseparable absorbing sets

Most of results of Bestvina and Mogilski [\textit{Characterizing certain incomplete infinite-dimensional absolute retracts}, Michigan Math. J. \textbf{33} (1986), 291--313] on strong $Z$-sets in ANR's and absorbing sets is generalized to nonseparable case. It is shown that if an ANR $X$ is locally homotopy dense embeddable in infinite-dimensional Hilbert manifolds and $w(U) = w(X)$ (where `$w$' is the topological weight) for each open nonempty subset $U$ of $X$,then $X$ itself is homotopy dense embeddable in a Hilbert manifold. It is also demonstrated that whenever $X$ is an AR, its weak product $W(X,*) = \{(x_n)_{n=1}^{\infty} \in X^{\omega}:\ x_n = * \textup{for almost all} n\}$ is homeomorphic to a pre-Hilbert space $E$ with $E \cong \Sigma E$. An intrinsic characterization of manifolds modelled on such pre-Hilbert spaces is given.Comment: 26 page

Protomers of Benzocaine: Solvent and Permittivity Dependence

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization (ESI) process. Here we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry (IM-MS) to yield gas-phase IR spectra of simultaneously m/z and drift-time resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species - the N- and O-protonated form. Density functional theory (DFT) calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation has been suggested