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

Strong HI Lyman-α\alpha variations from the 11 Gyr-old host star Kepler-444: a planetary origin ?

Kepler-444 provides a unique opportunity to probe the atmospheric composition and evolution of a compact system of exoplanets smaller than the Earth. Five planets transit this bright K star at close orbital distances, but they are too small for their putative lower atmosphere to be probed at optical/infrared wavelengths. We used the Space Telescope Imaging Spectrograph instrument onboard the Hubble Space Telescope to search for the signature of the planet's upper atmospheres at six independent epochs in the Ly-$\alpha$ line. We detect significant flux variations during the transits of both Kepler-444e and f (~20%), and also at a time when none of the known planets was transiting (~40%). Variability in the transition region and corona of the host star might be the source of these variations. Yet, their amplitude over short time scales (~2-3 hours) is surprisingly strong for this old (11.2+-1.0Gyr) and apparently quiet main-sequence star. Alternatively, we show that the in-transits variations could be explained by absorption from neutral hydrogen exospheres trailing the two outer planets (Kepler-444e and f). They would have to contain substantial amounts of water to replenish such hydrogen exospheres, which would reveal them as the first confirmed ocean-planets. The out-of-transit variations, however, would require the presence of a yet-undetected Kepler-444g at larger orbital distance, casting doubt on the planetary origin scenario. Using HARPS-N observations in the sodium doublet, we derived the properties of two Interstellar Medium clouds along the line-of-sight toward Kepler-444. This allowed us to reconstruct the stellar Ly-$\alpha$ line profile and to estimate the XUV irradiation from the star, which would still allow for a moderate mass loss from the outer planets after 11.2Gyr. Follow-up of the system at XUV wavelengths will be required to assess this tantalizing possibility.Comment: Accepted for publication in A&A Name of the system added to the title in most recent versio

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

Protein Kinase A Regulates Molecular Chaperone Transcription and Protein Aggregation

Heat shock factor 1 (HSF1) regulates one of the major pathways of protein quality control and is essential for deterrence of protein-folding disorders, particularly in neuronal cells. However, HSF1 activity declines with age, a change that may open the door to progression of neurodegenerative disorders such as Huntington's disease. We have investigated mechanisms of HSF1 regulation that may become compromised with age. HSF1 binds stably to the catalytic domain of protein kinase A (PKAcα) and becomes phosphorylated on at least one regulatory serine residue (S320). We show here that PKA is essential for effective transcription of HSP genes by HSF1. PKA triggers a cascade involving HSF1 binding to the histone acetylase p300 and positive translation elongation factor 1 (p-TEFb) and phosphorylation of the c-terminal domain of RNA polymerase II, a key mechanism in the downstream steps of HSF1-mediated transcription. This cascade appears to play a key role in protein quality control in neuronal cells expressing aggregation-prone proteins with long poly-glutamine (poly-Q) tracts. Such proteins formed inclusion bodies that could be resolved by HSF1 activation during heat shock. Resolution of the inclusions was inhibited by knockdown of HSF1, PKAcα, or the pTEFb component CDK9, indicating a key role for the HSF1-PKA cascade in protein quality control

Converging Neuronal Activity in Inferior Temporal Cortex during the Classification of Morphed Stimuli

How does the brain dynamically convert incoming sensory data into a representation useful for classification? Neurons in inferior temporal (IT) cortex are selective for complex visual stimuli, but their response dynamics during perceptual classification is not well understood. We studied IT dynamics in monkeys performing a classification task. The monkeys were shown visual stimuli that were morphed (interpolated) between pairs of familiar images. Their ability to classify the morphed images depended systematically on the degree of morph. IT neurons were selected that responded more strongly to one of the 2 familiar images (the effective image). The responses tended to peak ∼120 ms following stimulus onset with an amplitude that depended almost linearly on the degree of morph. The responses then declined, but remained above baseline for several hundred ms. This sustained component remained linearly dependent on morph level for stimuli more similar to the ineffective image but progressively converged to a single response profile, independent of morph level, for stimuli more similar to the effective image. Thus, these neurons represented the dynamic conversion of graded sensory information into a task-relevant classification. Computational models suggest that these dynamics could be produced by attractor states and firing rate adaptation within the population of IT neurons

Recommendations for reporting ion mobility mass spectrometry measurements

© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. 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

Decreased Striatal RGS2 Expression Is Neuroprotective in Huntington's Disease (HD) and Exemplifies a Compensatory Aspect of HD-Induced Gene Regulation

The molecular phenotype of Huntington's disease (HD) is known to comprise highly reproducible changes in gene expression involving striatal signaling genes. Here we test whether individual changes in striatal gene expression are capable of mitigating HD-related neurotoxicity.We used protein-encoding and shRNA-expressing lentiviral vectors to evaluate the effects of RGS2, RASD2, STEP and NNAT downregulation in HD. Of these four genes, only RGS2 and RASD2 modified mutant htt fragment toxicity in cultured rat primary striatal neurons. In both cases, disease modulation was in the opposite of the predicted direction: whereas decreased expression of RGS2 and RASD2 was associated with the HD condition, restoring expression enhanced degeneration of striatal cells. Conversely, silencing of RGS2 or RASD2 enhanced disease-related changes in gene expression and resulted in significant neuroprotection. These results indicate that RGS2 and RASD2 downregulation comprises a compensatory response that allows neurons to better tolerate huntingtin toxicity. Assessment of the possible mechanism of RGS2-mediated neuroprotection showed that RGS2 downregulation enhanced ERK activation. These results establish a novel link between the inhibition of RGS2 and neuroprotective modulation of ERK activity.Our findings both identify RGS2 downregulation as a novel compensatory response in HD neurons and suggest that RGS2 inhibition might be considered as an innovative target for neuroprotective drug development

A continuum from clear to cloudy hot-Jupiter exoplanets without primordial water depletion

Thousands of transiting exoplanets have been discovered, but spectral analysis of their atmospheres has so far been dominated by a small number of exoplanets and data spanning relatively narrow wavelength ranges (such as 1.1–1.7 micrometres). Recent studies show that some hot-Jupiter exoplanets have much weaker water absorption features in their near-infrared spectra than predicted. The low amplitude of water signatures could be explained by very low water abundances, which may be a sign that water was depleted in the protoplanetary disk at the planet’s formation location, but it is unclear whether this level of depletion can actually occur. Alternatively, these weak signals could be the result of obscuration by clouds or hazes, as found in some optical spectra. Here we report results from a comparative study of ten hot Jupiters covering the wavelength range 0.3–5 micrometres, which allows us to resolve both the optical scattering and infrared molecular absorption spectroscopically. Our results reveal a diverse group of hot Jupiters that exhibit a continuum from clear to cloudy atmospheres. We find that the difference between the planetary radius measured at optical and infrared wavelengths is an effective metric for distinguishing different atmosphere types. The difference correlates with the spectral strength of water, so that strong water absorption lines are seen in clear-atmosphere planets and the weakest features are associated with clouds and hazes. This result strongly suggests that primordial water depletion during formation is unlikely and that clouds and hazes are the cause of weaker spectral signatures