Gas-Phase Protein Structure Characterization with Ion Mobility Mass Spectrometry and Molecular Dynamics Simulations

Over the last few decades, the widespread application of soft ionization techniques such as electrospray ionization (ESI) coupled with mass spectrometry (MS) facilitated the characterization of large biomolecules in the gas phase. Under suitable conditions and during the short timescale of the desolvation process associated with ESI (10-12-102 s), the solvent-free protein ions preserve significant portions of their native solution-phase structure and are presumed to be kinetically protected from thermodynamic destabilization such as unfolding-refolding processes occurring in the gas phase that could yield an inside-out structure.;The combination of ESI with ion mobility spectrometry- mass spectrometry (IMS-MS) provides information regarding higher-order structure of proteins and their complexes. IMS-MS has the ability to resolve and probe conformers of protein ions of a particular charge state based on their mobility through an inert buffer gas in drift tube under the influence of a constant electric field. An ion\u27s mobility is dependent upon its charge and shape and can be used to determine the orientationally-averaged collision cross section (CCS) of the ion with the buffer gas. Comparison of experimentally measured CCS values with theoretical CCS numbers obtained from a series of computer-assisted molecular dynamics simulations (MD) which explore the conformational space of protein ions provides insight into candidate structures for each conformer.;Although, CCS values provide a rough estimate of the overall shape of different molecules, IMS-MS alone cannot distinguish three dimensional structures of a series of conformers that represent the same mobility and thus would arrive at the same time at the exit region of the drift tube. The combination of IMS-MS with hydrogen-deuterium exchange (HDX) experiments as a gas-phase chemical probe of structure provides the opportunity to distinguish among these conformer types.;In this work, the gas-phase ion conformers of a model peptide have been studied through CCS measurements, HDX behavior analysis and extensive (MD) simulations.;Initially, an advanced protocol is introduced in order to achieve an impartial sampling of phase space targeting both higher-energy and more thermodynamically-stable structures. The gas-phase transport properties of the ion conformers - including their dynamics at experimental temperatures- have been monitored, and, combined with an optimized clustering and data mining method, accurate CCS determination has been accomplished. These data provided the first criterion to filter through a substantial pool of conformations in order to obtain a series of candidate structures (CCS matched) with significant structural variation.;A hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model is applied to the candidate structures obtained from MD simulations. The HAS-NEC model produced hypothetical, per-residue deuterium uptake values. This information then provided the overall structural contribution from each in-silico structure leading to the best match to experimental results. The comparison of predicted and experimentally observed isotopic envelopes of various mass spectral fragment ions supported the accuracy of the model. With these results, the hypothetical HDX data were employed as a second dimension to narrow the sampled phase space and, together with the accurate CCS values, 13 nominal conformers with specific population contributions to the gas-phase ions were selected.;In the final installment of this work, extensive simulations of the ESI process were performed to monitor the behavior of the peptide ion, charge carriers and the droplets involved in the ionization process. The results provided a series of structures that match the nominal conformers obtained through CCS calculations and the HAS-NEC model. This method validation confirmed the accuracy of the HAS-NEC model in successfully predicting the representative gas-phase structures on a computationally-affordable timescale

Protein Structure

Since the dawn of recorded history, and probably even before, men and women have been grasping at the mechanisms by which they themselves exist. Only relatively recently, did this grasp yield anything of substance, and only within the last several decades did the proteins play a pivotal role in this existence. In this expose on the topic of protein structure some of the current issues in this scientific field are discussed. The aim is that a non-expert can gain some appreciation for the intricacies involved, and in the current state of affairs. The expert meanwhile, we hope, can gain a deeper understanding of the topic

Online learning of physics during a pandemic: A report from an academic experience in Italy

The arrival of the Sars-Cov II has opened a new window on teaching physics in academia. Frontal lectures have left space for online teaching, teachers have been faced with a new way of spreading knowledge, adapting contents and modalities of their courses. Students have faced up with a new way of learning physics, which relies on free access to materials and their informatics knowledge. We decided to investigate how online didactics has influenced students’ assessments, motivation, and satisfaction in learning physics during the pandemic in 2020. The research has involved bachelor (n = 53) and master (n = 27) students of the Physics Department at the University of Cagliari (N = 80, 47 male; 33 female). The MANOVA supported significant mean differences about gender and university level with higher values for girls and master students in almost all variables investigated. The path analysis showed that student-student, student-teacher interaction, and the organization of the courses significantly influenced satisfaction and motivation in learning physics. The results of this study can be used to improve the standards of teaching in physics at the University of Cagliar

Planetary Science Vision 2050 Workshop : February 27–28 and March 1, 2017, Washington, DC

This workshop is meant to provide NASA’s Planetary Science Division with a very long-range vision of what planetary science may look like in the future.Organizer, Lunar and Planetary Institute ; Conveners, James Green, NASA Planetary Science Division, Doris Daou, NASA Planetary Science Division ; Science Organizing Committee, Stephen Mackwell, Universities Space Research Association [and 14 others]PARTIAL CONTENTS: Exploration Missions to the Kuiper Belt and Oort Cloud--Future Mercury Exploration: Unique Science Opportunities from Our Solar System’s Innermost Planet--A Vision for Ice Giant Exploration--BAOBAB (Big and Outrageously Bold Asteroid Belt) Project--Asteroid Studies: A 35-Year Forecast--Sampling the Solar System: The Next Level of Understanding--A Ground Truth-Based Approach to Future Solar System Origins Research--Isotope Geochemistry for Comparative Planetology of Exoplanets--The Moon as a Laboratory for Biological Contamination Research--“Be Careful What You Wish For:” The Scientific, Practical, and Cultural Implications of Discovering Life in Our Solar System--The Importance of Particle Induced X-Ray Emission (PIXE) Analysis and Imaging to the Search for Life on the Ocean Worlds--Follow the (Outer Solar System) Water: Program Options to Explore Ocean Worlds--Analogies Among Current and Future Life Detection Missions and the Pharmaceutical/ Biomedical Industries--On Neuromorphic Architectures for Efficient, Robust, and Adaptable Autonomy in Life Detection and Other Deep Space Missions

Microscopy Conference 2017 (MC 2017) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2017", die vom 21. bis 25.08.2017, in Lausanne stattfand

Microscopy Conference 2017 (MC 2017) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2017", die vom 21. bis 25.08.2017, in Lausanne stattfand