Global insight into microwave stoneware firing: Macro and micro structural changes

In this paper we have characterized the lineage of two traits associated with the coat proteins (CPs) of the tombusvirids: Silencing suppression and HR elicitation in Nicotiana species. We considered that the tombusvirid CPs might collectively be considered an effector, with the CP of each CP-encoding species comprising a structural variant within the family. Thus, a phylogenetic analysis of the CP could provide insight into the evolution of a pathogen effector. The phylogeny of the CP of tombusvirids indicated that CP representatives of the family could be divided into four clades. In two separate clades the CP triggered a hypersensitive response (HR) in Nicotiana species of section Alatae but did not have silencing suppressor activity. In a third clade the CP had a silencing suppressor activity but did not have the capacity to trigger HR in Nicotiana species. In the fourth clade, the CP did not carry either function. Our analysis illustrates how structural changes that likely occurred in the CP effector of progenitors of the current genera led to either silencing suppressor activity, HR elicitation in select Nicotiana species, or neither trait.

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Cryo-EM structure of 90S small ribosomal subunit precursors in transition states

Science ◽

10.1126/science.aba9690 ◽

2020 ◽

Vol 369 (6510) ◽

pp. 1477-1481 ◽

Cited By ~ 3

Author(s):

Yifei Du ◽

Weidong An ◽

Xing Zhu ◽

Qi Sun ◽

Jia Qi ◽

...

Keyword(s):

Structural Changes ◽

Critical Role ◽

Ribosomal Subunit ◽

Rna Degradation ◽

Ribosomal Subunits ◽

Cryo Electron Microscopy ◽

Nuclear Exosome ◽

Assembly Intermediate ◽

Insight Into

The 90S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40S ribosome. Here, we gained insight into this transition by determining cryo–electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90S to the pre-40S. The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5′ external transcribed spacer (5′ ETS) is degraded within 90S, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90S through helicase Mtr4 and is primed to digest the 3′ end of the 5′ ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5′ ETS degradation in 90S progression.

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OS4-5 Mechanical and structural changes in the cartilage-bone system as a function of degeneration : New insight into the mechanobiology of osteoarthritis(OS4: Advanced Clinical Joint Biomechanics)

The Proceedings of the Asian Pacific Conference on Biomechanics emerging science and technology in biomechanics ◽

10.1299/jsmeapbio.2015.8.91 ◽

2015 ◽

Vol 2015.8 (0) ◽

pp. 91

Author(s):

Ashvin Thambyah ◽

Emily Hargrave-Thomas ◽

Mieke Nickien ◽

Rebekah Kim ◽

Neil Broom

Keyword(s):

Structural Changes ◽

Joint Biomechanics ◽

Insight Into

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Scanning Probe Microscopy of Bacterial Red Light Photoreceptors

MRS Proceedings ◽

10.1557/opl.2012.1006 ◽

2012 ◽

Vol 1465 ◽

Author(s):

Fernando G. Tobias ◽

Anna Gawedzka ◽

Max S. Goldmeier ◽

Alexandra C. Sakols ◽

Emina A. Stojković ◽

...

Keyword(s):

Scanning Probe Microscopy ◽

Structural Changes ◽

Structural Model ◽

Fluorescent Protein ◽

Red Light ◽

Hexagonal Lattice ◽

Scanning Probe ◽

Scanning Tunneling ◽

Probe Microscopy ◽

Insight Into

ABSTRACTBacteriophytochromes (Bphs) are red-light photoreceptors found in photosynthetic and non-photosynthetic bacteria that have been engineered into infrared fluorescent protein markers. Bphs are composed of a photosensory module that is covalently linked to an effector/regulatory module, usually a histidine kinase (HK) domain. Light-induced, global structural changes are proposed to originate within the covalently attached biliverdin chromophore, a linear tetrapyrrole, and propagate through the protein. Bphs undergo reversible photoconversion between two distinct red and far-red light absorbing states, denoted Pr and Pfr respectively. For most Bphs, Pr is the dark-adapted state. The energy dissipated during Pr/Pfr photoconversion is proposed to directly impact the infrared fluorescence quantum yield. At this time, only structures of three different Bphs have been published, all of truncated proteins in their respective dark-adapted states. We have utilized scanning probe microscopy (SPM) to investigate the structure of intact Bphs in the light-adapted state in order to gain new insight into the mechanism of photoconversion and fluorescence. Scanning tunneling microscopy (STM) analysis of a pair of Bphs from photosynthetic bacterium R. palustris, RpBphP2 (P2) and RpBphP3 (P3) in their light-adapted states is presented in these proceedings. The concentration of the depositing protein has a key role in the molecular arrangements observed on the highly-ordered pyrolytic graphite (HOPG) surface. For example, at a high protein concentration, a hexagonal lattice of Bphs is observed by STM on a HOPG surface. Upon dilution, the photoreceptors self-organize into fiber-like structures on the surface. In these fibers, the dimer interface and the individual domains of the Bphs can be assigned and directly compared to a structural model of the intact, full-length proteins. In summary, SPM has potential to be an effective method for gaining new insight into Bph structure and dynamics.

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Gaining insight into structural changes with dynamic diffraction methods

Thermochimica Acta ◽

10.1016/0040-6031(95)02523-5 ◽

1995 ◽

Vol 269-270 ◽

pp. 33-42 ◽

Cited By ~ 2

Author(s):

Matthias Epple

Keyword(s):

Structural Changes ◽

Dynamic Diffraction ◽

Insight Into ◽

Gaining Insight

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Genetic and functional odorant receptor variation in the Homo lineage

10.1101/2021.09.13.460146 ◽

2021 ◽

Author(s):

Claire A. de March ◽

Hiroaki Matsunami ◽

Masashi Abe ◽

Matthew Cobb ◽

Kara C. Hoover

Keyword(s):

Structural Changes ◽

Odorant Receptor ◽

Odorant Receptors ◽

Receptor Function ◽

Functional Variation ◽

Receptor Proteins ◽

Local Adaptations ◽

The Road ◽

Specific Anosmia ◽

Insight Into

AbstractThe largest and rapidly evolving gene family of odorant receptors detect odors to variable degrees due to amino acid sequence and protein structure. Hybridization between humans, Neandertals, and Denisovans implies shared behavior1,2, although some speculate that Neandertals were poor smellers 3,4. We identified genetic and functional variation in humans and extinct lineages in 30 receptors with known function. We show that structural changes in receptor proteins altered odor sensitivity not specificity, indicating a common repertoire across lineages. In humans, variation in receptors may change odor perception or induce odor-specific anosmia 5,6. Variation in sensitivity may reflect local adaptations (e.g., Denisovan sensitivity to honey, Neandertals sensitivity to grass and sulphur). Extinct human lineages had highly conserved receptor genes and proteins. We observe a similar pattern in the Neandertal OR5P3 variant, which produced no response to ∼350 odors. Our data suggest that receptor structure was highly conserved in our closest relatives, but not in living humans. The diversity of geographic adaptations in humans may have produced greater functional variation, increasing our olfactory repertoire and expanding our adaptive capacity 5. Our results provide insight into odorant receptor function and shed light on the olfactory ecology of ancient humans and their extinct relatives. By studying the function of ancient odorant receptor genes, we have been able to get a glimpse of the sensory world of our extinct ancestors and relatives, with some of the variants giving specific insights into potential adaptations shown by these long-dead populations. The functional variability we have identified in the molecular structure of the odorant receptor proteins will aid in the more general problem of understanding the function of odorant receptor proteins and the neurons they are carried by, opening the road to linking receptor function to perception.

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Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD-ACE2 Binding

10.1101/2021.09.20.461041 ◽

2021 ◽

Author(s):

Abhishek Aggarwal ◽

Supriyo Naskar ◽

Nikhil Maroli ◽

Biswajit Gorai ◽

Narendra M Dixit ◽

...

Keyword(s):

Structural Changes ◽

Underlying Mechanism ◽

Free Energy Calculations ◽

Target Cells ◽

Original Strain ◽

Binding Affinities ◽

Receptor Binding Domain ◽

Wild Type ◽

Dynamics Simulations ◽

Insight Into

Some recent SARS-CoV-2 variants appear to have increased transmissibility than the original strain. An underlying mechanism could be the improved ability of the variants to bind receptors on target cells and infect them. In this study, we provide atomic-level insight into the binding of the receptor binding domain (RBD) of the wild-type SARS-CoV-2 spike protein and its single (N501Y), double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants to the human ACE2 receptor. Using extensive all-atom molecular dynamics simulations and advanced free energy calculations, we estimate the associated binding affinities and binding hotspots. We observe significant secondary structural changes in the RBD of the mutants, which lead to different binding affinities. We find higher binding affinities of the double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants than the wild type and the N501Y variant, which could contribute to the higher transmissibility of recent variants containing these mutations.

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