Cinnamaldehyde and Phenyl Ethyl Alcohol promote the entrapment of intermediate species of HEWL, as revealed by structural, kinetics and thermal stability studies

AbstractNumerous efforts have been directed towards investigating the different stages leading to the fibrillation process in neurodegenerative diseases and finding the factors modulating it. In this study, using a wide range of molecular techniques as well as fibrillation kinetics coupled with differential scanning fluorimetry (DSF) and crystal structure determination of HEWL treated with cinnamaldehyde (Cin) and Phenyl ethyl alcohol (PEA) in their aroma form during fibrillation, we were able to identify the binding positions of Cin and PEA in HEWL. Additionally, crystal structures were used to suggest residues Thr43, Asn44, Arg45 and Arg68 as a plausible ‘hotspot’ promoting entrapment of intermediate species in the process of fibril formation in HEWL. We were also able to use DSF to show that Cin can significantly decrease the thermal stability of HEWL, promoting the formation of partially unfolded intermediate species. In conclusion, our data led us to emphasize that compounds in their ‘aroma form’ can influence the structure and stability of protein molecules and suggest reconsideration of HEWL as a model protein for fibrillation studies related to neurodegenerative diseases based on the initial structure of the proteins, whether globular (HEWL) or intrinsically disordered.

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Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

Current Alzheimer Research ◽

10.2174/1567205017666201109094908 ◽

2020 ◽

Vol 17 ◽

Author(s):

Ibrahim Yagiz Akbayrak ◽

Sule Irem Caglayan ◽

Zilan Ozcan ◽

Vladimir N. Uversky ◽

Orkid Coskuner-Weber

Keyword(s):

Neurodegenerative Diseases ◽

Computer Simulations ◽

Conformational Changes ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Computational Studies ◽

Accurate Data ◽

Aggregation Propensity ◽

Intrinsically Disordered ◽

Future Developments

: Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations – including our own – revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

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Morphometric and Molecular Analyses of Ostertagia leptospicularis Assadov, 1953 from Ruminants: Species Diversity or Host Influence?

Animals ◽

10.3390/ani11010182 ◽

2021 ◽

Vol 11 (1) ◽

pp. 182

Author(s):

Anna Wyrobisz-Papiewska ◽

Jerzy Kowal ◽

Elżbieta Łopieńska-Biernat ◽

Paweł Nosal ◽

Iwona Polak ◽

...

Keyword(s):

Host Species ◽

Roe Deer ◽

Bos Taurus ◽

Capreolus Capreolus ◽

Nematode Species ◽

Molecular Techniques ◽

Systematic Classification ◽

Morphological Variations ◽

Wide Range ◽

Induced Changes

Ostertagia leptospicularis Assadov, 1953 was formally described in roe deer Capreolus capreolus and has been reported in a wide range of ruminants, including other Cervidae, as well as Bovidae. Nematode specimens derived from various host species exhibit morphological similarity; however, some differences can be observed. It is unclear if this is due to the differential reaction of one nematode species in different host species (i.e., host-induced changes) or because of distinct nematode species in these hosts (i.e., species complex). This paper focuses on specimens resembling O. leptospicularis f. leptospicularis and its closely related species (Ostertagia ostertagi f. ostertagi) collected from various hosts. Morphometric and molecular techniques were applied to assess host-induced changes in nematode morphology and to clarify its systematic classification. There was an overall effect of host species on measurements of nematodes resembling O. leptospicularis (both males and females), but the distinctiveness of the specimens from cattle Bos taurus were highlighted. The results obtained may suggest that the specimens of O. leptospicularis from cattle in Germany and cervids in central Europe belong to different strains. Furthermore, nematodes from the cervid strain appear to circulate within particular host species, which can be seen in the stated morphological variations.

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Intracellular Ionic Strength Sensing Using NanoLuc

International Journal of Molecular Sciences ◽

10.3390/ijms22020677 ◽

2021 ◽

Vol 22 (2) ◽

pp. 677

Author(s):

Tausif Altamash ◽

Wesam Ahmed ◽

Saad Rasool ◽

Kabir H. Biswas

Keyword(s):

Thermal Stability ◽

Phase Separation ◽

Drug Discovery ◽

Ionic Strength ◽

Cellular Signaling ◽

Live Cells ◽

Protein Activity ◽

Cellular Survival ◽

Cellular Processes ◽

Wide Range

Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.

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Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis

Canadian Journal of Plant Science ◽

10.4141/cjps2011-240 ◽

2012 ◽

Vol 92 (6) ◽

pp. 1121-1133 ◽

Cited By ~ 9

Author(s):

S. C. Debnath ◽

Y. L. Siow ◽

J. Petkau ◽

D. An ◽

N. V. Bykova

Keyword(s):

Genetic Diversity ◽

Antioxidant Activity ◽

Molecular Markers ◽

Molecular Techniques ◽

Diversity Analysis ◽

Full Potential ◽

Genetic Diversity Analysis ◽

Wide Range ◽

Berry Crops ◽

Improvement Programs

Debnath, S. C., Siow, Y. L., Petkau, J., An, D. and Bykova, N. V. 2012. Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis. Can. J. Plant Sci. 92: 1121–1133. An improved understanding of important roles of dietary fruits in maintaining human health has led to a dramatic increase of global berry crop production. Berry fruits contain relatively high levels of vitamin C, cellulose and pectin, and produce anthocyanins, which have important therapeutic values, including antitumor, antiulcer, antioxidant and anti-inflammatory activities. There is a need to develop reliable methods to identify berry germplasm and assess genetic diversity/relatedness for dietary properties in berry genotypes for practical breeding purposes through genotype selection in a breeding program for cultivar development, and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic materials independent of environmental influences. Significant progress has been made in diversity analysis of wild cranberry, lowbush blueberry, lingonberry and cloudberry germplasm, and in strawberry and raspberry cultivars and advanced breeding lines developed in Canada. Inter simple sequence repeat (ISSR) markers detected an adequate degree of polymorphism to differentiate among berry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in the current berry improvement programs. Although multiple factors affect antioxidant activity, a wide range of genetic diversity has been reported in wild and cultivated berry crops. Diversity analysis based on molecular markers did not agree with those from antioxidant activity. The paper also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques including expressed sequence tag-polymerase chain reaction (EST-PCR) analysis to develop improved environment-friendly berry cultivars suited to the changing needs of growers and consumers.

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Visualising intrinsic disorder and conformational variation in protein ensembles

Faraday Discussions ◽

10.1039/c3fd00138e ◽

2014 ◽

Vol 169 ◽

pp. 179-193 ◽

Cited By ~ 6

Author(s):

Julian Heinrich ◽

Michael Krone ◽

Seán I. O'Donoghue ◽

Daniel Weiskopf

Keyword(s):

Intrinsic Disorder ◽

Molecular Graphics ◽

Post Translational Modifications ◽

3D Structures ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Wide Range ◽

Conformational Variations ◽

Protein Ensembles ◽

Traditional Approaches

Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination—however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our goal in this paper is to improve this situation by augmenting traditional approaches (molecular graphics and principal components) with methods from human–computer interaction and information visualisation, especially parallel coordinates. We present a new tool integrating these approaches, and demonstrate how it can dissect ensembles to reveal functional insights into conformational variation and intrinsic disorder.

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Heparin remodels the microtubule-binding repeat R3 of Tau protein towards fibril-prone conformations

Physical Chemistry Chemical Physics ◽

10.1039/d1cp02651h ◽

2021 ◽

Author(s):

Xuewei Dong ◽

Ruxi Qi ◽

Qin Qiao ◽

Xuhua Li ◽

Fangying Li ◽

...

Keyword(s):

Neurodegenerative Diseases ◽

Tau Protein ◽

Amyloid Fibrils ◽

Microtubule Binding ◽

Wide Range

Abnormal aggregation of proteins into pathological amyloid fibrils are implicated in a wide range of devastating human neurodegenerative diseases. Intracellular fibrillary inclusions formed by Tau protein are characterized as the...

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Effects of handedness on olfactory event-related potentials in a simple olfactory task

Rhinology Journal ◽

10.4193/rhino14.204 ◽

2015 ◽

Vol 53 (2) ◽

pp. 149-153

Author(s):

Marie Gottschlich ◽

Thomas Hummel

Keyword(s):

Hydrogen Sulfide ◽

Ethyl Alcohol ◽

Healthy Subjects ◽

Event Related Potentials ◽

Major Influence ◽

Chemical Senses ◽

Phenyl Ethyl Alcohol ◽

Related Potentials ◽

The Rose

The purpose of the present study was to re-investigate the influence of handedness on simple olfactory tasks to further clarify the role of handedness in chemical senses. Similar to language and other sensory systems, effects of handedness should be expected. Young, healthy subjects participated in this study, including 24 left-handers and 24 right-handers, with no indication of any major nasal or health problems. The two groups did not differ in terms of sex and age (14 women and 10 men in each group). They had a mean age of 24.0 years. Olfactory event-related potentials were recorded after left or right olfactory stimulation with the rose-like odor phenyl ethyl alcohol (PEA) or the smell of rotten eggs (hydrogen sulfide, H2S). Results suggested that handedness has no major influence on amplitude or latency of olfactory event-related potentials when it comes to simple olfactory tasks.

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The influence of sex on the olfactory function in healthy subjects

Zbornik Matice srpske za prirodne nauke ◽

10.2298/zmspn0201083s ◽

2002 ◽

pp. 83-89

Author(s):

Slobodan Savovic ◽

Vladimir Pilija ◽

Slobodanka Lemajic ◽

Maja Buljcik ◽

Dejan Nincic ◽

...

Keyword(s):

Sex Hormones ◽

Ethyl Alcohol ◽

Mental State ◽

Healthy Subjects ◽

Age Groups ◽

Protective Role ◽

Olfactory Function ◽

Age Group ◽

Phenyl Ethyl Alcohol

The sense of smell is the least examined of all senses. The significance of the organs of smell is in their influence on the mental state as well as on the vegetative, visceral and sexual functions. The objective of this experiment was to define the influence of sex on the olfactory function. It was performed on 120 subjects (60 females and 60 males) divided into three age groups (20 - 30; 31 - 40; 41 - 50 years of age). The experiment was carried out by the Fortunato-Niccolini olfactometric method using six odorous experimental substances: A - anethol, PH - phenyl-ethyl-alcohol, C citral, M - menthol, V- vanillin and P - pyridine, the thresholds of perception (TP) and identification (TI) being defined for each odorous substance. The examined females had slightly lower thresholds of perception (TP) and identification (TI) in relation to the males of the same age group. However, the differences were not statistically significant except for the group of subjects between 41 and 50 years of age where the females, being in the pre-menopause, had significantly better olfactory functions. The results can be explained by the weakening of the olfactory power as a result of ageing in both sexes, however, the females still experienced the protective role of sex hormones.

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Ударно-волновой полиморфный переход в пористом графите

Журнал технической физики ◽

10.21883/jtf.2021.11.51532.139-21 ◽

2021 ◽

Vol 91 (11) ◽

pp. 1707

Author(s):

С.А. Кинеловский

Keyword(s):

Phase Transition ◽

Shock Wave ◽

Elastic Energy ◽

Polymorphic Transformation ◽

Polymorphic Transition ◽

Initial Structure ◽

Graphite Phase ◽

Proposed Model ◽

Porous Graphite ◽

Wide Range

For the polymorphic transformation of porous graphite in the shock, the previously proposed model linking the process of graphite phase transition with a change in the elastic energy of a substance has been tested. It is shown that the model plausibly describes the experimental results outside the transition zone in a fairly wide range of changes in the porosity of samples with their different initial structure. It is discussed how the model under consideration changes the currently existing ideas about the thermodynamics of the polymorphic transition of matter in a shock wave.

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Thermal fractionation of soil organic matter produces fine-scale distributions of SOM age

10.5194/egusphere-egu21-15968 ◽

2021 ◽

Author(s):

Shane Stoner ◽

Carlos Sierra ◽

Marion Schrumpf ◽

Sebastian Dötterl ◽

Susan Trumbore

Keyword(s):

Thermal Stability ◽

Organic Matter ◽

Soil Organic Matter ◽

Chemical Oxidation ◽

Fine Scale ◽

Mineral Association ◽

Density Fractions ◽

Chemical Complexity ◽

Wide Range ◽

Carbon Release

Soil organic matter (SOM) is a complex collection of organic molecules of varying origin, structure, chemical activity, and mineral association. A wide array of laboratory methods exists to separate SOM based on qualitative, biological, chemical, and physical characteristics. However, all present conceptual and logistical limitations, including the requirement of a substantial amount soil material.An newly applied alternative method of fractionation relies on a conceptual analogue between biochemical stability in soil and thermal stability, e.g. more persistent SOM will require higher temperatures (greater energy inputs) to decompose than less persistent SOM. This accounts for both chemical complexity and mineral association as main factors in determining SOM persistence.In this method, carbon is released by heating SOM to 900&#176;C at a constant rate. The peaks of carbon release are grouped into activation energy pools, CO2 is collected, and analyzed for 13C and 14C. We seek to describe in finer detail the distribution of soil radiocarbon by adding another fractionation step following a different paradigm of SOM stability, and explore mineralogical effects on SOM quality and stability using thermal analysis, radiocarbon, and gas chromatography.Here, we analyzed bulk soil and soil fractions derived from density separation and chemical oxidation, as well as mineral horizons dominated by diverse mineralogies. Density fractions contained a wide range of radiocarbon activities and that young SOM is stabilized across multiple fractions, likely due to organomineral complexation. Initial results showed that soil minerals with limited stabilization potential released C at lower temperatures than those with diverse stabilization mechanisms. High-temperature sub-fractions contained the oldest carbon across fractions and minerals, thus supporting the assumption that thermal stability can be used as a limited analogue for stability in soil. We present a fine-scale distribution of radiocarbon in SOM and discuss the potential of this method for comparison with other fractionation techniques.

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