Few Ramachandran Angle Changes Provide Interaction Strength Increase in Aβ42 versus Aβ40 Amyloid Fibrils

Bastidas, Oscar; Green, Ben; Sprague, M.; Peters, Michael

doi:10.1038/srep36499

Cited by 5 publications

(3 citation statements)

References 45 publications

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“…This has become a scarce and expensive resource. As a consequence, levels of EPA and DHA in farmed fish have fallen considerably since 2006, such that at least two servings/week of farmed salmon are now required to deliver 250 mg/day of EPA and DHA 12 .…”

Section: Introductionmentioning

confidence: 99%

Omega-3 index and blood pressure responses to eating foods naturally enriched with omega-3 polyunsaturated fatty acids: a randomized controlled trial

Stanton

James

Brennan

et al. 2020

Sci Rep

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Diets low in seafood omega-3 polyunsaturated fatty acids (PUFAs) are very prevalent. Such diets have recently been ranked as the sixth most important dietary risk factor—1.5 million deaths and 33 million disability-adjusted life-years worldwide are attributable to this deficiency. Wild oily fish stocks are insufficient to feed the world’s population, and levels of eicosapentaenoic acid and docosahexaenoic acid (DHA) in farmed fish have more than halved in the last 20 years. Here we report on a double-blinded, controlled trial, where 161 healthy normotensive adults were randomly allocated to eat at least three portions/week of omega-3-PUFA enriched (or control) chicken-meat, and to eat at least three omega-3-PUFA enriched (or control) eggs/week, for 6 months. We show that regular consumption of omega-3-PUFA enriched chicken-meat and eggs significantly increased the primary outcome, the red cell omega-3 index (mean difference [98.75% confidence interval] from the group that ate both control foods, 1.7% [0.7, 2.6]). Numbers of subjects with a very high-risk omega-3 index (index < 4%) were more than halved amongst the group that ate both enriched foods. Furthermore, eating the enriched foods resulted in clinically relevant reductions in diastolic blood pressure (− 3.1 mmHg [− 5.8, − 0.3]). We conclude that chicken-meat and eggs, naturally enriched with algae-sourced omega-3-PUFAs, may serve as alternative dietary sources of these essential micronutrients. Unlike many lifestyle interventions, long-term population health benefits do not depend on willingness of individuals to make long-lasting difficult dietary changes, but on the availability of a range of commonly eaten, relatively inexpensive, omega-3-PUFA enriched foods.

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Section: Introductionmentioning

confidence: 99%

Omega-3 index and blood pressure responses to eating foods naturally enriched with omega-3 polyunsaturated fatty acids: a randomized controlled trial

Stanton

James

Brennan

et al. 2020

Sci Rep

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“…Secondary structures of protein isolates were significantly affected by extraction pH. The α‐helical structure of proteins could be stabilized by the hydrogen bonds between carbonyl oxygen and amino hydrogen, 19 and the electrostatic interaction between amino acids 20 . CD spectra of all the extracted proteins exhibited two negative peaks at 222 and 208 nm, which are the predominant signals of α‐helical structure 21 .…”

Section: Resultsmentioning

confidence: 99%

Protein extraction pH and cross‐linking affect physicochemical and textural properties of protein gels made from channel catfish by‐products

Tan

Chang

2021

J Sci Food Agric

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BACKGROUND Channel catfish farming is very important aquaculture industry in the southern states of the USA. However, huge amounts of by‐products are generated from catfish fillet‐processing. The by‐products (mostly heads and bone frames) are excellent sources of proteins. Currently, catfish by‐product has little value, and is regarded as a ‘waste’, which if not utilized properly could cause serious environmental pollution. Therefore, to find a way to utilize those by‐products is critical for the economy of aquaculture. METHOD Protein isolates were extracted from the mixture of catfish by‐products (heads and frames) under different alkaline conditions (pH 7.5–11) and made into protein gels. Secondary structures of extracted protein isolates were studied. Microbial transglutaminase (MTGase, 0–4 U g–1 proteins) was incorporated to improve gel structure. Gelling, physicochemical, textural and thermal properties of protein gels treated with/without MTGase were investigated. Protein pattern changes of MTGase‐treated protein gels were studied and the microstructure of the protein gels was analyzed. RESULTS Alpha‐helicity of protein isolates made at pH 11 was 21.5% lower than that extracted at pH 8.5. Storage modulus (G′) of protein gel decreased with increasing extraction pH (pH > 9) of the corresponding protein isolate. MTGase treatment exhibited significant effects on denaturation temperature and enthalpy of protein gels. Excessive MTGase (>2 U g–1) could weaken the gel structure. CONCLUSION Protein isolates can be extracted from catfish by‐products and made into protein gels, which are a value‐added product. © 2021 Society of Chemical Industry

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“…Following our recently published study on Aβ 42 amyloid fibrils [ 10 ], we analyzed the recently published trimeric structures of SARS-CoV-2 Spike protein (S) (PDB ID’s: 6VSB and 6VYB) according to the Coulombic (charge and partial atomic charge) and Lennard-Jones (Born and van der Waals forces) atom-atom interaction forces as laid out in the open-source energy mapping algorithm developed by Krall et al [ 11 ]. This mapping algorithm efficiently parses the strongest non-covalent atom-atom interactions and their inter-atomic distances from structure file data according to empirically established criteria based on the AMBER 03 force field model to ensure that all dominant interactions are accounted for.…”

Section: Methodsmentioning

confidence: 99%

Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of “Up” versus “Down” protomer states

et al. 2020

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The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion.

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Few Ramachandran Angle Changes Provide Interaction Strength Increase in Aβ42 versus Aβ40 Amyloid Fibrils

Cited by 5 publications

References 45 publications

Omega-3 index and blood pressure responses to eating foods naturally enriched with omega-3 polyunsaturated fatty acids: a randomized controlled trial

Omega-3 index and blood pressure responses to eating foods naturally enriched with omega-3 polyunsaturated fatty acids: a randomized controlled trial

Protein extraction pH and cross‐linking affect physicochemical and textural properties of protein gels made from channel catfish by‐products

Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of “Up” versus “Down” protomer states

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