scholarly journals The Impact of Capsid Proteins on Virus Removal and Inactivation during Water Treatment Processes

2015 ◽  
Vol 8s2 ◽  
pp. MBI.S31441 ◽  
Author(s):  
Brooke K. Mayer ◽  
Yu Yang ◽  
Daniel W. Gerrity ◽  
Morteza Abbaszadegan

This study examined the effect of the amino acid composition of protein capsids on virus inactivation using ultraviolet (UV) irradiation and titanium dioxide photocatalysis, and physical removal via enhanced coagulation using ferric chloride. Although genomic damage is likely more extensive than protein damage for viruses treated using UV, proteins are still substantially degraded. All amino acids demonstrated significant correlations with UV susceptibility. The hydroxyl radicals produced during photocatalysis are considered nonspecific, but they likely cause greater overall damage to virus capsid proteins relative to the genome. Oxidizing chemicals, including hydroxyl radicals, preferentially degrade amino acids over nucleotides, and the amino acid tyrosine appears to strongly influence virus inactivation. Capsid composition did not correlate strongly to virus removal during physicochemical treatment, nor did virus size. Isoelectric point may play a role in virus removal, but additional factors are likely to contribute.

2000 ◽  
Vol 66 (4) ◽  
pp. 1354-1359 ◽  
Author(s):  
Liesbeth Rijnen ◽  
Pascal Courtin ◽  
Jean-Claude Gripon ◽  
Mireille Yvon

ABSTRACT The first step of amino acid degradation in lactococci is a transamination, which requires an α-keto acid as the amino group acceptor. We have previously shown that the level of available α-keto acid in semihard cheese is the first limiting factor for conversion of amino acids to aroma compounds, since aroma formation is greatly enhanced by adding α-ketoglutarate to cheese curd. In this study we introduced a heterologous catabolic glutamate dehydrogenase (GDH) gene into Lactococcus lactis so that this organism could produce α-ketoglutarate from glutamate, which is present at high levels in cheese. Then we evaluated the impact of GDH activity on amino acid conversion in in vitro tests and in a cheese model by using radiolabeled amino acids as tracers. The GDH-producing lactococcal strain degraded amino acids without added α-ketoglutarate to the same extent that the wild-type strain degraded amino acids with added α-ketoglutarate. Interestingly, the GDH-producing lactococcal strain produced a higher proportion of carboxylic acids, which are major aroma compounds. Our results demonstrated that a GDH-producing lactococcal strain could be used instead of adding α-ketoglutarate to improve aroma development in cheese.


2013 ◽  
Vol 110 (6) ◽  
pp. 981-987 ◽  
Author(s):  
Atsushi Kanda ◽  
Kyosuke Nakayama ◽  
Tomoyuki Fukasawa ◽  
Jinichiro Koga ◽  
Minoru Kanegae ◽  
...  

It is well known that ingestion of a protein source is effective in stimulating muscle protein synthesis after exercise. In addition, there are numerous reports on the impact of leucine and leucine-rich whey protein on muscle protein synthesis and mammalian target of rapamycin (mTOR) signalling. However, there is only limited information on the effects of whey protein hydrolysates (WPH) on muscle protein synthesis and mTOR signalling. The aim of the present study was to compare the effects of WPH and amino acids on muscle protein synthesis and the initiation of translation in skeletal muscle during the post-exercise phase. Male Sprague–Dawley rats swam for 2 h to depress muscle protein synthesis. Immediately after exercise, the animals were administered either carbohydrate (CHO), CHO plus an amino acid mixture (AA) or CHO plus WPH. At 1 h after exercise, the supplements containing whey-based protein (AA and WPH) caused a significant increase in the fractional rate of protein synthesis (FSR) compared with CHO. WPH also caused a significant increase in FSR compared with AA. Post-exercise ingestion of WPH caused a significant increase in the phosphorylation of mTOR levels compared with AA or CHO. In addition, WPH caused greater phosphorylation of ribosomal protein S6 kinase and eukaryotic initiation factor 4E-binding protein 1 than AA and CHO. In contrast, there was no difference in plasma amino acid levels following supplementation with either AA or WPH. These results indicate that WPH may include active components that are superior to amino acids for stimulating muscle protein synthesis and initiating translation.


2009 ◽  
Vol 37 (1) ◽  
pp. 248-252 ◽  
Author(s):  
Deborah C.I. Goberdhan ◽  
Margret H. Ögmundsdóttir ◽  
Shubana Kazi ◽  
Bruno Reynolds ◽  
Shivanthy M. Visvalingam ◽  
...  

mTOR (mammalian target of rapamycin) plays a key role in determining how growth factor, nutrient and oxygen levels modulate intracellular events critical for the viability and growth of the cell. This is reflected in the impact of aberrant mTOR signalling on a number of major human diseases and has helped to drive research to understand how TOR (target of rapamycin) is itself regulated. While it is clear that amino acids can affect TOR signalling, how these molecules are sensed by TOR remains controversial, perhaps because cells use different mechanisms as environmental conditions change. Even the question of whether they have an effect inside the cell or at its surface remains unresolved. The present review summarizes current ideas and suggests ways in which some of the models proposed might be unified to produce an amino acid detection system that can adapt to environmental change.


2018 ◽  
Author(s):  
Björn F. Koel ◽  
David F. Burke ◽  
Stefan van der Vliet ◽  
Theo M. Bestebroer ◽  
Guus F. Rimmelzwaan ◽  
...  

AbstractWe previously showed that single amino acid substitutions at seven positions in hemagglutinin determined major antigenic change of influenza H3N2 virus. Here, the impact of two such substitutions was tested in eleven representative H3 hemagglutinins to investigate context-dependence effects. The antigenic effect of substitutions introduced at hemagglutinin position 145 was fully independent of the amino acid context of the representative hemagglutinins. Antigenic change caused by substitutions introduced at hemagglutinin position 155 was variable and context-dependent. Our results suggest that epistatic interactions with contextual amino acids in the hemagglutinin can moderate the magnitude of antigenic change.


2018 ◽  
Author(s):  
Jeffrey I. Boucher ◽  
Troy W. Whitfield ◽  
Ann Dauphin ◽  
Gily Nachum ◽  
Carl Hollins ◽  
...  

AbstractThe evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution are interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available dataset of 32,163 sequenced isolates from drug-naïve individuals. The most common amino acids in sequenced isolates supported robust experimental fitness, indicating that the experimental fitness landscape captured key features of selection acting on protease during viral infections of hosts. Amino acid changes requiring multiple mutations from the likely ancestor were slightly less likely to support robust experimental fitness than single mutations, consistent with the genetic code favoring chemically conservative amino acid changes. Amino acids that were common in sequenced isolates were predominantly accessible by single mutations from the likely protease ancestor. Multiple mutations commonly observed in isolates were accessible by mutational walks with highly fit single mutation intermediates. Our results indicate that the prevalence of multiple base mutations in HIV-1 protease is strongly influenced by mutational sampling.


Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 555
Author(s):  
Emily L. Gordon ◽  
Rebecca T. Kimball ◽  
Edward L. Braun

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.


Biology ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 64 ◽  
Author(s):  
Akanksha Pandey ◽  
Edward L. Braun

Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. We focused on a dataset that appeared to have a mixture of signals and we found that the most striking difference in phylogenetic signal reflected relative solvent accessibility. Analyses of exposed sites (residues located on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge+ctenophore clade. These differences in phylogenetic signal were not ameliorated when we conducted analyses using a set of maximum-likelihood profile mixture models. These models are very similar to the Bayesian CAT model, which has been used in many analyses of deep metazoan phylogeny. In contrast, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acid trees estimated using the exposed and buried site both supported placement of ctenophores sister to all other animals. Although the central conclusion of our analyses is that sites in different structural environments yield distinct trees when analyzed using models of protein evolution, our amino acid recoding analyses also have implications for metazoan evolution. Specifically, our results add to the evidence that ctenophores are the sister group of all other animals and they further suggest that the placozoa+cnidaria clade found in some other studies deserves more attention. Taken as a whole, these results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.


2019 ◽  
Author(s):  
Marc Weber ◽  
Raul Burgos ◽  
Eva Yus ◽  
Jae-Seong Yang ◽  
Maria Lluch-Senar ◽  
...  

AbstractThe C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains unknown. Here, we identified C-terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine) while hydrophobic amino acids and threonine are lower. In highly abundant proteins, the C-terminal residue is more conserved. We then studied the impact of C-terminal composition on protein levels in a library of M. pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to 4-fold. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels and is under selective pressure in highly expressed proteins.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 922-922
Author(s):  
Heather N. Colvin ◽  
Elmira Alipour ◽  
Jordan Buzzett ◽  
Glen Marrs ◽  
Daniel B. Kim-Shapiro ◽  
...  

Abstract The capacity of mature red blood cells (RBCs) to respond to oxidative stress is limited due to lack of a full complement of organelles and as such, when faced with an oxidative environment, they rely on their endogenous antioxidant capacity (including superoxide dismutase, catalase, peroxiredoxin and glutathione) to protect against cellular damage. Low blood glutathione activity has been reported in several red cell disorders leading to increased oxidative stress. Targeting oxidative stress has thus been proposed as a secondary treatment in multiple anemia-causing diseases, such as sickle cell disease (SCD) and malaria, although its overall efficacy remains unclear. As glutathione itself is not permeable through the RBC membrane, treatment with cell-permeable amino acid precursors of glutathione (glutamine, cysteine and/or glycine) is a potential strategy to expand the RBC's antioxidant capacity and alleviate oxidative stress. Indeed, L-glutamine has recently been approved as a therapeutic for SCD, although the mechanistic basis for its effect is not clear. To fill this gap in our understanding, we performed detailed characterization of biophysical phenotype, morphology, and intracellular redox environment of oxidatively stressed RBCs in environments with varying amounts of available precursor amino acids. To assess the impact of exogenous amino acid precursors on the RBC's glutathione antioxidant capacity, we exposed mature RBCs from healthy adults to hydrogen peroxide (H 2O 2) and co-incubated with media that included glutamine, cysteine, and/or glycine. As catalase has the ability to scavenge high levels of exogenously fluxed H 2O 2, we performed these experiments using sodium azide to block catalase activity, enabling us to model oxidatively stressed RBCs. We performed osmotic gradient ektacytometry to quantify RBC deformability and hydration status, and assessed RBC morphology using osmotic-adjusted fixation techniques and scanning electron microscopy. As previously documented, H 2O 2 exposure in sodium azide-treated healthy RBCs was associated with decreased deformability, decreased hydration and increased numbers of echinocytes in a dose-dependent manner. We monitored red cell phenotypic changes following co-incubation with glutamine, cysteine, and/or glycine individually and in combination to test whether these amino acids extended the RBC's antioxidant abilities and contributed to improved function and morphology. We found that supplementation with all three amino acids in combination significantly improved both deformability and hydration of H 2O 2-stressed RBCs, as opposed to treatment with glutamine alone. To directly assess whether the exogenous amino acids were in fact contributing to less intracellular oxidative stress in RBCs, we quantified intracellular reactive oxygen species (ROS) using 2', 7' -dichlorofluorescein diacetate (DCFDA), a cell permeable dye used to measure ROS production. As expected, H 2O 2 exposure alone was associated with elevated intracellular ROS inside RBCs in both a time- and dose-dependent manner. Supplementation with the three amino acid cocktail during H 2O 2 stress resulted in a reduction in the level of intracellular ROS activity. In summary, we documented that exogenous added amino acids reduce oxidative damage in RBCs and we hypothesize that this protection occurs via the glutathione antioxidant pathways. In future studies, we plan to investigate the impact of exogenous amino acids on sickled and irreversibly sickled RBCs (ISCs) in the context of SCD, and on uninfected and infected RBCs in the context of malaria. Disclosures Kim-Shapiro: Beverage Operations LLC: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties: co-inventor on a patent related to the use of nitrite under cardiovascular conditions, and a co-author on patents related to treatment of hemolysis.


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