Converting Amino Acid Alignment Scores into Measures of Evolutionary Time: A Simulation Study of Various Relationships

1997 ◽  
Vol 44 (4) ◽  
pp. 361-370 ◽  
Author(s):  
Da-Fei Feng ◽  
Russell F. Doolittle
Keyword(s):  
Amino Acid ◽  
Simulation Study ◽  
Evolutionary Time ◽  
Amino Acid Alignment

scholarly journals NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Philip L. Tzou ◽  
Xiaoqiu Huang ◽  
Robert W. Shafer
Keyword(s):  
Amino Acid ◽  
Gene Sequences ◽  
Virus Gene ◽  
Amino Acid Alignment

scholarly journals ERG11 Polymorphism in Voriconazole-Resistant Candida tropicalis: Weak Role of ERG11 Expression, Ergosterol Content, and Membrane Permeability

2020 ◽  
Vol 65 (1) ◽  
pp. e00325-20
Author(s):  
Patricia Navarro-Rodríguez ◽  
Loida López-Fernández ◽  
Adela Martin-Vicente ◽  
Josep Guarro ◽  
Javier Capilla
Keyword(s):  
Amino Acid ◽  
Membrane Permeability ◽  
Candida Tropicalis ◽  
Gene Sequencing ◽  
Missense Mutations ◽  
Sterol Content ◽  
Content Type ◽  
Ergosterol Content ◽  
Amino Acid Alignment

ABSTRACTMutations in ERG11 were detected by gene sequencing and amino acid alignment in 18 Candida tropicalis strains with different degrees of sensitivity to voriconazole (VRC). ERG11 expression, sterol content, and membrane permeability were also evaluated. We report three missense mutations in ERG11 that resulted in resistance to VRC. The transcriptional levels of ERG11 as well as the ergosterol content and membrane permeability demonstrated no correlation to only a slight correlation with the obtained MIC values, but the data did suggest a tendency toward such a correlation.

scholarly journals Evolutionary Profile for (Host and Viral) MLKL Indicates Its Activities as a Battlefront for Extensive Counteradaptation

2021 ◽  
Author(s):  
Suzette N Palmer ◽  
Sruthi Chappidi ◽  
Chelsea Pinkham ◽  
Dustin C Hancks
Keyword(s):  
Amino Acid ◽  
Rapid Evolution ◽  
Amino Acid Replacement ◽  
Vital Role ◽  
Evolutionary Time ◽  
Cytokine Induction ◽  
Regulated Cell Death ◽  
Mouse Cells ◽  
Selection For ◽  
Human And Mouse

Abstract Pathogen infection triggers host innate defenses which may result in the activation of regulated cell death (RCD) pathways such as apoptosis. Given a vital role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptosis. Yet, it is unclear whether components of this emerging RCD pathway display signatures associated with pathogen conflict that are rare in combination but common to key host defense factors, namely, rapid evolution, viral homolog (virolog), and cytokine induction. We leveraged evolutionary sequence analysis that examines rates of amino acid replacement, which revealed: 1) strong and recurrent signatures of positive selection for primate and bat RIPK3 and MLKL, and 2) elevated rates of amino acid substitution on multiple RIPK3/MLKL surfaces suggestive of past antagonism with multiple, distinct pathogen-encoded inhibitors. Furthermore, our phylogenomics analysis across poxvirus genomes illuminated volatile patterns of evolution for a recently described MLKL viral homolog. Specifically, poxviral MLKLs have undergone numerous gene replacements mediated by duplication and deletion events. In addition, MLKL protein expression is stimulated by interferons in human and mouse cells. Thus, MLKL displays all three hallmarks of pivotal immune factors of which only a handful of factors like OAS1 exhibit. These data support the hypothesis that over evolutionary time MLKL functions—which may include execution of necroptosis—have served as a major determinant of infection outcomes despite gene loss in some host genomes.

Investigating the adsorption mechanism of glycine in comparison with catechol on cristobalite surface using density functional theory for bio-adhesive materials

RSC Advances ◽  
2016 ◽  
Vol 6 (115) ◽  
pp. 114313-114319 ◽  
Author(s):  
Shabeer Ahmad Mian ◽  
Younas Khan ◽  
Uzair Ahmad ◽  
Mohammad Adil Khan ◽  
Gul Rahman ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Amino Acid ◽  
Simulation Study ◽  
Density Functional ◽  
Adsorption Mechanism ◽  
Functional Theory ◽  
Adhesive Materials

Amino acid proteins exist in Mussel's adhesive (mefp's) of which glycine has a significant amount. A density functional theory simulation study was performed in a belief that all the proteins in mefp's are responsible for the versatile adhesion.

scholarly journals A Molecular Dynamics Simulation Study of Two Dipeptide Based Molecular Micelles: Effect of Amino Acid Order

2013 ◽  
Vol 03 (01) ◽  
pp. 20-29 ◽  
Author(s):  
Kevin F. Morris ◽  
Eugene J. Billiot ◽  
Fereshteh H. Billiot ◽  
Kenny B. Lipkowitz ◽  
William M. Southerland ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation
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