Improved mitochondrial amino acid substitution models for metazoan evolutionary studies [PDF]
BMC Evolutionary Biology, 2017 Background Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species.
Vinh Sy Le, Cuong Cao Dang, Quang Si Le
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CodonTest: modeling amino acid substitution preferences in coding sequences. [PDF]
PLoS Computational Biology, 2010 Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged.
Wayne Delport +5 more
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nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models. [PDF]
Syst Biol, 2022 Abstract Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality.
Dang CC +6 more
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PON-All: Amino Acid Substitution Tolerance Predictor for All Organisms [PDF]
Frontiers in Molecular Biosciences, 2022 Genetic variations are investigated in human and many other organisms for many purposes (e.g., to aid in clinical diagnosis). Interpretation of the identified variations can be challenging.
Yang Yang +3 more
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The amino acid substitution affects cellular response to mistranslation [PDF]
G3: Genes, Genomes, Genetics, 2021 Mistranslation, the misincorporation of an amino acid not specified by the “standard” genetic code, occurs in all organisms. tRNA variants that increase mistranslation arise spontaneously and engineered tRNAs can achieve mistranslation frequencies ...
Matthew D Berg +10 more
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AI‐Based D‐Amino Acid Substitution for Optimizing Antimicrobial Peptides to Treat Multidrug‐Resistant Bacterial Infection [PDF]
Advanced ScienceD‐amino acid substitution provides an effective strategy for optimizing antimicrobial peptides (AMPs) by enhancing their stability. However, the absence of universal rules renders traditional screening methods time‐consuming and labor‐intensive ...
Yinuo Zhao +14 more
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A single amino acid substitution in SED-2 β-lactamase leads to increased inhibitor resistance and an extended substrate spectrum [PDF]
Microbiology Spectrumβ-Lactamases are the leading mechanism of resistance to β-lactam antibiotics in Enterobacterales. Here, we report the detection and characteristics of SED-2, a new member of the Citrobacter sedlakii class A chromosomal β-lactamase SED family.
S. Laviad-Shitrit +11 more
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Creation of photocyclic vertebrate rhodopsin by single amino acid substitution [PDF]
eLife, 2022 Opsins are universal photoreceptive proteins in animals and can be classified into three types based on their photoreaction properties. Upon light irradiation, vertebrate rhodopsin forms a metastable active state, which cannot revert back to the original
Kazumi Sakai +3 more
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Reduced purine biosynthesis in humans after their divergence from Neandertals
eLife, 2021 We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other ...
Vita Stepanova +25 more
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Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. [PDF]
PLoS Computational Biology, 2008 Substitutions of individual amino acids in proteins may be under very different evolutionary restraints depending on their structural and functional roles. The Environment Specific Substitution Table (ESST) describes the pattern of substitutions in terms
Sungsam Gong, Tom L Blundell
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