The process of amino acid replacement in proteins is context-dependent, with substitution rates influenced by local structure, functional role, and amino acids at other locations. Predicting how these differences affect replacement processes is difficult. To make such inference easier, it is often assumed that the acceptabilities of different amino acids at a position are constant. However, evolutionary interactions among residue positions will tend to invalidate this assumption. Here, we use simulations of purple acid phosphatase evolution to show that amino acid propensities at a position undergo predictable change after an amino acid replacement at that position. After a replacement, the new amino acid and similar amino acids tend to become gradually more acceptable over time at that position. In other words, proteins tend to equilibrate to the presence of an amino acid at a position through replacements at other positions. Such a shift is reminiscent of the spectroscopy effect known as the Stokes shift, where molecules receiving a quantum of energy and moving to a higher electronic state will adjust to the new state and emit a smaller quantum of energy whenever they shift back down to the original ground state. Predictions ...Continue Reading
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center
Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients
Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models
A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes
Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs
Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex
BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling
Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling
Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins
The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model
Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence
Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints
Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau
Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach
In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus
Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation
Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root
Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates
A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site
Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates
Epistatic contributions promote the unification of incompatible models of neutral molecular evolution
mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria
Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision
Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants
Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Synthetic Genetic Array Analysis
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Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.
Neural Activity: Imaging
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Chronic Fatigue Syndrome
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Cell Atlas of the Human Eye
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STING Receptor Agonists
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