Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties
Sign Up to like & getrecommendations! Published in 2022 at "ACS Chemical Biology"
DOI: 10.1021/acschembio.2c00318
Abstract: Protein-based nanoparticles are useful models for the study of self-assembly and attractive candidates for drug delivery. Virus-like particles (VLPs) are especially promising platforms for expanding the repertoire of therapeutics that can be delivered effectively as… read more here.
Keywords: like particles; fitness landscape; surface; landscape ... See more keywords
Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA
Sign Up to like & getrecommendations! Published in 2019 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.8b13298
Abstract: Molecular evolution can be conceptualized as a walk over a “fitness landscape”, or the function of fitness (e.g., catalytic activity) over the space of all possible sequences. Understanding evolution requires knowing the structure of the… read more here.
Keywords: self aminoacylating; ribozyme; landscape; fitness landscape ... See more keywords
Epistasis shapes the fitness landscape of an allosteric specificity switch
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-25826-7
Abstract: Epistasis is a major determinant in the emergence of novel protein function. In allosteric proteins, direct interactions between inducer-binding mutations propagate through the allosteric network, manifesting as epistasis at the level of biological function. Elucidating… read more here.
Keywords: fitness landscape; allosteric proteins; epistasis shapes; specificity ... See more keywords
Inferring the intrinsic mutational fitness landscape of influenzalike evolving antigens from temporally ordered sequence data.
Sign Up to like & getrecommendations! Published in 2022 at "Physical review. E"
DOI: 10.1103/physreve.105.024401
Abstract: There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. To find such… read more here.
Keywords: mutational fitness; fitness landscape; sequence; fitness ... See more keywords
Local Fitness Landscape Exploration Based Genetic Algorithms
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Access"
DOI: 10.1109/access.2023.3234775
Abstract: Genetic algorithms (GAs) have been used to evolve optimal/sub-optimal solutions of many problems. When using GAs for evolving solutions, often fitness evaluation is the most computationally expensive, and this discourages researchers from applying GAs for… read more here.
Keywords: landscape exploration; fitness; fitness landscape; multi objective ... See more keywords
Mapping the in vivo fitness landscape of a tethered ribosome
Sign Up to like & getrecommendations! Published in 2023 at "Science Advances"
DOI: 10.1126/sciadv.ade8934
Abstract: Fitness landscapes are models of the sequence space of a genetic element that map how each sequence corresponds to its activity and can be used to guide laboratory evolution. The ribosome is a macromolecular machine… read more here.
Keywords: vivo fitness; fitness landscape; mapping vivo; tethered ribosome ... See more keywords
Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability
Sign Up to like & getrecommendations! Published in 2017 at "BMC Bioinformatics"
DOI: 10.1186/s12859-017-1608-x
Abstract: BackgroundThe canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its… read more here.
Keywords: code; fitness; canonical code; fitness landscape ... See more keywords
Exploring the sequence fitness landscape of a bridge between protein folds
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DOI: 10.1371/journal.pcbi.1008285
Abstract: Most foldable protein sequences adopt only a single native fold. Recent protein design studies have, however, created protein sequences which fold into different structures apon changes of environment, or single point mutation, the best characterized… read more here.
Keywords: protein; exploring sequence; fitness landscape;
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
Sign Up to like & getrecommendations! Published in 2021 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1008596
Abstract: The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism… read more here.
Keywords: aero types; biology; fitness; fitness landscape ... See more keywords
Rare-event sampling analysis uncovers the fitness landscape of the genetic code
Sign Up to like & getrecommendations! Published in 2022 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1011034
Abstract: The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear… read more here.
Keywords: genetic code; fitness landscape; rare event; event sampling ... See more keywords
Predicting Egg Passage Adaptations to Design Better Vaccines for the H3N2 Influenza Virus
Sign Up to like & getrecommendations! Published in 2022 at "Viruses"
DOI: 10.3390/v14092065
Abstract: Seasonal H3N2 influenza evolves rapidly, leading to an extremely poor vaccine efficacy. Substitutions employed during vaccine production using embryonated eggs (i.e., egg passage adaptation) contribute to the poor vaccine efficacy (VE), but the evolutionary mechanism… read more here.
Keywords: h3n2 influenza; virus; fitness landscape; passage ... See more keywords