Fitness spectrum among random mutants on Mt. Fuji-type fitness landscape

Journal of Theoretical Biology
T Aita, Y Husimi

Abstract

Statistical properties of a Mt. Fuji-type fitness landscape on a multi-valued sequence space were analysed. We constructed the model landscape based on additivity of the free energy contributed by each residue on a biopolymer, introducing "tolerance functions" that describe tolerance to residue substitution at each site. The fitness spectrum among a random mutant population around a wild-type sequence was theoretically obtained as the probability density distribution function of fitness. As the Hamming distance from the wild-type to the mutants increases, the mean fitness of the mutant population gradually decreases, and the variance of the fitness increases. These features are originated from the anisotropy of the landscape. On the assumption that the free energy is statistically additive around a wild-type in a sequence space of a real biopolymer, one can estimate the Hamming distance from the wild-type to the optimal biopolymer and the fitness of the optimum. Two sets of experimental data were analysed: (1) a promoter strength spectrum of a mutant population produced by the random mutagenesis of a wild-type lac promoter; (2) four stepwise optimization processes of different peptide mixtures evaluated with ligand binding affi...Continue Reading

Citations

Sep 1, 2002·Journal of Biological Physics·Y HusimiI Tabuchi
May 24, 2014·PLoS Computational Biology·Devin Greene, Kristina Crona
Apr 1, 2014·Molecular Biology and Evolution·Mariona Parera, Miguel Angel Martinez
Nov 15, 2001·Protein Engineering·T AitaY Husimi
Oct 21, 2017·Reports on Progress in Physics·Uri ObolskiLilach Hadany
Jan 27, 1999·Nature Biotechnology·T MatsuuraI Urabe
Dec 17, 2003·FEBS Letters·Koichiro KitamuraKoichi Nishigaki
Jan 3, 2019·Annual Review of Biophysics·Celia BlancoIrene A Chen
Mar 3, 2006·The Journal of Biological Chemistry·Masahiro IwakuraKunihiko Gekko
May 29, 2015·Physical Biology·Michael Manhart, Alexandre V Morozov
Jan 7, 1998·Trends in Biotechnology·O Kuchner, F H Arnold
Mar 27, 2019·Journal of the American Chemical Society·Abe D PressmanIrene A Chen

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.