- 著者
- Akira R. Kinjo
- 出版者
- The Biophysical Society of Japan
- 雑誌
- Biophysics and Physicobiology (ISSN:21894779)
- 巻号頁・発行日
- vol.12, pp.117-119, 2015 (Released:2015-12-11)
- 参考文献数
- 16
- 被引用文献数
- 1 1
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract “direct” correlations between distant sites that are latent in “indirect” correlations observed in a protein multiple-sequence alignment. I show that the direct correlation can be obtained by using a formulation analogous to the Ornstein-Zernike integral equation in liquid theory. This formulation intuitively illustrates how the indirect or apparent correlation arises from an infinite series of direct correlations, and provides interesting insights into protein structure prediction.
- 著者
- Ken Nishikawa Akira R. Kinjo
- 出版者
- 日本生物物理学会
- 雑誌
- BIOPHYSICS (ISSN:13492942)
- 巻号頁・発行日
- vol.10, pp.99-108, 2014 (Released:2014-12-17)
- 参考文献数
- 50
- 被引用文献数
- 1 12
We propose the cooperative model of phenotype-driven evolution, in which natural selection operates on a phenotype caused by both genetic and epigenetic factors. The conventional theory of evolutionary synthesis assumes that a phenotypic value (P) is the sum of genotypic value (G) and environmental deviation (E), P=G+E, where E is the fluctuations of the phenotype among individuals in the absence of environmental changes. In contrast, the cooperative model assumes that an evolution is triggered by an environmental change and individuals respond to the change by phenotypic plasticity (epigenetic changes). The phenotypic plasticity, while essentially qualitative, is denoted by a quantitative value F which is modeled as a normal random variable like E, but with a much larger variance. Thus, the fundamental equation of the cooperative model is given as P=G+F where F includes the effect of E. Computer simulations using a genetic algorithm demonstrated that the cooperative model realized much faster evolution than the evolutionary synthesis. This accelerated evolution was found to be due to the cumulative evolution made possible by a ratchet mechanism due to the epigenetic contribution to the phenotypic value. The cooperative model can well account for the phenomenon of genetic assimilation, which, in turn, suggests the mechanism of cumulative selection. The cooperative model may also serve as a theoretical basis to understand various ideas and phenomena of the phenotypedriven evolution such as genetic assimilation, the theory of facilitated phenotypic variation, and epigenetic inheritance over generations.
- 著者
- Akira R. Kinjo
- 出版者
- 一般社団法人 日本生物物理学会
- 雑誌
- Biophysics and Physicobiology (ISSN:21894779)
- 巻号頁・発行日
- vol.13, pp.45-62, 2016 (Released:2016-04-22)
- 参考文献数
- 33
- 被引用文献数
- 8
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interactions, I analyzed the globin and V-set domains by increasing the “temperature” and by “mutating” a site. The correlations between residue conservation and various measures of the system’s stability indicate that the long-range interactions make the conservation pattern more specific to the structure, and increasingly stabilize better conserved residues.