103 citations · 749 across the 31 of their papers we have counts for
31 papers
Funnel-like protein energy landscapes emerge from functional evolution under thermal fluctuations
Norifumi Maruyama, Macoto Kikuchi
Foldable proteins exhibit funnel-like energy landscapes, but their evolution under selection for function remains unclear. We study this in a lattice protein model, defining fitnes…
Phenotype selection due to mutational robustness
Macoto Kikuchi
The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. W…
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
Tadamune Kaneko, Macoto Kikuchi
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene reg…
Emergence of cooperative bistability and robustness of gene regulatory networks
Shintaro Nagata, Macoto Kikuchi
Gene regulatory networks (GRNs) are complex systems in which many genes regulate mutually to adapt the cell state to environmental conditions. In addition to function, the GRNs pos…
The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation
Nobu C. Shirai, Macoto Kikuchi
α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly c…
Structural flexibility of intrinsically disordered proteins induces stepwise target recognition
Nobu C. Shirai, Macoto Kikuchi
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-targe…