Related papers: Physical principles underpinning molecular-level p…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
It is a common belief that metamorphic proteins challenge the Anfinsen thermodynamic hypothesis (or dogma). Here we argue against this view aims to show that metamorphic proteins not just fulfill the Anfinsen dogma but also exhibit marginal…
Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will…
The problem of the rate and mechanisms of biological evolution was considered. It was shown that species could not be formed due to undirected mutations in characteristic times of about one million years. A mechanism of deterministic…
We consider a particular instance of the lift of controlled systems recently proposed in the theory of irreversible thermodynamics and show that it leads to a variational principle for an optimal control in the sense of Pontryagin. Then we…
An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple…
Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can…
Proteins display generic properties that are challenging to explain by direct selection, notably allostery, the capacity to be regulated through long-range effects, and evolvability, the capacity to adapt to new selective pressures. An…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
Information is a key concept in evolutionary biology. Information is stored in biological organism's genomes, and used to generate the organism as well as to maintain and control it. Information is also "that which evolves". When a…
Dispersal is a well recognized driver of ecological and evolutionary dynamics, and simultaneously an evolving trait. Dispersal evolution has traditionally been studied in single-species metapopulations so that it remains unclear how…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution…