Related papers: Residue mobility has decreased during protein evol…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
The main objective of this work is to shed light on the effect of fiber plasticity on the macroscopic response and domain formation in soft biological composites. This goal is pursued by analyzing the plane-strain response of two-phase…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
The dependence of the scaling properties of the structure factor on space dimensionality, range of interaction, initial and final conditions, presence or absence of a conservation law is analysed in the framework of the large-N model for…
Viral capsids are structurally constrained by interactions amongst the amino acids of the constituting proteins. Therefore, epistasis is expected to evolve amongst sites engaged in physical interactions, and to influence their substitution…
Rigidity is an emergent property of materials - it is not a feature of individual components that comprise the structure, but instead arises from interactions between many constituent parts. Recently, it has been recognized that…
We study translocation of semiflexible polymers driven by force $f_d$ inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time $\tau$ increases with increasing bending rigidity…
Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the stabilities of the proteins increase compared to the…
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
The enhancement of mobility at the surface of an amorphous alloy is studied using a combination of molecular dynamic simulations and normal mode analysis of the non-uniform distribution of Debye-Waller factors. The increased mobility at the…
Artificial neural networks used for reinforcement learning are structurally rigid, meaning that each optimized parameter of the network is tied to its specific placement in the network structure. It also means that a network only works with…
Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Flexibility-rigidity index (FRI) has been developed as a robust, accurate and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and…
The type IV pilus retraction motor is found in many important bacterial pathogens. It is the strongest known linear motor protein and is required for bacterial infectivity. We characterize the dynamics of type IV pilus retraction in terms…
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
We study the influence of filament elasticity on the motion of collective molecular motors. It is found that for a backbone flexibility exceeding a characteristic value (motor stiffness divided through the mean displacement between attached…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…