Related papers: Residue mobility has decreased during protein evol…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…
Fragility index and cooperativity length characterizing the molecular mobility in the amorphous phase are for the first time calculated in drawn polylactide (PLA). The microstructure of the samples is investigated from wide-angle X-ray…
The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…
Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a non-uniform force F(y). We considered linear-gradient, parabolic and delta-like driving-force profiles.…
Grain structure plays a key role in the mechanical properties of alloy materials. Engineering the grain structure requires a comprehensive understanding of the evolution of grain boundaries (GBs) when a material is subjected to various…
Skeletal muscle modeling has a vital role in movement studies and the development of therapeutic approaches. In the current study, a Huxley-based model for skeletal muscle is proposed, which demonstrates the impact of impairments in muscle…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
Liberal evolution of interacting binaries has been proposed previously by several authors in order to meet various observed binary characteristics better than conservative evolution does. Since Algols are eclipsing binaries the distribution…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
Protein flexibility, measured by the B-factor or Debye-Waller factor, is essential for protein functions such as structural support, enzyme activity, cellular communication, and molecular transport. Theoretical analysis and prediction of…
Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
The elastic properties of the $B_1$-structured transition-metal nitrides and their carbide counterparts are studied using the {\it ab initio\} density functional perturbation theory. The linear response results of elastic constants are in…
Unstable systems of fluidized grains in a very-narrow vertical tube can auto-defluidize after some time, the settling particles forming either a glass- or crystal-like structure. We carried out experiments using different polymer spheres,…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
Through experiments, we idealise a plant leaf as a flexible, thin, rectangular plate clamped at the midpoint and positioned perpendicular to an airflow. Flexibility of the structure is considered as an advantage at moderate flow speed…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…