Related papers: Sensitivity of protein rigidity analysis to small …
The paper presents a systematic approach for stiffness modeling of manipulators with complex and hybrid structures using matrix structural analysis. In contrast to previous results, it is suitable for mixed architectures containing…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
When a thin elastic sheet crumples, the elastic energy condenses into a network of folding lines and point vertices. These folds and vertices have elastic energy densities much greater than the surrounding areas, and most of the work…
The rigidity and flexibility of homologous psychrophilic(P), mesophilic(M) and thermophilic(T) proteins have been investigated at the global and local levels in terms of packing factor and atomic fluctuations obtained from B-factors. For…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
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…
Many mechanical structures, both engineered and biological, combine heavy rigid elements such as bones and beams with lightweight flexible ones such as cables and membranes. These are referred to as tensegrities, reflecting that cables can…
The characterization of protein-nanoparticle assemblies in solution remains a challenge. We demonstrate a technique based on a graphene microelectrode for structural-functional analysis of model systems composed of nanoparticles enclosed in…
Collagen fibrils, cable-like assemblies of long biological molecules, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Elastoplastic lattice models for the response of solids to deformation typically incorporate structure only implicitly via a local yield strain that is assigned to each site. However, the local yield strain can change in response to a…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
This paper presents a set of general strategies for the analysis of structure in amorphous materials and a general approach to assessing the utility of a selected structural description. Measures of structural diversity and utility are…
Successful adaptation helped the emergence of complexity. Alternating plastic- and rigid-like states were recurrently considered to play a role in adaptive processes. However, this extensive knowledge remained fragmented. In this paper I…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
The sliding friction force exerted by stochastic linkers interacting with a moving filament is calculated. The elastic properties of the substrate on which the linkers are anchored are shown to strongly influence the friction force. In some…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…