Related papers: Comparative analysis of rigidity across protein fa…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
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…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
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…
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
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…
Adhesion is a fundamental phenomenon that plays a role in many engineering and biological applications. This paper concerns the use of machine learning to characterize the effective adhesive properties when a thin film is peeled from a…
While cracking is a complex dynamics that involves material intrinsic properties like grain shape and size distribution, elastic properties of grain and cementing materials, and extrinsic properties of loading, in this work, the focus has…
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.…
Understanding the mechanical behaviour of bones up to failure is necesary for diagnosis and prevention of accident and trauma. As far as we know, no authors have yet studied the tensile behaviour of compact bone including failure under…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
Hydrogels have the ability to undergo large deformations and yet fail like brittle materials. The development of biocompatible hydrogels with high strength and toughness is an ongoing challenge in many applications. We crosslinked bovine…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…