Related papers: Are proteins ultrametric?
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
Following a review of metric, ultrametric and generalized ultrametric, we review their application in data analysis. We show how they allow us to explore both geometry and topology of information, starting with measured data. Some themes…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
As protein informatics advances rapidly, the demand for enhanced predictive accuracy, structural analysis, and functional understanding has intensified. Transformer models, as powerful deep learning architectures, have demonstrated…
Mathematical diffraction theory is concerned with the analysis of the diffraction image of a given structure and the corresponding inverse problem of structure determination. In recent years, the understanding of systems with continuous and…
In cell membranes, proteins and lipids are organized into sub-micrometric nanodomains of varying size, shape and composition, performing specific functions. Despite their biological importance, the detailed morphology of these nanodomains…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins…
Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types…
Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion…
An ultrametric topology formalizes the notion of hierarchical structure. An ultrametric embedding, referred to here as ultrametricity, is implied by a hierarchical embedding. Such hierarchical structure can be global in the data set, or…