Related papers: Critical fluctuations in proteins native states
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Passive mechanical response of skeletal muscles at fast time scales is dominated by long range interactions inducing cooperative behavior without breaking the detailed balance. This leads to such unusual "material properties" as negative…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Proteins are regularly described with some general indices (mass fractal dimension, surface fractal dimension, entropy, enthalpy, free energies, hydrophobicity, denaturation temperature etc..), which are inherently statistical in nature.…
The exploration of the rich dynamics of electrons is a frontier in fundamental nano-physics. The dynamical behavior of electrons is dominated by random and chaotic thermal motion with ultrafast ($\approx$ ps) and nanoscale scatterings. This…
We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a…
There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are…
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…
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…
A mass ejection model in a time-dependent random environment with both temporal and spatial correlations is introduced. When the environment has a finite correlation length, individual particle trajectories are found to diffuse at large…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
Microstructural dynamics in amorphous particle packings is commonly probed by quantifying particle displacements. While rigidity in particle packings emerges when displacement of particles are hindered, it is not obvious how the typically…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
We investigate magnetic fluctuations of a mesoscopic critical region at the interface induced by smooth time-independent spacial changes of a control parameter across its critical value. Near the spatial critical point, the order parameter…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…