相关论文: The role of topology on protein thermal stability

Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…

We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…

Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we…

The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method…

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…

We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…

Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…

The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…

Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…

A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…

We compute the topological entropy of the toric code models in arbitrary dimension at finite temperature. We find that the critical temperatures for the existence of full quantum (classical) topological entropy correspond to the…

Topological entanglement entropy is a topological invariant which can detect topological order of quantum many-body ground state. We assume an existence of such order parameter at finite temperature which is invariant under smooth…

Production of heat shock proteins are induced when a living cell is exposed to a rise in temperature. The heat shock response of protein DnaK synthesis in E.coli for temperature shifts from temperature T to T plus 7 degrees, respectively to…

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…

What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…

Temperature fluctuations of a finite system follows the Landau bound $\delta T^2 = T^2/C(T)$ where $C(T)$ is the heat capacity of the system. In turn, the same bound sets a limit to the precision of temperature estimation when the system…

The impact of temperature-induced deformations and shape fluctuations on the particle stability and decay processes has been investigated across the isotopes of hot nuclear systems with $Z = 28$ to $50$, with focus on astrophysically…