Related papers: Sidechain Dynamics and Protein Folding
In this study, one-dimensional systems of masses connected by springs, i.e., spring-chain systems, are investigated numerically. The average kinetic energy of chain-end particles of these systems is larger than that of other particles,…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
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…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
We investigate the relation between backbone and side-chain ordering in a small protein. For this purpos e we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used to y model in protein studies.…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
A hierarchy of timescales is ubiquitous in biological systems, where enzymatic reactions play an important role because they can hasten the relaxation to equilibrium. We introduced a statistical physics model of interacting spins that also…
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…
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…
An adiabatic transition between two equilibrium states corresponding to different stiffnesses in an infinite chain of particles is studied. Initially, the chain particles have random displacements and random velocities corresponding to a…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…