Related papers: Protein Folding and Spin Glass
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
See chem-ph/9505003.
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
We argue that the first order folding transitions of proteins observed at physiological chemical conditions end in a critical point for a given temperature and chemical potential of the surrounding water. We investigate this critical point…
We review phenomenological and microscopic theories of the structural glass transition
Kinetic lattice-gas models display fragile glass behavior, in spite of their trivial Gibbs-Boltzmann measure. This suggests that the nature of glass transition might be, at least in some cases, understood in purely kinetic or dynamical…
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…
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…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Using an effective potential method, a replica formulism is set up for describing supercooled liquids near their glass transition. The resulting potential is equivalent to that for an Ising spin glass in a magnetic field. Results taken from…
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…
Simple theoretical concepts and models have been helpful to understand the folding rates and routes of single-domain proteins. As reviewed in this article, a physical principle that appears to underly these models is loop closure.
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
In an effort to understand the glass transition, the dynamics of a non-randomly frustrated spin model has been analyzed. The phenomenology of the spin model is similar to that of a supercooled liquid undergoing the glass transition. The…
The prediction of protein secondary and tertiary structures from the primary amino acid sequence is both an incredibly important and incredibly difficult problem. Accurate prediction of a protein's native structure can provide critical…
A simple and predictive model is put forward explaining the experimentally observed substantial shift of the glass transition temperature, Tg, of sufficiently thin polymer films. It focuses on the limit of small molecular weight, where…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
I give a very brief non-technical introduction to the intersection of the fields of spin systems and computational complexity. The focus is on spin glasses and their relationship to NP-complete problems.