We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilizing interactions, and folding rates themselves, leads to a model of the energy hypersurface that is characterized by the structure of diffusive "hypergutters" as well as the familiar "funnels". Several general predictions result: 1), intermediate ...

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein...

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein...

Do stable intermediates form very early in the protein folding process? New results and a quantity of literature that bear on this issue are examined here. Results available provide little support for early intermediate accumulation before an initial search-dependent nucleation barrier.

Analysis of individual RNA folding reactions reveals that, as in proteins, cooperative interactions selectively drive RNA toward its biologically active, native conformation. This new work establishes a platform for future investigations of the physical principles underlying the assembly of large RNA enzymes.

Fix an n ≥ 3. Consider the following two operations: given a line with a specified point on the line we can construct a new line through the point which forms an angle with the new line which is a multiple of π/n (folding); and given two lines we can construct the point where they cross (intersection). Starting with the line y = 0 and the points (0, 0) and (1, 0) we determine which points in th...

Biological and technological systems process information by means of cascades of signals. Be they interacting genes, spiking neurons or electronic transistors, information travels across these systems, producing, for each set of external conditions, an appropriate response. In technology, circuits performing specific complex tasks are designed by humans. In biology, however, design has to be ru...

A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational pr...

The GroE chaperones of Escherichia coli promote the folding of other proteins under conditions where no spontaneous folding occurs. One requirement for this reaction is the trapping of the nonnative protein inside the chaperone complex. Encapsulation may be important to prevent unfavorable intermolecular interactions during folding. We show here that, especially for oligomeric proteins, the tim...

We use infrared spectroscopy to study the evolution of protein folding intermediate structures on arbitrarily slow time scales by rapidly quenching thermally unfolded hen egg white lysozyme in a glassy matrix, followed by reheating of the protein to refold; upon comparison with differential scanning calorimetric experiments, low-temperature structural changes that precede the formation of energ...