How native state topology affects the folding of Dihydrofolate Reductase and Interleukin-1beta

Abstract

The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The predictive power of these models suggest that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed and much of the structural heterogeneity observed in the intermediates and the transition state ensembles is determined by topological effects.

Proc. Natl. Acad. Sci. USA, in press (11 pages, 4 color PS figures) Higher resolution PS files can be found at http://www-physics.ucsd.edu/~cecilia/pub_list.html

References in corpus (1)

• Protein structures and optimal folding emerging from a geometrical variational principle

Cited by in corpus (13)

• Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models
• Investigation of routes and funnels in protein folding by free energy functional methods
• Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin
• Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding
• Exact Partition Function Zeros of the Wako-Saito-Muñoz-Eaton Protein Model
• Buffed energy landscapes: Another solution to the kinetic paradoxes of protein folding
• Effective potentials for Folding Proteins
• Mean Field Approach for a Statistical Mechanical Model of Proteins
• Solvation Effects and Driving Forces for Protein Thermodynamic And Kinetic Cooperativity: How Adequate Is Native-Centric Topological Modeling?
• Unbiased simulation of structural transitions in calmodulin
• Folding of a Small Helical Protein Using Hydrogen Bonds and Hydrophobicity Forces
• Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition
• Energetic frustrations in protein folding at residue resolution: a simulation study of homologous immunoglobulin-like \b{eta}-sandwich proteins