Protein three-helix bundles

E. M. Boczko and C. L. Brooks III. First principles calculation of the folding free energy of a three helix bundle protein. Science, 269 393-396, 1995. 

Berriz GF, Shakhnovich El. Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model. J Mol Biol 2001 310 673-85. 

Dyer, R.B. Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein. Biochemistry 2004, 43, 3582-3589. 

Trialdehyde Template for the Synthesis of a Three-Helix-Bundle Protein by... 

T. A. Knotts, N. Rathore, and J. J. de Pablo (2005) Structure and stability of a model three-helix-bundle protein on tailored surfaces. Proteins-Structure Function and bioinformatics 61, pp. 385-397... 

The other explanation is the diffusion-collision model in which the secondary structure forms very fast [5,17]. These secondary structure elements then diffuse in a random walk fashion until they collide in the proper way and form the tertiary structure. Islam et al. used this model to analyze the folding of a three helix bundle proteins [17]. 

S. Islam, M. Karpins, D. Weaver (2002) Application of the diffusion-collision model to the folding of three-helix bundle proteins. J. Mol. Biol. 318, pp. 199-215... 

Exploring the Folding Free Energy Surface of a Three-helix Bundle Protein. 

The probability P(TP ig) calculated from (96) can be used to assess the quality of reaction coordinates. For a good reaction coordinate, all transition states, i.e., the states x with large probability P(TP x), should correspond to approximately the same value of the reaction coordinate. Hence, the probability E (TP ) should be a sharply peaked function with a maximum at the transition state value of q. For a poor reaction coordinate, on the other hand, P(TP ) is expected to be rather featureless according to (95), as in this case no strong correlation between the value of q x) and the probability P(TP x) exists. Best and Hummer have successfully used this approach to test reaction coordinates for the folding of a simple three-helix bundle protein and the collective dipole flip of ordered one-dimensional chains of hydrogen-bonded water molecules in narrow carbon nanotubes [261]. 

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