Abstract:
:We present a method for calculating the configurational-dependent diffusion coefficient of a globular protein as a function of the global folding process. Using a coarse-grained structure-based model, we determined the diffusion coefficient, in reaction coordinate space, as a function of the fraction of native contacts formed Q for the cold shock protein (TmCSP). We find nonmonotonic behavior for the diffusion coefficient, with high values for the folded and unfolded ensembles and a lower range of values in the transition state ensemble. We also characterized the folding landscape associated with an energetically frustrated variant of the model. We find that a low-level of frustration can actually stabilize the native ensemble and increase the associated diffusion coefficient. These findings can be understood from a mechanistic standpoint, in that the transition state ensemble has a more homogeneous structural content when frustration is present. Additionally, these findings are consistent with earlier calculations based on lattice models of protein folding and more recent single-molecule fluorescence measurements.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Oliveira RJ,Whitford PC,Chahine J,Wang J,Onuchic JN,Leite VBdoi
10.1016/j.bpj.2010.04.041subject
Has Abstractpub_date
2010-07-21 00:00:00pages
600-8issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(10)00539-4journal_volume
99pub_type
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