NDLI: Capillarity-like growth of protein folding nuclei

Content Provider	PubMed Central
Author	Qi, Xianghong Portman, John J.
Abstract	A full structural description of transition state ensembles in protein folding includes the specificity of the ordered residues composing the folding nucleus as well as spatial density. To our knowledge, the spatial properties of the folding nucleus and interface of specific nuclei have yet to receive significant attention. We analyze folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory that assumes the volume of the folded core of the nucleus grows with chain length as V f ≈ N 3ν. For 27 two-state proteins studied, the scaling exponent ν ranges from 0.2 to 0.45 with an average of 0.33. This average value corresponds to packing of rigid objects, although generally the effective monomer size in the folded core is larger than the corresponding volume per particle in the native-state ensemble. That is, on average, the folded core of the nucleus is found to be relatively diffuse. We also study the growth of the folding nucleus and interface along the folding route in terms of the density or packing fraction. The evolution of the folded core and interface regions can be classified into three patterns of growth depending on how the growth of the folded core is balanced by changes in density of the interface. Finally, we quantify the diffuse versus polarized structure of the critical nucleus through direct calculation of the packing fraction of the folded core and interface regions. Our results support the general picture of describing protein folding as the capillarity-like growth of folding nuclei.
Related Links	http://dx.doi.org/10.1073/pnas.0711527105
Starting Page	11164
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	32
Volume Number	105
Language	English
Publisher	National Academy of Sciences
Publisher Date	2008-08-12
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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