Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 334, Issue 2, Pages 309-325Publisher
ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2003.09.047
Keywords
bacteriophage lambda protein W; SH3 domain; alpha beta-plait; immunity protein; acyl-coenzyme A-binding protein
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Funding
- NIGMS NIH HHS [GM48807] Funding Source: Medline
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The use of simple theoretical models has provided a considerable contribution to our present understanding of the means by which proteins adopt their native fold from the plethora of available unfolded states. A common assumption in building computationally tractable models has been the neglect of stabilizing non-native interactions in the class of models described as G (o) over baro-like. The focus of this study is the characterization of the folding of a number of proteins via a G (o) over bar -like model, which aims to map a maximal amount of information reflecting the protein sequence onto a minimalist skeleton. This model is shown to contain sufficient information to reproduce the folding transition states of a number of proteins, including topologically analogous proteins that fold via different transition states. Remarkably, these models also demonstrate consistency with the general features of folding transition states thought to be stabilized by non-native interactions. This suggests that native interactions are the primary determinant of most protein folding transition states, and that non-native interactions lead only to local structural perturbations. A prediction is also included for an asymmetrical folding transition state of bacteriophage lambda protein W, which has yet to be subjected to experimental characterization. (C) 2003 Elsevier Ltd. All rights reserved.
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