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	Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments
	Badasyan, Artem ; Liu, Zhirong ; Chan, Hue Sun
	2009
英文摘要	Coarse-grained chain simulations were used to study fragments of two homologous proteins of the peripheral subunit-binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2-oxo-glutarate dehydrogenase PSBD (BBL). To ascertain a robust rank order of folding cooperativity, native-centric intraprotein interactions were modeled by (i) a common Go-like potential, and (ii) native-centric potentials with desolvation barriers or (iii) many-body terms. Homologous proteins can possess substantially different folding cooperativity. Consistent with experiment, our calculations indicated that E3BD fragments fold more cooperatively than BBL fragments of approximately the same chain length. For a given fragment, native contacts deduced from Protein Data Bank structures can vary significantly depending on the number of residues that the structure encompasses in addition to those of the fragment itself, resulting in variation in model folding cooperativity predicted using different native contact sets for the same fragment. This observation underscores that folding cooperativity of these fragments can be extremely sensitive to change in chain length. Thus, a ?40-residue protein fragment's folding cooperativity, or lack thereof, does not necessarily imply essentially identical behaviors for super- or sub-fragments with only several residues more, or less, than the given fragment. Ramifications for experimental investigations of downhill folding are discussed. ? 2009 Wiley Periodicals, Inc.; EI; 0
语种	英语
DOI标识	10.1002/qua.22272
内容类型	其他
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/263244]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Badasyan, Artem,Liu, Zhirong,Chan, Hue Sun. Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments. 2009-01-01.

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