RNA and protein folding: Common themes and variations

被引:218
作者
Thirumalai, D [1 ]
Hyeon, C
机构
[1] Univ Maryland, Inst Phys Sci & Technol, Biophys Program, College Pk, MD 20742 USA
[2] Univ Maryland, Inst Phys Sci & Technol, Dept Chem & Biochem, College Pk, MD 20742 USA
关键词
D O I
10.1021/bi047314+
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Visualizing the navigation of an ensemble of unfolded molecules through the bumpy energy landscape in search of the native state gives a pictorial view of biomolecular folding. This picture, when combined with concepts in polymer theory, provides a unified theory of RNA and protein folding. Just as for proteins, the major folding free energy barrier for RNA scales sublinearly with the number of nucleotides, which allows us to extract the elusive prefactor for RNA folding. Several folding scenarios can be anticipated by considering variations in the energy landscape that depend on sequence, native topology, and external conditions. RNA and protein folding mechanism can be described by the kinetic partitioning mechanism (KPM) according to which a fraction (Phi) of molecules reaches the native state directly, whereas the remaining fraction gets kinetically trapped in metastable conformations. For two-state folders Phi approximate to 1. Molecular chaperones are recruited to assist protein folding whenever Phi is small. We show that the iterative annealing mechanism, introduced to describe chaperonin-mediated folding, can be generalized to understand protein-assisted RNA folding. The major differences between the folding of proteins and RNA arise in the early stages of folding. For RNA, folding can only begin after the polyelectrolyte problem is solved, whereas protein collapse requires burial of hydrophobic residues. Cross-fertilization of ideas between the two fields should lead to an understanding of how RNA and proteins solve their folding problems.
引用
收藏
页码:4957 / 4970
页数:14
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