Kinetic barriers and the role of topology in protein and RNA folding

Abstract

This review compares the folding behavior of proteins and RNAs. Topics covered include the role of topology in the determination of folding rates, major folding events including collapse, properties of denatured states, pathway heterogeneity, and the influence of the mode of initiation on the folding pathway.Keywords: protein structure/folding; RNA folding Proteins and RNAs must fold into specific structures in order to carry out their functions within the cell. For both biomolecules, the stability and specificity of the native fold results from the burial of hydrophobic and aromatic side groups, and the formation of hydrogen bonds. Nevertheless, their folding behavior differs in many important ways (Thirumalai and Hyeon 2005)( Table 1). Proteins have a higher folding cooperativity with secondary structure (SecStr) and collapse occurring in the same kinetic event. In contrast, RNA SecStr typically forms at low ionic conditions with collapse and tertiary structure (TertStr) formation occurring only upon the addition of counterions that shield the repulsion of the negatively charged RNA phosphodiester backbone. Specific Mg 2+ binding often helps assemble the preformed RNA SecStrs into tertiary architectures (Cate et al. 1997;Batey et al. 1999;Klein et al. 2004). As a result, the protein folding landscape has fewer stable intermediates than the RNA folding landscape (Thirumalai and Woodson 1996;Treiber et al. 1998;Thirumalai et al. 2001;Treiber and Williamson 2001;Das et al. 2003;Baird et al. 2007). Folding rates and chain topologyWhen interpreting data and identifying the critical folding events, one must distinguish between the intrinsic (unavoidable) kinetic barriers from the optional barriers, which arise on some pathways but not on others. Proteins and RNAs can fold directly to the native state or be trapped by kinetic barriers related to undoing errors formed early in the pathway (Bryngelson and Wolynes 1989;Abkevich et al. 1994a;Sosnick et al. 1994;Guo and Thirumalai 1995;Thirumalai and Woodson 1996;Pan and Sosnick 1997;Pan et al. , 1999bTreiber and Williamson 1999;Russell et al. 2002). The nature of the errors include premature collapse and nonnative secondary structure formation. These optional barriers obscure the intrinsic barriers, those unavoidable steps that determine folding rates in the absence of error correction. Protein foldingThe error-free folding of proteins had been proposed to be a nucleation process where the chain attains a coarse

A “Link‐Psi” strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable

“…32,50 Secondly, many TSEs contain a high fraction of the native structure and topology (e.g., the TSE has $70% of the native state's relative contact order). [20][21][22]32,51 This high level eliminates many otherwise possible transition state structures, and further reduces the amount of heterogeneity.…”

RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways

“…In contrast, folding rates are independent of topological complexity for fast folding molecules (Sosnick and Pan 2004). From the limited information comparing folding of a few RNA classes, it is generally believed that a correlation between folding rate and topology depends upon whether the ratelimiting step involves disruption of non-native interactions or small local conformational changes that act as nucleation scaffolds (Treiber and Williamson 2001a;Sosnick 2008).…”

DEAD-box protein facilitated RNA folding in vivo

“…[1][2][3][4][5] Of the studies that monitored intracellular RNA structure formation, only few have attempted a comprehensive correlation of in vitro versus in vivo folding paradigms. 6,12 As the folding pathway of the ai5γ ribozyme has been thoroughly studied in vitro at non-physiological conditions, 1 we aimed at elucidating how this large, multidomain RNA, which depends on the helicase Mss116p for efficient splicing in vivo, folds in yeast.…”

“…However, the precise site of action of Mss116p during the early folding steps remains enigmatic both in vitro and in vivo. In any case folding of the scaffolding domain appears to be a critical step at non-physiological conditions, 21 near-physiological conditions with 3 and without Mss116p 19 as well as in yeast mitochondria. Aside from accelerating the Mg 2+ -induced collapse of ai5γ in an ATP-independent manner, it has been shown that ATP hydrolysis is necessary for the protein's turnover and that Mss116p does not stabilize the native state of the ribozyme, but that such stabilization results from binding of flanking exons.…”

“…So far significant progress has been made in describing RNA structure and associated folding pathways in vitro. [1][2][3][4][5] From these studies several interesting folding paradigms have emerged portraying the diversity of RNA biophysical behaviors. However, little is known about RNA structure formation in vivo and a comparison of RNA folding paradigms observed in vitro versus in vivo has also been the focus of only very few studies.…”