The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics

Makarov, Dmitrii E.

doi:10.1110/ps.0220003

Cited by 179 publications

(254 citation statements)

References 93 publications

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“…The amide and hydrocarbon ASA results and structural analysis presented here provide strong experimental support for a general mechanism of protein folding in which most if not all of the native elements of secondary structure form before TS, and begin to coalesce into more native-like structures in TS, as previously proposed (2,4,(44)(45)(46). A rapidly equilibrating mixture of largely unfolded chains with various subsets of these elements of 2°structure comprises the ensemble of early folding intermediates.…”

Section: Analysis Of All-2°and More Advanced Structural Models Of Folsupporting

confidence: 77%

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Guinn¹,

Kontur

Tsodikov

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Protein folding has been extensively studied, but many questions remain regarding the mechanism. Characterizing early unstable intermediates and the high-free-energy transition state (TS) will help answer some of these. Here, we use effects of denaturants (urea, guanidinium chloride) and temperature on folding and unfolding rate constants and the overall equilibrium constant as probes of surface area changes in protein folding. We interpret denaturant kinetic m-values and activation heat capacity changes for 13 proteins to determine amounts of hydrocarbon and amide surface buried in folding to and from TS, and for complete folding. Predicted accessible surface area changes for complete folding agree in most cases with structurally determined values. We find that TS is advanced (50-90% of overall surface burial) and that the surface buried is disproportionately amide, demonstrating extensive formation of secondary structure in early intermediates. Models of possible pre-TS intermediates with all elements of the native secondary structure, created for several of these proteins, bury less amide and hydrocarbon surface than predicted for TS. Therefore, we propose that TS generally has both the native secondary structure and sufficient organization of other regions of the backbone to nucleate subsequent (post-TS) formation of tertiary interactions. The approach developed here provides proof of concept for the use of denaturants and other solutes as probes of amount and composition of the surface buried in coupled folding and other large conformational changes in TS and intermediates in protein processes.etermination of the mechanism of protein folding [unfolded (U) → folded (F)] is a long-standing goal of biophysical research. Folding of a single domain globular protein is a very highly cooperative (thermodynamically two-state) process. From analysis of folding kinetic data for CI2 and barnase, Fersht et al.(1) concluded that proteins fold through a high-free-energy transition state (TS) with partially formed elements of native structure. Recently, Barrick and Sosnick (2) concluded that an ensemble of unstable, rapidly reversible intermediates form early in the folding mechanism, and that the most advanced and unstable of these undergoes a rate-determining conformational change with transition state TS. This transit step, slower than the reverse direction of previous rapidly reversible steps, is followed by rapid propagation of folding. Most proposals for the initial intermediates invoke unstable regions of α-helix and/or β-sheet; these are thought to coalesce and/or rearrange to form TS. Kay and coworkers (3) characterized a marginally stable early intermediate of Fyn SH3 domain and found that interactions of amide groups formed earlier in the folding pathway than interactions of methyl groups, indicating that 2°structure formed before the 3°fold. Recent hydrogen exchange pulse-labeling experiments analyzed with mass spectrometry by Englander, Marqusee, and collaborators (4) indicate that folding of RNase H occurs t...

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Section: Analysis Of All-2°and More Advanced Structural Models Of Folsupporting

confidence: 77%

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Guinn¹,

Kontur

Tsodikov

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…One important insight from experimental studies is that for many proteins the rate of folding is inversely correlated to the density of sequence-distant contacts (referred to as "contact order") in the native state [3,15]. This correlation suggests that the overall fold or "topology" of the native-state is established in the rate-limiting step in folding [16]. At a more detailed resolution, rate-equilibrium relationships of single-residue protein variants (and so-called "Φ-values") indicate that detailed side-chain packing interactions vary in their extent of formation in the rate-limiting, or transition-state ensemble, often remaining unformed until the native state is formed (for a review of Φ-values in globular proteins, see the article by Royer in this issue).…”

Section: Recent Observations and Related Questions In Folding Of Globmentioning

confidence: 99%

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Kloss

Courtemanche

Barrick

2008

Archives of Biochemistry and Biophysics

101

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Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings. KeywordsRepeat-protein; Ankyrin repeat; protein folding; energy landscape; atomic force microscopy In the last twenty-five years, advances in experimental studies and in computation and theory have greatly improved our understanding of protein folding. On the experimental side, advances have come from new and improved techniques, including site-directed mutagenesis, hydrogen exchange (HX) methods, improvements to rapid mixing devices, and development of single-molecule fluorescence and force spectroscopy. Experimental advances have also come in the form of generalizations and insights from expanding databases of thermodynamic and kinetic constants for protein folding [1][2][3][4][5].On the computational side, advances in our understanding of protein folding have come from huge increases in computer speed and storage capacity, in innovative methods to study energetics of folding such as ensemble-based approaches and replica exchange methods [6,7], and distributed computing methods [8]. As with experiment, computational studies of folding, and in particular, fold prediction, have greatly benefited from expanding databases of protein structure [9,10]. On the theoretical side, the application of ideas from condensed-matter *Correspondence: barrick@jhu.edu, (410) 516-0409. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptArch Biochem Biophys. Author manuscript; available in PMC 2009 January ...

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“…Even in the worst-case scenario where the entire ECO 3 subgraph is searched, the maximum number of microstates that must be enumerated is 75, yielding a search efficiency of SE = − log 10 (75/15037) ≈ 2.3, orders of magnitude faster than random search. (12)(13)(14)(15)(16)(17)(18) and low-ECO zipping strategies. The global performance of the zipping and assembly algorithm across all foldable sequences displays an inverse relationship between the average search efficiency (SE ≡ − log 10 (Ω/Ω 0 )) for zippable sequences and the fraction of foldable sequences which are zippable.…”

Section: Conclusion: Zipping and Assembly Is A Viable Folding Principlementioning

confidence: 99%

“…In addition, there have been efforts to identify transition states of protein folding, in order to elucidate the folding mechanisms. Sampling the chain topomers has also been proposed as the main folding event 12,13 , although this class of models has recently been shown to be either inconsistent with experimental data or requiring unphysical search characteristics 14,15 .…”

Section: Introductionmentioning

confidence: 99%

Exploring zipping and assembly as a protein folding principle

Voelz

Dill

2007

Proteins

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It has been proposed that proteins fold by a process called "Zipping & Assembly" (Z&A). Zipping refers to the growth of local substructures within the chain, and assembly refers to the coming together of already-formed pieces. Our interest here is in whether Z&A is a general method that can fold most of sequence space, to global minima, efficiently. Using the HP model, we can address this question by enumerating full conformation and sequence spaces. We find that Z&A reaches the global energy minimum native states, even though it searches only a very small fraction of conformational space, for most sequences in the full sequence space. We find that Z&A, a mechanism-based search, is more efficient in our tests than the Replica Exchange search method. Folding efficiency is increased for chains having: (a) small loop-closure steps, consistent with observations by Plaxco et al. 1 that folding rates correlate with contact order, (b) neither too few nor too many nucleation sites per chain, and (c) assembly steps that do not occur too early in the folding process. We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms.

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The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics

Cited by 179 publications

References 93 publications

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Exploring zipping and assembly as a protein folding principle

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