One-state Downhill versus Conventional Protein Folding

Ferguson, Neil; Schartau, P.J.; Sharpe, Timothy D.; Sato, Satoshi; Fersht, Alan R.

doi:10.1016/j.jmb.2004.09.069

Cited by 72 publications

(155 citation statements)

References 22 publications

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“…Although the new scenario of global downhill protein folding for BBL protein and three PSBD homologues has been proposed, we demonstrated evidences of two-state cooperative (first order phase) transition for these proteins by using an extended ME model that uses an exact free energy landscape, an exact analysis of relaxation eigenmodes from a master equation, and an out-of-equilibrium relaxation kinetics via kinetic Monte Carlo simulation. Our exact and numerical results are in a qualitative agreement with the recent experimental results (15,16,24) and properly address the fundamental controversy related to the global downhill folding not in terms of the statistical dispute but by the fundamental principles of equilibrium thermodynamics and out-ofequilibrium relaxation kinetics. We believe that our work provides a resolution to the long-standing controversy of global downhill protein folding, whose applicability for other proteins needs to be exercised with caution.…”

Section: Resultssupporting

confidence: 86%

“…Whereas Naganathan et al (18) argued that the experimental data in ref. 15 support the global downhill folding scenario, Fersht and coworkers (16) believe that the conclusion drawn by Muñoz and coworkers was obtained by an incorrect assumption and analysis of the data in refs. 13 and 18.…”

mentioning

confidence: 90%

“…They not only suggested that Naf-BBL follows the global downhill folding scenario but also claimed that the same scenario holds for other PSBD homologues (13). In contrast, Fersht and coworkers (15,16) examined the structural, denaturation, and kinetic properties of PSBD homologues from E. coli [unlabeled wild-type BBL, Protein Data Bank (PDB) entry 1W4H], Bacillus stearothermophilus (E3BD F166W, PDB entry 1W4E), and Pyrobaculumaerophilum (POB Y166W L146A, PDB entry 1W4J) (17) and found that 1W4H, 1W4E, and 1W4J follow the typical two-state folding scheme. Whereas Naganathan et al (18) argued that the experimental data in ref.…”

mentioning

confidence: 99%

“…However, Ferguson et al (20) and Zhou and Bai (21) argued back again that the new data presented by Sadqi et al (19) could well be described by a twoor three-state model. Such an ongoing fundamental controversy (13)(14)(15)(16)(18)(19)(20)(21)(22)(23)(24)(25) about the folding mechanism for Naf-BBL and PSBD homologues would reshape our concept on protein folding. Faced with these conflicting and ambiguous assertions from experiment, we have attempted to resolve such a controversy by carrying out an exact analysis of thermodynamic and kinetic properties for folding-unfolding of an unlabeled BBL (BBL short, PDB entry 1BBL) with no naphthyl moiety and three PSBD homologues.…”

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confidence: 99%

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Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Chung

Cheon

et al. 2008

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

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Recent experiments claiming that Naf-BBL protein follows a global downhill folding raised an important controversy as to the folding mechanism of fast-folding proteins. Under the global downhill folding scenario, not only do proteins undergo a gradual folding, but folding events along the continuous folding pathway also could be mapped out from the equilibrium denaturation experiment. Based on the exact calculation using a free energy landscape, relaxation eigenmodes from a master equation, and Monte Carlo simulation of an extended Muñoz-Eaton model that incorporates multiscale-heterogeneous pairwise interactions between amino acids, here we show that the very nature of a two-state cooperative transition such as a bimodal distribution from an exact free energy landscape and biphasic relaxation kinetics manifest in the thermodynamics and folding-unfolding kinetics of BBL and peripheral subunit-binding domain homologues. Our results provide an unequivocal resolution to the fundamental controversy related to the global downhill folding scheme, whose applicability to other proteins should be critically reexamined.protein folding mechanism ͉ global downhill folding ͉ protein thermodynamics ͉ relaxation kinetics of protein O ur understanding of protein folding is primarily based on interpretation of the thermodynamics and kinetics from a simple protein folding model (1-10). The principle of minimal frustration and structural consistency captured by the Go model allowed us to describe the complicated nature of protein folding at a coarse-grained level (5, 6). Bryngelson et al. (6,7) posited a phenomenological picture of free energy landscape of a protein-like heteropolymer and classified protein folding into three scenarios depending on whether the free energy landscape is unistable or bistable and also whether a glass transition occurs. Shakhnovich and Gutin (8) presented microscopic statisticalmechanical theories for heteropolymer model, whose consequences provided important insights into the thermodynamics, kinetics, and nature of free energy landscape for protein folding. The conventional view of protein folding assumes a discrete two-state transition between a native state and a denatured ensemble of protein conformations that are separated by a folding barrier (9). The other view termed as one-state (or global) downhill folding asserts that there is a continuous change of protein conformation during folding without distinct free energy barrier (7, 10). The former could be understood as the first order (cooperative) phase transition whereas the latter as the second order (noncooperative) phase transition between a native and a denatured ensemble of protein conformation. An in-depth analysis for possible downhill folding was performed by Abkevich et al. (10) where it was shown that the major determinant for the cooperativity of protein folding is the relative abundance of nonlocal versus local contacts between residues in the native structure of a protein, which also simultaneously compete with the loss of conform...

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Section: Resultssupporting

confidence: 86%

mentioning

confidence: 90%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Chung

Cheon

et al. 2008

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

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“…Most of the previous experiments on BBL based on bulk measurements are consistent with both unimodal downhill folding and barrier-limited folding with a heterogeneous native state, but the steep chevron plot favors a conventional folding mechanism with a transition state (7,(29)(30)(31). The SM-FRET experiments here show directly that BBL does occupy native and denatured states separated by an energy barrier.…”

Section: Discussionsupporting

confidence: 80%

Direct observation of barrier-limited folding of BBL by single-molecule fluorescence resonance energy transfer

Huang

Ying

Fersht

2009

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

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One controversial area in protein folding mechanisms is whether some small, ultra-fast-folding proteins exist in distinct native and denatured state ensembles, separated by an energy barrier, or if there is a continuum of states between native and denatured. In theory, the simplest way of distinguishing between single-state barrierless or ''downhill'' folding and conventional separate state folding is by single-molecule spectroscopy, which can detect either distinct populations of proteins or a continuum. But, the time resolution of approximately 1 ms of most confocal fluorescence microscopes for single-molecule fluorescence resonance energy transfer (SM-FRET) is longer than that for the structural relaxation of proteins such as BBL, whose mechanism of folding is controversial. We have constructed a highly sensitive confocal fluorescence microscope and measured the distribution of . The key protein in the unimodal hypothesis is BBL, a member of the peripheral subunit binding domain family, which is claimed to be a global downhill folder based especially on the dispersion of melting temperature for individual residues (2). It is extremely difficult to falsify unimodal folding because most equilibrium and kinetic data can be interpreted by numerous alternative mechanisms, especially when the rate of interconversion of D and N states is on a faster time scale than that of observation (6). The dependence of rates of folding and unfolding on denaturant concentration is good evidence for the nature of the mechanism-classical chevron plots with a steep limb are compatible with only a folding scenario with a free energy barrier and a transition state, so there is a significant change of solvent-accessible surface between the ground and transition states (6-8). That evidence combined with a rationalization of the anomalous behavior of BBL has been used as evidence that the folding of BBL can be accommodated by a barrier limited folding model, with some heterogeneity of the native state (9-12). Direct observation of distinct states of BBL in the transition region at equilibrium would provide compelling evidence for barrier limited folding (6, 13). The current method of choice is single-molecule fluorescence resonance energy transfer (SM-FRET) experiments, which has been widely applied in the studies of protein folding, structure, and function, and is especially useful in detection of heterogeneity of populations (14-21).We have applied SM-FRET to the B-domain of Protein A (BDPA) and directly observed the denatured and native states of this protein in its transition region (6), the signature of barrier-limited folding. We were not able to use SM-FRET to resolve unambiguously the folding mechanism of BBL because it folds in a fraction of a millisecond at room temperature, whereas the typical time resolution of SM-FRET was, until very recently, typically 1 ms (6,21,22), in which time BBL would rapidly equilibrate and appear as a time-averaged structure of the separate states if it folds by a barrier limited transition (23, 2...

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Catalyst‐Controlled Regioselective Approach to 1‐Aminoisoquinolines and/or 1‐Aminoisoindolines through Aminative Domino Cyclization of 2‐Alkynylbenzonitriles

2015

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One-state Downhill versus Conventional Protein Folding

Cited by 72 publications

References 22 publications

Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Direct observation of barrier-limited folding of BBL by single-molecule fluorescence resonance energy transfer

Catalyst‐Controlled Regioselective Approach to 1‐Aminoisoquinolines and/or 1‐Aminoisoindolines through Aminative Domino Cyclization of 2‐Alkynylbenzonitriles

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One-state Downhill versus Conventional Protein Folding

Cited by 72 publications

References 22 publications

Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Direct observation of barrier-limited folding of BBL by single-molecule fluorescence resonance energy transfer

Catalyst‐Controlled Regioselective Approach to 1‐Aminoisoquinolines and/or 1‐Aminoisoindolines through Aminative Domino Cycliza­tion of 2‐Alkynylbenzonitriles

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Product

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About

Catalyst‐Controlled Regioselective Approach to 1‐Aminoisoquinolines and/or 1‐Aminoisoindolines through Aminative Domino Cyclization of 2‐Alkynylbenzonitriles