The problem was to find the problem

Baldwin, Robert L.

doi:10.1002/pro.5560060924

Cited by 9 publications

(11 citation statements)

References 14 publications

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“…26 These results suggest that hidden intermediates might occur commonly in small proteins and are consistent with the hypothesis that proteins fold in a step-wise manner through partially unfolded intermediates. [27][28][29] Interpretation of the unfolding free energy and m-values measured by fluorescence…”

Section: The Partially Unfolded Form Is a Hidden Intermediatementioning

confidence: 99%

Detection of a Hidden Folding Intermediate of the Third Domain of PDZ

Feng

Bai

2005

Journal of Molecular Biology

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Section: The Partially Unfolded Form Is a Hidden Intermediatementioning

confidence: 99%

Detection of a Hidden Folding Intermediate of the Third Domain of PDZ

Feng

Bai

2005

Journal of Molecular Biology

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“…Since the establishment of the thermodynamic hypothesis of protein folding by Anfinsen (44) in the 1960s, a critical issue has been how, in a biologically meaningful time scale, protein molecules find the native state in the enormously large conformational space. A straightforward hypothesis for solving this puzzle has been the existence of folding intermediates (45). For example, assuming that each amino acid contributes three conformations, the total number of conformations for a polypeptide chain with 100 aa is 3 100 or 10 48 .…”

Section: The Folding Pathway Of Rd-apocyt B562 With Intermediates At mentioning

confidence: 99%

A protein folding pathway with multiple folding intermediates at atomic resolution

Feng

Zhou

Bai

2005

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

115

129

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Using native-state hydrogen-exchange-directed protein engineering and multidimensional NMR, we determined the high-resolution structure (rms deviation, 1.1 Å) for an intermediate of the fourhelix bundle protein: Rd-apocytochrome b 562. The intermediate has the N-terminal helix and a part of the C-terminal helix unfolded. In earlier studies, we also solved the structures of two other folding intermediates for the same protein: one with the N-terminal helix alone unfolded and the other with a reorganized hydrophobic core. Together, these structures provide a description of a protein folding pathway with multiple intermediates at atomic resolution. The two general features for the intermediates are (i) native-like backbone topology and (ii) nonnative side-chain interactions. These results have implications for important issues in protein folding studies, including large-scale conformation search, -value analysis, and computer simulations.hidden folding intermediate ͉ native-state hydrogen exchange ͉ NMR structure ͉ protein engineering ͉ protein structure

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“…They allow stepwise folding, drastically reducing the scale of conformational search. In that view-which was supported by experiments on sufficiently long proteins [4]-the protein folding problem is reduced to relaxation in a finite number of states [2]. Still it was unclear how the protein reaches one of those intermediates, since now the Levinthal's paradox can be reformulated with respect to partial relaxation.…”

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confidence: 99%

“…This power-efficiency dilemma motivated a search for the efficiency that would generally characterize the maximal power regime. One candidate for this is the Curzon-Ahlborn efficiency η CA = 1 − T 2 /T 1 [2], which is however crucially tied to the linear regime T 1 ≈ T 2 [3,4]. Beyond this regime η CA is a lower bound of η for a class of model engines [5].…”

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Carnot Cycle at Finite Power: Attainability of Maximal Efficiency

et al. 2013

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We want to understand whether and to which extent the maximal (Carnot) efficiency for heat engines can be reached at a finite power. To this end we generalize the Carnot cycle so that it is not restricted to slow processes. We show that for realistic (i.e. not purposefully-designed) enginebath interactions, the work-optimal engine performing the generalized cycle close to the maximal efficiency has a long cycle time and hence vanishing power. This aspect is shown to relate to the theory of computational complexity. A physical manifestation of the same effect is the Levinthal's paradox in the protein folding problem. The resolution of this paradox for realistic proteins allows to construct engines that can extract at a finite power 40 % of the maximally possible work reaching 90 % of the maximal efficiency. For purposefully designed engine-bath interactions, the Carnot efficiency is achievable at a large power. Reciprocating heat engines extract work operating cyclically between two thermal baths at temperatures T 1 and T 2 (T 1 > T 2 ) [1]. They have two basic characteristics: (i) efficiency, η = W/Q 1 , is the work W extracted per cycle divided by the heat input Q 1 from the hightemperature bath. (ii) Power W/τ , where τ is the cycle duration. Both these quantities have to be large for a good engine: if η is small, lot of energy is wasted; if the power is small, no sizable work is delivered over a reasonable time [1].The second law establishes the Carnot efficiency η C = 1 − T2 T1 as an upper bound for η [1]. The Carnot cycle reaches the bounding value η C in the (useless) limit, where the power goes to zero [1]. Conversely, realistic engines are not efficient, since they have to be powerful, e.g. the efficiency of Diesel engines amounts to 35-40 % of the maximal value. This power-efficiency dilemma motivated a search for the efficiency that would generally characterize the maximal power regime. One candidate for this is the Curzon-Ahlborn efficiency η CA = 1 − T 2 /T 1 [2], which is however crucially tied to the linear regime T 1 ≈ T 2 [3,4]. Beyond this regime η CA is a lower bound of η for a class of model engines [5]. Several recent models for the efficiency at the maximal power overcome η CA with η * = ηC 2−ηC [6]. As argued in [5,7,8], the maximal power regime allows for the Carnot efficiency, at least for certain models. But it is currently an open question whether the maximal efficiency is attained under realistic conditions (see e.g.[9] versus [7]), and how to characterize the very realism of those conditions. Even more generally: what is the origin of the power-efficiency dilemma? We answer these questions by analyzing a generalized Carnot cycle, which in contrast to the original Carnot cycle is not restricted to slow processes. We now summarize our answers.(1) When the N -particle engine operates at the maximal work extracted per cycle, its efficiency reaches the Carnot bound η C for N 1, while the cycle time isgiven by the relaxation time of the engine. The maximal work and the Carnot efficiency are...

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The problem was to find the problem

Cited by 9 publications

References 14 publications

Detection of a Hidden Folding Intermediate of the Third Domain of PDZ

Detection of a Hidden Folding Intermediate of the Third Domain of PDZ

A protein folding pathway with multiple folding intermediates at atomic resolution

Carnot Cycle at Finite Power: Attainability of Maximal Efficiency

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