Statistical mechanics of kinetic proofreading in protein folding in vivo.

Gulukota, Kamalakar; Wolynes, Peter G.

doi:10.1073/pnas.91.20.9292

Cited by 53 publications

(50 citation statements)

References 19 publications

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“…This seems a further development of the "kinetic proofreading" model of Gulukota and Wolynes (1994). Zahn and his colleagues further suggested that chaperonins have an ongoing annealing function (i.e., local bindinghnbinding) within the polypeptide-chaperonin complex, perhaps distinct from active unfolding (Zahn et al, 1996b).…”

Section: Conformational Changes In the Substrate Proteinmentioning

confidence: 98%

GroEL‐Mediated protein folding

1997

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I. Architecture of GroEL and GroES and the reaction pathwayA. Architecture of the chaperonins B. Reaction pathway of GroEL-GroES-mediated folding 3. 4. 5.Role of hydrophobicity in recognition Homologous proteins with differing recognition-differences in primary structure versus effects on folding Concluding remarksKeywords: chaperonin; GroES; Hsp60; kinetic partitioning; mechanism of action; X-ray structureThe early studies of Anfinsen and co-workers established that the 1973). Under physiologic conditions inside the cell, however, the primary structure of a protein contains all the information necesfolding process for many proteins, particularly those with multisary to direct the native secondary and tertiary fold (Anfinsen, domain structures, is prone to producing a variety of misfolded species and aggregates. Recent studies indicate that a specialized

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Section: Conformational Changes In the Substrate Proteinmentioning

confidence: 98%

GroEL‐Mediated protein folding

1997

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“…The cycle of ATP hydrolysis, release, partitioning, and rebinding (Fig. 2B It is useful to contrast the IAM to the kinetic proofreading model for chaperonin action (7). In the latter, the chaperonins are assumed to provide a bias in the folding to the native state that is argued to be responsible for the rate enhancement.…”

Section: Rugged Energy Landscapes and The Kinetic Partitioning Mechanismmentioning

confidence: 99%

“…We show here that these two seemingly disparate approaches to protein folding can be unified by the theory of iterative annealing to account for chaperonin-facilitated protein folding. Theoretical studies have also begun to consider the role of chaperonins in protein folding (6)(7)(8)(9).…”

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confidence: 99%

Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism.

Todd

Lorimer²,

Thirumalai³

1996

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

249

279

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We develop a heuristic model for chaperonin-facilitated protein folding, the iterative annealing mechanism, based on theoretical descriptions of "rugged" conformational free energy landscapes for protein folding, and on experimental evidence that (i) folding proceeds by a nucleation mechanism whereby correct and incorrect nucleation lead to fast and slow folding kinetics, respectively, and (ii) chaperonins optimize the rate and yield of protein folding by an active ATP-dependent process. The

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“…Eq. 1 has the form of the Ising spin-glass Hamiltonian, and a similar expression was used in the model of folding of proteins (17). Although Eq.…”

Section: Modelmentioning

confidence: 99%

Evolution of the folding ability of proteins through functional selection

Saito

Sasai

Yomo

1997

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

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An evolutionary process is simulated with a simple spin-glass-like model of proteins to examine the origin of folding ability. At each generation, sequences are randomly mutated and subjected to a simulation of the folding process based on the model. According to the frequency of local configurations at the active sites, sequences are selected and passed to the next generation. After a few hundred generations, a sequence capable of folding globally into a native conformation emerges. Moreover, the selected sequence has a distinct energy minimum and an anisotropic funnel on the energy surface, which are the imperative features for fast folding of proteins. The proposed model reveals that the functional selection on the local configurations leads a sequence to fold globally into a conformation at a faster rate.Natural proteins are known to fold into unique threedimensional structures. Though this folding ability must have emerged in the course of evolution, most investigations have focused not so much on the origin as on the mechanism of the folding process.In dealing with the mechanism of the folding process, recent theoretical work with lattice models (1-4) and with spin-glass ideas (5-8) suggests that completely random heteropolymers do not have the same tendency to fold into a unique conformation as natural proteins do. To attain a single conformation from all the possible ones within a biological time scale, the peptide chain must have an energetically highly distinctive minimum and a so-called folding funnel (2)-i.e., a biased energy surface. This design principle of the energy landscape is called the principle of minimum frustration (5-7). Several hypotheses have been presented of the origin of minimally frustrated peptides (9-11).Partial successes in obtaining catalytic antibodies (12) and some functional peptides (13, 14) through functional selection imply the possibility that most polypeptides, if not all, have been tuned through positive selections on function during their evolution. Therefore, it is worth asking whether the existence of an accessible unique conformation evolves from random polypeptides when sequences are selected on the basis of their function alone. In fact, one of the authors and his colleagues (15) synthesized random peptides with 140 residues and showed that 10% of those peptides were water soluble. Some of the soluble peptides have weak hydrolyzing activity whose strength depends on the sequence of the random proteins (unpublished results).The function of a protein is, in general, governed directly by some active site residues. The spatial configuration of each active site is arranged in a certain way to possess a high functional activity. Then, one could ask whether such local configurational adaptation dictates the folding of the whole protein. In other words, does a globally properly folded peptide chain evolve through the restriction on the local configurations? Pande et al. (10) raised a related question whether sequences with a lower total energy of the protein-subst...

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Statistical mechanics of kinetic proofreading in protein folding in vivo.

Cited by 53 publications

References 19 publications

GroEL‐Mediated protein folding

GroEL‐Mediated protein folding

Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism.

Evolution of the folding ability of proteins through functional selection

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