Unfolding of Triosephosphate Isomerase from Trypanosoma brucei: Identification of Intermediates and Insight into the Denaturation Pathway Using Tryptophan Mutants

Chánez‐Cárdenas, María Elena; Fernández‐Velasco, D. Alejandro; Vázquez‐Contreras, Edgar; Coria, Roberto; Saab‐Rincón, Gloria; Pérez‐Montfort, Ruy

doi:10.1006/abbi.2001.2749

Cited by 40 publications

(78 citation statements)

References 51 publications

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“…However, this result is consistent with that of several other dimeric proteins including factor for inversion stimulation protein, 50 the ATPase SecA, 72 organophosphorus hydrolase, 73 triosephosphate isomerase 74,75 and glutathione reductase 76 where a dimeric intermediate has been observed. Like apo-S100B, each of these proteins has the appearance of a transition corresponding to a F 2 ⇄ I 2 step at relatively low GuHCl concentrations (b 2 M), indicative that the dissociation of the dimer is a less favourable process.…”

Section: Discussionsupporting

confidence: 92%

Identification of a Dimeric Intermediate in the Unfolding Pathway for the Calcium-Binding Protein S100B

Shaw

Marlatt

Ferguson

et al. 2008

Journal of Molecular Biology

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Section: Discussionsupporting

confidence: 92%

Identification of a Dimeric Intermediate in the Unfolding Pathway for the Calcium-Binding Protein S100B

Shaw

Marlatt

Ferguson

et al. 2008

Journal of Molecular Biology

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“…16 Two intermediates were found in unfolding experiments of Trypanosoma brucei TIM, but unfolding of Triosephosphate Isomerase Folding this form of TIM was generally not reversible. 17 Results of an early study on the folding of rabbit muscle TIM showed that reactivation of the enzyme is second-order at low protein concentration and first-order at higher concentrations. 18 Another study of rabbit TIM folding found no evidence for an intermediate when the protein was folded in water, but did find evidence for an intermediate when the protein was folded in reverse micelles.…”

Section: Partially Folded Intermediates In Tim Folding/ Unfoldingmentioning

confidence: 98%

Equilibrium and Kinetic Folding of Rabbit Muscle Triosephosphate Isomerase by Hydrogen Exchange Mass Spectrometry

Pan

Raza

Smith

2004

Journal of Molecular Biology

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“…(vi) Sperm whale apomyoglobin was subdivided into two fragments, helices A-E and helices F-H; the latter fragment resembles an isolated apomyoglobin equilibrium intermediate (37) N-terminal unit into two domains, each containing one helical cluster. (viii) KSHV protease was divided into two domains: residues 4-161, the protein core, and residues 162-226, most of which is known to be unfolded in the monomeric form but folded upon dimerization (40 (18), raising the possibility that human TIM also has an alternative three-domain structure. Neither CATH nor SCOP detected the intermediates detailed above in eight of these nine cases (Table S1), a vivid demonstration that visually based methods are blind to thermodynamics.…”

Section: Qualifying Ratiomentioning

confidence: 99%

“…Again, early visual assessment found that triosephosphate isomerase "cannot be plausibly subdivided [into domains]" (16). Later experimental evidence, however, suggests that TIM barrels comprise two or even three domains (18,19). Clearly, a rigorous, quantitative domain definition is needed.…”

mentioning

confidence: 99%

A thermodynamic definition of protein domains

Porter

Rose

2012

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

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Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structurebased decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose mvalue is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.protein folding | protein structure | protein architecture | protein parsing D omains are visually arresting protein substructures with an influential history in protein biochemistry (1). These familiar, self-contained structural units were first noticed in some of the earliest solved protein structures (2, 3) and soon came to be recognized as common features of protein architecture (4).Dissecting proteins into their constituent domains provides a simple, intuitive approach to classifying protein structure, a molecular application of the time-honored principle of "carving nature at its joints" (5). Many structure-based computer algorithms have been devised to parse the ever-increasing number of solved proteins into discrete units; a highly abbreviated sample includes (6-13). Today, CATH (14) and SCOP (15) are the two most widely used domain classifications. Both are based on computational algorithms but rely ultimately on the human eye as the final arbiter of domain boundaries.However, seeing can be deceiving. The dependence on visual intuition introduces an unavoidable element of ambiguity into procedures for domain recognition. The most enduring domain definition, "potentially independent, stable folding uni...

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Unfolding of Triosephosphate Isomerase from Trypanosoma brucei: Identification of Intermediates and Insight into the Denaturation Pathway Using Tryptophan Mutants

Cited by 40 publications

References 51 publications

Identification of a Dimeric Intermediate in the Unfolding Pathway for the Calcium-Binding Protein S100B

Identification of a Dimeric Intermediate in the Unfolding Pathway for the Calcium-Binding Protein S100B

Equilibrium and Kinetic Folding of Rabbit Muscle Triosephosphate Isomerase by Hydrogen Exchange Mass Spectrometry

A thermodynamic definition of protein domains

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