Manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c′

Tanveer A. Dar, R. Dustin Schaeffer, Valerie Daggett, Bruce E. Bowler

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

To provide insight into the role of local sequence in the nonrandom coil behavior of the denatured state, we have extended our measurements of histidine-heme loop formation equilibria for cytochrome c†to 6 M guanidine hydrochloride. We observe that there is some reduction in the scatter about the best fit line of loop stability versus loop size data in 6 M versus 3 M guanidine hydrochloride, but the scatter is not eliminated. The scaling exponent, γ3, of 2.5 ± 0.2 is also similar to that found previously in 3 M guanidine hydrochloride (2.6 ± 0.3). Rates of histidine-heme loop breakage in the denatured state of cytochrome c′ show that some histidine-heme loops are significantly more persistent than others at both 3 and 6 M guanidine hydrochloride. Rates of histidine-heme loop formation more closely approximate random coil behavior. This observation indicates that heterogeneity in the denatured state ensemble results mainly from contact persistence. When mapped onto the structure of cytochrome c′, the histidine-heme loops with slow breakage rates coincide with chain reversals between helices 1 and 2 and between helices 2 and 3. Molecular dynamics simulations of the unfolding of cytochrome c′ at 498 K show that these reverse turns persist in the unfolded state. Thus, these portions of the primary structure of cytochrome c′ set up the topology of cytochrome c′ in the denatured state, predisposing the protein to fold efficiently to its native structure.

Original languageEnglish (US)
Pages (from-to)1029-1041
Number of pages13
JournalBiochemistry
Volume50
Issue number6
DOIs
StatePublished - Feb 15 2011

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Rhodopseudomonas
Cytochromes c
Heme
Histidine
Guanidine
Topology
Molecular Dynamics Simulation
Molecular dynamics
Computer simulation

ASJC Scopus subject areas

  • Biochemistry

Cite this

Manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c′. / Dar, Tanveer A.; Schaeffer, R. Dustin; Daggett, Valerie; Bowler, Bruce E.

In: Biochemistry, Vol. 50, No. 6, 15.02.2011, p. 1029-1041.

Research output: Contribution to journalArticle

Dar, Tanveer A. ; Schaeffer, R. Dustin ; Daggett, Valerie ; Bowler, Bruce E. / Manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c′. In: Biochemistry. 2011 ; Vol. 50, No. 6. pp. 1029-1041.
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