VCD spectroscopic and molecular dynamics analysis of the Trp-cage miniprotein TC5b

Jeffrey Copps, Richard F. Murphy, Sándor Lovas

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

TC5b is a 20 residue polypeptide notable for its compact tertiary structure, a rarity for a short peptide. This structure is due to the "Trp-cage" motif, an association of aromatic, Pro, and Gly residues. The structure of TC5b has been fully characterized by NMR and electronic circular dichroism (ECD) studies, but has never been studied with vibrational circular dichroism (VCD) spectroscopy, which may reveal finer structure. In this study, we examine the VCD spectra of TC5b to characterize the spectroscopic signature of the peptide and its comprising structural elements. TC5b exhibited a negative-positive-negative triplet which is associated with α-helical structure in deuterated solvents but also signs of a polyproline II (PPII) helix in the amide I' region. Detection of this element was complicated by the aforementioned triplet form, as well as by an upfrequency shift in PPII helical elements due to the use of the deuterated organic solvents DMSO-d6 and TFE-d1. Nevertheless, while ECD spectra showed only α-helical structure for TC5b, VCD spectroscopy revealed a more complex structure which was in agreement with NMR results. VCD spectroscopy also showed a rapid conformational change of the peptide at temperatures above 35°C in D2O and in aqueous solvent with greater than 75% DMSO-d6 content. Molecular dynamics (MD) simulations to investigate this latter effect of DMSO-d6 on TC5b were conducted in DMSO and 50% (v/v) DMSO in H2O. In DMSO unfolding of the peptide was rapid while in 50% (v/v) DMSO in H2O the unfolding was more gradual.

Original languageEnglish
Pages (from-to)427-437
Number of pages11
JournalBiopolymers
Volume88
Issue number3
DOIs
StatePublished - 2007

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Molecular Dynamics Simulation
Circular Dichroism
Circular dichroism spectroscopy
Dimethyl Sulfoxide
Vibrational spectroscopy
Dynamic analysis
Peptides
Molecular dynamics
Dichroism
Nuclear magnetic resonance
Spectrum Analysis
Polypeptides
Amides
Chemical elements
Organic solvents
Association reactions
Polytetrafluoroethylene
Computer simulation
Temperature

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

VCD spectroscopic and molecular dynamics analysis of the Trp-cage miniprotein TC5b. / Copps, Jeffrey; Murphy, Richard F.; Lovas, Sándor.

In: Biopolymers, Vol. 88, No. 3, 2007, p. 427-437.

Research output: Contribution to journalArticle

Copps, Jeffrey ; Murphy, Richard F. ; Lovas, Sándor. / VCD spectroscopic and molecular dynamics analysis of the Trp-cage miniprotein TC5b. In: Biopolymers. 2007 ; Vol. 88, No. 3. pp. 427-437.
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abstract = "TC5b is a 20 residue polypeptide notable for its compact tertiary structure, a rarity for a short peptide. This structure is due to the {"}Trp-cage{"} motif, an association of aromatic, Pro, and Gly residues. The structure of TC5b has been fully characterized by NMR and electronic circular dichroism (ECD) studies, but has never been studied with vibrational circular dichroism (VCD) spectroscopy, which may reveal finer structure. In this study, we examine the VCD spectra of TC5b to characterize the spectroscopic signature of the peptide and its comprising structural elements. TC5b exhibited a negative-positive-negative triplet which is associated with α-helical structure in deuterated solvents but also signs of a polyproline II (PPII) helix in the amide I' region. Detection of this element was complicated by the aforementioned triplet form, as well as by an upfrequency shift in PPII helical elements due to the use of the deuterated organic solvents DMSO-d6 and TFE-d1. Nevertheless, while ECD spectra showed only α-helical structure for TC5b, VCD spectroscopy revealed a more complex structure which was in agreement with NMR results. VCD spectroscopy also showed a rapid conformational change of the peptide at temperatures above 35°C in D2O and in aqueous solvent with greater than 75{\%} DMSO-d6 content. Molecular dynamics (MD) simulations to investigate this latter effect of DMSO-d6 on TC5b were conducted in DMSO and 50{\%} (v/v) DMSO in H2O. In DMSO unfolding of the peptide was rapid while in 50{\%} (v/v) DMSO in H2O the unfolding was more gradual.",
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