Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: Helix-coil transition kinetics

Seongeun Yang, Minhaeng Cho

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20 Citations (Scopus)

Abstract

Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)21-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K ∼ 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 310-helix and type Iβ -turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining Tm by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.

Original languageEnglish
Pages (from-to)605-617
Number of pages13
JournalJournal of Physical Chemistry B
Volume111
Issue number3
DOIs
Publication statusPublished - 2007 Jan 25

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Denaturation
biopolymer denaturation
helices
Peptides
peptides
Molecular dynamics
coils
infrared spectra
Amides
amides
molecular dynamics
Infrared radiation
Kinetics
Water
Computer simulation
kinetics
predictions
water
field theory (physics)
simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

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title = "Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: Helix-coil transition kinetics",
abstract = "Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)21-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K ∼ 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 310-helix and type Iβ -turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining Tm by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.",
author = "Seongeun Yang and Minhaeng Cho",
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T1 - Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra

T2 - Helix-coil transition kinetics

AU - Yang, Seongeun

AU - Cho, Minhaeng

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