Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy

Yun Xiang, Lili Duan, John Zhang

Research output: Contribution to journalArticle

Abstract

Understanding protein folding is of fundamental and practical importance in chemistry and biology. Despite the great success that has been made in tackling this problem, a detailed knowledge of how the elementary processes such as hydrogen-bond formation occur during protein folding has remained largely elusive. Using the combined power of molecular dynamics simulation with electrostatic polarization and coherent two-dimensional infrared spectroscopy, we are able to delineate the order of the hydrogen-bond formation event of a 17-residue peptide during its folding from an extended state to the native α-helix state. The folding is carried out by a single trajectory room-temperature molecular dynamics simulation that includes the polarization effect of hydrogen bonding, which is critical to the successful folding of the peptide. The onset and evolution of the isotope-labeled amide I vibration diagonal and cross peaks on the simulated 2DIR spectra allow us to build a structure-spectrum connection, and thus provide a microscopic picture of the helix folding process.

Original languageEnglish (US)
Pages (from-to)15681-15688
Number of pages8
JournalPhysical Chemistry Chemical Physics
Volume12
Issue number48
DOIs
StatePublished - Dec 28 2010

Fingerprint

folding
Protein folding
Infrared spectroscopy
Hydrogen bonds
infrared spectroscopy
proteins
Molecular dynamics
room temperature
Polarization
Peptides
Proteins
Computer simulation
Amides
Isotopes
helices
Temperature
peptides
Electrostatics
Trajectories
hydrogen bonds

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Physics and Astronomy(all)

Cite this

Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy. / Xiang, Yun; Duan, Lili; Zhang, John.

In: Physical Chemistry Chemical Physics, Vol. 12, No. 48, 28.12.2010, p. 15681-15688.

Research output: Contribution to journalArticle

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