Computational spectroscopy of ubiquitin: Comparison between theory and experiments

Jun Ho Choi, Hochan Lee, Kyung Koo Lee, Seungsoo Hahn, Minhaeng Cho

Research output: Contribution to journalArticle

72 Citations (Scopus)

Abstract

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.

Original languageEnglish
Article number045102
JournalJournal of Chemical Physics
Volume126
Issue number4
DOIs
Publication statusPublished - 2007 Mar 13

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Ubiquitin
Amides
amides
Spectroscopy
dichroism
spectroscopy
Experiments
proteins
Quantum chemistry
quantum chemistry
Proteins
Hessian matrices
Hamiltonians
Computer simulation
refining
Dichroism
Computational methods
electronic spectra
cancellation
vibrational spectra

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Computational spectroscopy of ubiquitin : Comparison between theory and experiments. / Choi, Jun Ho; Lee, Hochan; Lee, Kyung Koo; Hahn, Seungsoo; Cho, Minhaeng.

In: Journal of Chemical Physics, Vol. 126, No. 4, 045102, 13.03.2007.

Research output: Contribution to journalArticle

Choi, Jun Ho ; Lee, Hochan ; Lee, Kyung Koo ; Hahn, Seungsoo ; Cho, Minhaeng. / Computational spectroscopy of ubiquitin : Comparison between theory and experiments. In: Journal of Chemical Physics. 2007 ; Vol. 126, No. 4.
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