Computational spectroscopy of ubiquitin: comparison between theory and experiments

• Published in: The Journal of chemical physics Vol. 126; no. 4; p. 045102
• Main Authors: Choi, Jun-Ho, Lee, Hochan, Lee, Kyung-Koo, Hahn, Seungsoo, Cho, Minhaeng
• Format: Journal Article
• Language: English
• Published: United States 28.01.2007
• Subjects: Circular Dichroism; Computer Simulation; Models, Chemical; Models, Molecular; Protein Conformation; Spectrophotometry, Infrared; Ubiquitin - chemistry; Ubiquitin - ultrastructure
• ISSN: 0021-9606
• DOI: 10.1063/1.2424711

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.