Structures and dynamics of helices in water and membrane environments studied by two -dimensional infrared spectroscopy

Chong Fang, University of Pennsylvania


Helix is a fundamental building block of proteins, whose biological functions depend upon their dynamics in specific environments. The 3D structures and conformational dynamics of a series of a α-helices in water and membrane environments have been studied by either the time domain or frequency domain interferometry incorporating the two-dimensional infrared (2D IR) technique and double isotope labeling strategy. Vital molecular information on a single-residue level is revealed through the detailed analysis of the cross peaks particularly in the isotopomer region. The waiting time dependence of the 2D correlation spectrum informs on the dynamics of the system on the sub-picosecond timescale with bond length scale precision. After the general introduction in Chapter I, the theoretical basis, operational principles and experimental setup were outlined in Chapter II. A series of doubly isotopically substituted 25-residue alanine-rich α-helices were measured by femtosecond three-pulse infrared time domain interferometry as presented in Chapter III. The magnitudes of three major coupling constants were obtained with signs determined to be β 12 > 0, β13 < 0 and β14 < 0. A series of singly 13C=18O labeled a -helices were measured by spectral interferometry (Chapter IV). The 13C=18O diagonal peaks appeared at ∼1571.3±0.8 cm-1, whereas residues 14 and 11 had wider structural distributions than 12 and 13. A small fast component in the correlation function was used to estimate the dynamics of these distributions whose structural origin was proposed to be the effect of nearby lysine residues on the intrahelical hydrogen-bond network. 2D IR spectroscopy was also adapted to probe the tertiary interactions within TM helices as shown in Chapter V. Residues Gly79 on the opposing TM dimer helices of GpA in SDS micelles were either 13C= 16O or 13C=18O substituted to obtain isotopomers. The 2D IR correlation spectra visualize the van der Waals packing force as cross peaks both above and below the diagonal line, with an off-diagonal anharmonicity of 3.8±0.6 cm-1 indicative of β ≈ +6.7±1.5 cm-1. The angle between the two Gly79 amide-I' transition dipoles was estimated to be ∼110°±8°. The waiting time dependence of the echo informs on the dynamics of different regions of the dimer either completely embedded in micelles or partially exposed to water.

Subject Area

Chemistry|Biophysics|Analytical chemistry

Recommended Citation

Fang, Chong, "Structures and dynamics of helices in water and membrane environments studied by two -dimensional infrared spectroscopy" (2006). Dissertations available from ProQuest. AAI3225454.