Measurements of dynamics, structure, and flexibility of macromolecules by pulsed Electron Spin Resonance

This thesis discusses the measurement of molecular dynamics and distances in spin-labeled macromolecules by pulsed electron spin resonance (ESR). We present a scheme to reduce the dead-time in a commercial ESR spectrometer. This achievement facilitates the acquisition of the ESR signal even when it is largely reduced due to short relaxation times. As a result, we obtain the two-dimensional (2D) ESR signal for a nitroxide labeled peptide over a temperature range of 192 K to 310 K. In that temperature range, molecular reorientations over the range of 10-10 to 10-4 s are sampled. The phase memory time (Tm) is measured at each experimental temperature. The phase memory times, Tm, as a function of rotational correlation are calculated using spectral simulations based on the stochastic Liouville equation. By comparing the plots of Tm versus temperature obtained from experiment and theoretical models, the details of molecular dynamics are elucidated. This accomplishment expands the application of 2D ESR to the measurement of dynamics in large proteins.The second part of this research employs a pulsed ESR technique, double electron-electron resonance (DEER), to measure large-scale distances in bis-peptide materials composed of 4-8 monomers. Constraints on overall structure and flexibility of the oligomers are rapidly determined by the end-to-end distance distribution measured from the DEER data. The distance distributions from DEER data are compared with those obtained from molecular dynamics (MD) simulations. Discrepancies between the DEER and MD results are evident, especially for longer oligomers. In order to rapidly predict the shapes of the oligomers, we introduce a joint stiff-segment model to represent the oligomer backbone. A scheme is established to exploit information on the end-to-end distance distribution functions obtained by ESR to optimize the force fields used in the joint-stiff segment model. The results provide information on the distribution of orientations of a monomer with respect to the preceding monomer. The model gives parameters that better fit the ESR results than those originally obtained from the MD simulations. The results enhance our ability to predict the shapes and flexibility of new oligomers constructed using an arbitrary number of monomer units