UV resonance raman study of solution environment effect on poly-L-lysine conformation and resolution enhancement mechanism of two dimensional correlation spectroscopy

How proteins fold into compact, highly ordered and functional three-dimensional structures continues to challenge the modern science. UV resonance Raman (UVRR) is one of the advanced technologies used to study protein folding problem. In this thesis, by using UVRR spectroscopy, we examined solution environment effect on poly-L-lysine (PLL) conformation in great detail.;We investigated the sidechain electrostatic control of PLL conformation by examining the PLL conformational dependence on pH, the presence of NaCl and NaClO4, and temperature. At pH value below 7, PLL adopts the extended polyproline II (PPII) and 2.51-helix conformations. Increasing pH and the addition of NaClO4 induces PLL to form a high content of a-helix-like conformations (alpha-helix, pi-bulge/helix and turn structures) by decreasing the sidechain electrostatic repulsion. In contrast to NaClO4, we found that high concentrations of NaCl has negligible impact on the PLL conformation at low pH. Utilizing UVRR, we also quantitatively tracked temperature and NaClO4 concentration induced conformation changes of PLL. We experimentally determined the conformational population distributions and the energy landscape of PLL along the Ramachandran Psi angle under different solution conditions.;We measured the NaClO4 concentration dependence of PLL amide hydrogen exchange kinetics at pH 2.8 using UVRR spectroscopy. We found NaClO 4 slows the hydrogen exchange rates for the extended conformations and conformational exchange rates between the extended and alpha-helix-like conformations. We proposed a NaClO4 protection mechanism.;This thesis also includes the study of the resolution enhancement mechanism of generalized two-dimensional correlation spectroscopy (2D COS). Despite extensive study, the origin of the 2D COS spectral patterns for overlapping bands and the resolution enhancement mechanisms are not completely understood. By using the simulation method, we elucidated the origin of 2D COS spectral features and identified the conditions to resolve overlapping bands.