Investigations of some biological molecules and processes via NMR spectroscopy and computer methods
Abstract
Presented here are investigations into biological signalling events, structure elucidation of the hormone salmon calcitonin, development of the computer program MORASS for relaxation matrix analysis of NOESY data, and parameter development for use of MORASS during structural refinement of macromolecules. In-vivo $\sp{31}$P NMR investigations of plant cell pH are presented in Chapter 2. Use of a flow cell/perfusion system to maintain metabolic integrity is illustrated. Results from pH titrations show that the intracellular pH is affected when nonbasal pH media is added extracellularly. Intracellular perturbations are greatest in the vacuole and are proportional to the deviation between the extracellular pH insult and the resting pH. Addition of chemical elicitors buffered to the basal pH value resulted in no change in internal pH during the first 30-45 minutes after elicitor addition. Chapter 3 describes NMR and modelling investigations of the 32 residue hormone salmon calcitonin (sCT) in 90% MeOH - 10% H$\sb2$O. In MeOH, sCT contains an $\alpha$ helical segment from Val-8 through Tyr-22 and a region of conformational heterogeneity (residues 20 through 25) resulting from the slow isomerism of the cis and trans forms of Pro-23. The C-terminal segment is found to exist in an extended conformation. Chapters 4 and 5 examine methods for distance determination from Nuclear Overhauser Effect Spectroscopy (NOESY). The two-spin approximation is examined, as is a complete matrix approach for analysis of the NOE. The ability of the matrix method to derive accurate relaxation rates with data simulated to include typical experimental errors is examined. Results show that the matrix method can absorb some experimental error and still produce interproton distances that are more accurate than the two-spin method. To overcome the problems of an incomplete NOESY map a complete matrix may be obtained by substitution of missing data from model geometries. This approach is analyzed in Chapter 5 for a DNA dodecamer duplex, d(CGCGAATTGCGC)$\sb2$. Results show that structures derived from the hybrid relaxation rate matrix analysis of the NOESY data are more accurate than those derived from a simple two-spin approximation analysis.
Degree
Ph.D.
Advisors
Gorenstein, Purdue University.
Subject Area
Biochemistry
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