Characterizing internal motions of peptides and proteins in solution by nuclear magnetic resonance spectroscopy

Lingyang Zhu, Purdue University

Abstract

Understanding protein function is an important goal of biological and medical research. It is generally acknowledged that protein function depends not only on the three-dimensional structure, or conformation, of the protein, but also on dynamics. However, details of the relationship between protein dynamics and function are still in question, especially regarding motions on the subnanosecond time scale. Assessment of this relationship is the ultimate goal of this thesis work. The principal focus was to validate and to further develop NMR relaxation techniques as applied to isotopically ($\sp{13}$C and $\sp{15}$N) enriched peptides and proteins. From NMR relaxation measurements interpreted using the Lipari and Szabo model-free approach, we have extracted amplitudes and rates of internal motions of peptides and proteins in solution on a residue-by-residue basis. Specific topics examined here include the evaluation of the accuracy of current relaxation techniques applied to AX$\sb2$ spin systems, finding pK$\sb{\rm a}$ values of the peptide melittin (MLT), measurement of the internal dynamics of MLT enriched with $\sp{15}$N at specific residues, and measurement of internal dynamics of rat intestinal fatty acid-binding protein (I-FABP), uniformly labeled with $\sp{15}$N, in the absence and presence of the fatty acid, palmitate. To further characterize the I-FABP system, the internal dynamics of palmitic acid itself, when bound to the protein, were also studied. The results helped clarify the applicability of NMR relaxation techniques to various spin systems, and led to a more complete understanding of the participation of charged groups in MLT in its self-aggregation. For I-FABP, distinct differences in internal dynamics of the liganded and unliganded forms of the protein were found. These data hold the promise of elucidating the relationship between protein-ligand dynamics and ligand binding.

Degree

Ph.D.

Advisors

Kemple, Purdue University.

Subject Area

Biophysics|Chemistry|Biochemistry

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