Structure and function relationship of cytochrome c studied by NMR and molecular dynamics simulations
Qi, Phoebe Xiurong
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https://hdl.handle.net/2142/21703
Description
Title
Structure and function relationship of cytochrome c studied by NMR and molecular dynamics simulations
Author(s)
Qi, Phoebe Xiurong
Issue Date
1995
Doctoral Committee Chair(s)
Wand, A. Joshua
Department of Study
Biochemistry
Discipline
Biochemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Chemistry, Biochemistry
Biophysics, General
Language
eng
Abstract
High resolution solution structures of ferro- and ferricytochrome c have been determined using a combination of multidimensional $\sp1$H-NMR techniques and hybridized distance geometry-simulated annealing calculations. A family of 44 individually refined structures was obtained for each redox state. The all-residue r.m.s.d. about the average structure for ferrocytochrome c is 0.35 $\pm$ 0.04 A for the backbone N, C$\alpha$ and C$\sp\prime$ atoms and 0.86 $\pm$ 0.04 A for all heavy atoms while 0.34 $\pm$ 0.04 A and 0.89 $\pm$ 0.05 A for the ferricytochrome c. Examination of long lived structural waters in both redox states reveal potentially significant redox-dependent structural changes. The orientation of the electron spin g-tensor was determined and the resulting pseudocontact shifts were used not only to independently confirm observed structural differences but also to address the accuracy and the precision of the determined structures. Electrostatic and midpoint potential calculations across the two families of structures were performed by computer assisted molecular dynamics simulations and found to be in close agreement with the experimental value. Specific electrostatic interactions such as heme propionic acids and heme ligands that were previously considered to modulate the midpoint potentials were examined. Finally, calculations of Marcus solvent reorganization energy were carried out using the determined solution structures to provide a fundamental understanding of the electron-transfer process of cytochrome c.
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