Structure and function relationship of cytochrome c studied by NMR and molecular dynamics simulations

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, Cα 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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2011

Author dc:creator

• Qi, Phoebe Xiurong

Contributors dc:contributor

• Wand, A. Joshua

• Chemistry, Biochemistry
• Biophysics, General

Statement dc:rights

• Copyright 1995 Qi, Phoebe Xiurong

Language dc:language

eng

Identifier

AAI9624464
(UMI)AAI9624464

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/21703