Thermodynamics and Kinetics of Ligand Photodissociation in Heme Proteins and Formation of DNA i-Motif

Authors

David S. ButcherFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Chemistry

First Advisor's Name

Jaroslava Miksovska

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Konstantinos Kavallieratos

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Yuk-Ching Tse-Dinh

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

Irina Agoulnik

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Joong Ho Moon

Fifth Advisor's Committee Title

Committee Member

Keywords

heme, heme protein, hemoglobin, photoacoustic, photoacoustic calorimetry, biophysical chemistry, i-motif, flavohemoglobin, non-symbiotic

Date of Defense

3-1-2017

Abstract

Heme proteins carry out a diverse array of functions in vivo while maintaining a well-conserved 3-over-3 α-helical structure. Human hemoglobin (Hb) is well-known for its oxygen transport function. Type 1 non-symbiotic hemoglobins (nsHb1) in plants and bacterial flavohemoglobins (fHb) from a variety of bacterial species have been predicted to carry out a nitric oxide dioxygenase function. In nsHb1 and fHb this function has been linked to protection from nitrosative stress. Herein, I combine photoacoustic calorimetry (PAC), transient absorption spectroscopy (TA), and classical molecular dynamics (cMD) simulations to characterize molecular mechanism of diatomic ligand interactions with a hexa-coordinate globin from plant (rice hemoglobin), bacterial flavohemoglobins and human hemoglobin.

In rice type 1 non-symbiotic hemoglobin (rHb1), the dynamics and energetics of structural changes associated with ligand photodissociation is strongly impacted by solvent and temperature, namely CO escape from the protein matrix is slower at pH = 6.0 compare to neutral pH (ns) due to the CD loop reorganization which forms a pathway for ligand escape. In human hemoglobin, exogenous allosteric effectors modulate energetics of conformational changes associated with the CO and O₂ escape although the effectors impact on rate constants for ligand association is small. The conformational dynamics associated with ligand photorelease from fHbs from Cupriavidus necator (FHP) and Staphylococcus aureus (HMP_Sa) are strongly modulated by the presence of azole drugs indicating that drug association modulates structural properties of the heme binding pocket.

In addition, we carried out a study of the formation of the DNA intercalated motif (i-motif). The formation of the structure is strongly favored at acidic pH; therefore, PAC was combined with a 2-nitrobenzaldehyde pH-jump to probe formation of the i-motif on fast timescales. i-Motif folding is two-step process with the initial protonation of cytosine residues being endothermic with ΔH_fast=8.5 ± 7.0 kcal mol^-1 and ΔV_fast=10.4 ± 1.6 mL mol^-1 and subsequent nucleation/i-motif folding (τ = 140 ns) with ΔH_slow=-51.5 ± 4.8 kcal mol^-1 and ΔV_slow=-6.6 ± 0.9 mL mol^-1. The above results indicate that PAC can be employed to study diverse biochemical reactions such as DNA folding, drug binding and ligand photorelease from proteins.

Identifier

FIDC001737

ORCID

0000-0002-1268-4150

Recommended Citation

Butcher, David S., "Thermodynamics and Kinetics of Ligand Photodissociation in Heme Proteins and Formation of DNA i-Motif" (2017). FIU Electronic Theses and Dissertations. 3259.
https://digitalcommons.fiu.edu/etd/3259