Development and Application of Novel ... - Jacobs University

The atomic level understanding of the subtle intertwining among structure,
dynamics and function of enzymes plays an important role to rationally design new or
improved functions. Second part of the thesis (Part II, Chapter 3 – 6) is based on molecular
modeling approach to gain insight into the structural and dynamic properties of P450BM-3
(CYP102) complex in water and in the presence of cobalt(II)sepulchrate (CoSep) as an
electron transfer (ET) mediator. P450BM-3, isolated from Bacillus megaterium is an
attractive target and model system for biochemical (catalyzes the wide variety of
industrially attractive substrates) and biomedical (being a bacterial model for microsomal
P450s system) applications. The comprehensive theoretical aspects of MD simulation are
provided in Chapter 3 with the overview about the system preparation for MD simulation
and the analysis of protein conformation and dynamics in the generated trajectory. In
Chapter 4, the structural and dynamic properties of P450BM-3 FMN (Flavin
mononucleotide) domain as holo-protein, with the cofactor in oxidized and reduced states
and as apo-protein are investigated. The results illustrate the effect of FMN cofactor and its
protonation state on the conformation and dynamics of the FMN domain that can be
related to ET pathway from FMN to HEME cofactor. The study is further extended to garner
insight into the binding modes and the structural determinant of inter-domain ET in
HEME/FMN complex of P450BM-3. MD simulations were performed on both FMN and
HEME domains, isolated and in their crystallographic complex and results are reported in
Chapter 5. HEME/FMN complex undergoes the rearrangement process to decrease the
distance between their redox centers to promote favorable ET rate under physiological
condition. In Chapter 6, MD simulation of P450BM-3 domains (isolated HEME domain and
HEME/FMN complex) were performed in the presence of CoSep, as ET mediator. The
results illustrate the preferential binding modes of CoSep in P450BM-3 domains and the
putative ET pathways from CoSep to the iron center of HEME cofactor and are in agreement
with the experimental findings.
v