5 research outputs found
Determination of Ligand Pathways in Globins: Apolar Tunnels Versus Polar Gates
Background: O2 pathways in animal hemoglobins and myoglobins are controversial.
Results: Ligands enter and exit sperm whale Mb and Cerebratulus lacteus Hb by completely different pathways.
Conclusion: Rational mutagenesis mapping can identify ligand migration pathways and provides experimental benchmarks for
testing molecular dynamics simulations.
Significance: Globins can use either a polar gate or an apolar tunnel for ligand entry
Molecular dynamics study of the allosteric control mechanisms of the glycolytic pathway
There is a growing body of interest to understand the regulation of allosteric proteins.
Allostery is a phenomenon of protein regulation whereby binding of an effector molecule at a
remote site affects binding and activity at the proteinâs active site. Over the years, these sites
have become popular drug targets as they provide advantages in terms of selectivity and
saturability. Both experimental and computational methods are being used to study and
identify allosteric sites. Although experimental methods provide us with detailed structures
and have been relatively successful in identifying these sites, they are subject to time and cost
limitations.
In the present dissertation, Molecular Dynamics Simulations (MDS) and Principal
Component Analysis (PCA) have been employed to enhance our understanding ofallostery
and protein dynamics. MD simulations generated trajectories which were then qualitatively
assessed using PCA. Both of these techniques were applied to two important trypanosomatid
drug targets and controlling enzymes of the glycolytic pathway - pyruvate kinase (PYK) and
phosphofructokinase (PFK).
Molecular Dynamics simulations were first carried out on both the effector bound and
unbound forms of the proteins. This provided a framework for direct comparison and
inspection of the conformational changes at the atomic level. Following MD simulations,
PCA was run to further analyse the motions. The principal components thus captured are in
quantitative agreement with the previously published experimental data which increased our
confidence in the reliability of our simulations. Also, the binding of FBP affects the allosteric
mechanism of PYK in a very interesting way. The inspection of the vibrational modes reveals
interesting patterns in the movement of the subunits which differ from the conventional
symmetrical pattern. Also, lowering of B-factors on effector binding provides evidence that
the effector is not only locking the R-state but is also acting as a general heat-sink to cool
down the whole tetramer. This observation suggests that protein rigidity and intrinsic heat
capacity are important factors in stabilizing allosteric proteins. Thus, this work also provides
new and promising insights into the classical Monod-Wyman-Changeux model of allostery