Redistribution of states and inducing new channels for conformational change: computational studies on calmodulin
Aykut, Ayşe Özlem (2013) Redistribution of states and inducing new channels for conformational change: computational studies on calmodulin. [Thesis]
In vitro experiments demonstrate that large conformational changes in many proteins are observed as “rare events” occurring on microsecond timescales. For proteins that sustain a plethora of functions, it is imperative that different conformational states be achieved readily under slightly differing environmental conditions in vivo. We investigate how perturbations that may be experienced by proteins in their fluctuating environments may be invoked to facilitate their access to different micro states, using the example of calcium loaded calmodulin (Ca2+-CaM). As perturbations, we introduce (i) mutation of a single residue, (ii) protonation of a group of residues to mimic the low pH environment, (iii) external forces applied on single residues, (iv) external displacements applied on single residues, and (v) increasing the ionic strength (IS) of the solution the protein resides in. After performing molecular dynamics simulations on the perturbed systems (i) and (ii), we observe distinct conformational changes within tens of nanoseconds, that otherwise occur on the time scales of microseconds. In particular, a reversible change between the extended and compact Ca2+-CaM structure may be invoked via the E31A mutation. This compact form bears a bent linker which is observed in many of the ligand bound forms of Ca2+- CaM. Protonation of ten acidic residues also leads to a large conformational change on the time scale of 100 ns. The structure attained is compact and although it does not have a bent linker, it is compatible with fluorescence resonance energy transfer and nuclear magnetic resonance experimental data. Barrier crossing between extended and compact forms of CaM, which is normally a rare event, is facilitated by shielding the repulsive electrostatic interactions between the two lobes. This is due to either the impact of lowering the pH in the environment or to allosteric interactions originating on the Nterminal domain and detected in the C-terminal domain as implicated by from the results of (iii) and (iv). We further find using scenario (v), at high IS there is depletion in the number of ions residing in close proximity of the protein. The loss of ionic screening results in rigidification of the linker fluctuations, leading to the slowing down of the dynamics of the system. Application of external perturbations to extended Ca2+- CaM in the form of forces (iv) as opposed to displacements (v) yield complementary results. We find that both approaches designate the same two regions on the protein structure, making these regions potential sites for manipulating conformational change. Local force perturbations implicate charged residues while local displacement perturbations find polar and hydrophobic residues in the same two regions. The observations reflect the differences inherent in the thermodynamic functions optimized by the two approaches, while confirming the universality of allosteric communication between the two lobes.
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