PDF, English (PhD thesis)
During communication processes, such as the allosteric regulation of enzymatic activity or the opening of mechanically-gated channels, biomolecules undergo conformational changes. Perturbations, like the binding of a ligand or stress in the cell membrane, act similar to the application of an external force. They trigger a response which is directly dependent on the receptor's mechanical properties, which can be characterized, among others, through Atomic Force Microscopy (AFM) experiments.
We introduce here Time-Resolved Force Distribution Analysis (TRFDA), an extension to Molecular Dynamics (MD) simulations, providing an engineer's view to in silico (bio)molecules. TRFDA reveals the internal distribution of forces and stresses in equilibrium states or during conformational changes, thereby exposing the propagation of an external force throughout the molecular structure. We also introduce the concept of punctual stress, an expression of stress at atomic level, which highlights the structural elements involved in the mechanical response.
We first apply TRFDA to study the indentation until rupture of a single layer graphene sheet, providing essential insight into the distribution of stress in molecular structures during material deformation and rupture. We find that stress accumulates under the AFM indenter tip much stronger than previously assumed, and it decays to almost background levels at distances as low as 5-10 times the indenter radius. The graphene rupture is initiated by thermal fluctuations in the stressed material, and the probability of rupture decreases exponentially as the distance from the indenter tip increases, explaining the locality of material failure observed experimentally.
The force-induced unfolding of two small proteins, ubiquitin and NuG2, represents a second application of TRFDA. In force-clamp MD simulations, we reproduce the stretched exponential kinetics reported experimentally for the unfolding of these proteins. The unfolding kinetic curves become more stretched with the decreasing mechanical resistance of the protein, suggesting that the the two-state kinetic model of protein unfolding should be augmented by a component expressing the protein elasticity. This finding is in line with the theory of glassy dynamics or static disorder in the transition states, proposed earlier as explanation for the stretched exponential kinetics. For different applied forces, we determine unfolding rates, then compare and combine them with experimental kinetic data in a single model, predicting equilibrium kinetic parameters which agree remarkably well with experimental ones. Using TRFDA, we identify the structural elements bearing most of the external force, and find that similarity in the secondary and tertiary structure is not a good predictor of similarity of unfolding mechanisms and mechanical properties. Our analysis of internal forces and stresses in tensed proteins also suggests that the stretched exponential kinetics is simply an expression of the protein elasticity.
By providing a dynamic view of forces and stress variations in MD simulations of dynamic processes, TRFDA can give insights in the structure and functionality of biomolecules, and is the ideal tool to complement experimental techniques in determining mechanical properties. We therefore hope that TRFDA will soon become a common tool for analyzing results from MD simulations of (bio)materials.
|Supervisor:||Russell, Prof. Dr. Robert B.|
|Date of thesis defense:||24 July 2013|
|Date Deposited:||11 Oct 2013 09:06|
|Faculties / Institutes:||The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences|
|Subjects:||570 Life sciences|
|Uncontrolled Keywords:||biophysics protein unfolding stress distribution kinetics graphene|