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Thesis Format

Integrated Article

Degree

Doctor of Philosophy

Program

Chemistry

Collaborative Specialization

Scientific Computing

Supervisor

Karttunen, Mikko

Abstract

We present molecular dynamics (MD) simulations of two protein targets for drug design: Triosephosphate isomerase (TIM) and Methyl CpG binding protein 2 (MeCP2). First, we studied three TIM proteins: TcTIM, TbTIM and a chimeric protein (Mut1). The first two are homologous enzymes with high sequence similarity, albeit different biophysical parameters. The chimeric protein has TbTIM’s sequence and 13 single point mutations, which are sufficient to obtain TcTIM-like behaviour in reactivation experiments. We analyzed the residue interaction networks observed in the all-atom MD simulations, as well as their electrostatic interactions and the impact of simulation length on them. A conserved salt bridge between catalytic residues Lys 14 and Glu 98 was observed in all three proteins, but key differences were found in other interactions concerning the catalytic amino acids. Although TcTIM forms less hydrogen bonds than TbTIM and Mut1, its hydrogen bond network spans almost the entire protein, connecting the residues in both monomers. Some of these interactions appeared only after the first microsecond of the simulation, and convergence in the number of hydrogen bonds was only reached during the last of the 3 μs of the simulation. Second, we performed MD simulations of the methyl DNA binding domain (MBD), which is the only domain in MeCP2 with an available structure. After characterizing its structure both in solution and in the presence of a surface in order to compare with high-speed atomic force microscopy experiments (HS-AFM), we built the rest of the protein structure by ab initio modelling using Modeller. This model was simulated in both all-atom and coarse-grained force fields. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. A similar two-globule conformation has been observed in the HS-AFM experiments. Our results are in good agreement with available experimental data. They predicted 4.1% of α-helical content, the experimental result is 4%. Finally, we compared the model predicted by AlphaFold to our Modeller model. Together, these simulations represent the first attempt to characterize the structure and dynamics of the full-length MeCP2 protein.

Summary for Lay Audience

We present molecular dynamics (MD) simulations of two proteins. The aim of an MD simulation is to provide the time-evolution of a system by solving iteratively its equations of motion. We first studied two Triosephosphate isomerase (TIM) proteins, one from Trypanosoma cruzi (TcTIM), the parasite that causes Chagas’ disease, and one from Trypanosoma brucei (TbTIM), causative agent of the African sleeping sickness, as well as a chimeric protein with some characteristics of both of them. Our simulations allowed us to study the electrostatic interactions between these proteins and explain why they behave differently even though they are extremely similar. Next, we focused our study on the Methyl CpG binding protein 2 (MeCP2). This protein is essential for growth and synaptic activity of neurons. Its malfunction is associated to Rett syndrome, the most common cause of cognitive impairment in females. This protein is an intrinsically disordered protein (IDP), a type of protein which does not have a unique tertiary structure. IDPs are highly flexible and conventional methods to study proteins are often not directly applicable to them. This is why the full-length structure of MeCP2 has not been solved yet. The only available structure solely contains ~17% of its amino acids, which represents the most ordered domain of this protein. We first performed MD simulations on this structure, and then used ab initio modelling to complete the rest of the protein. Since all-atom simulations of this model were not enough to guarantee adequate sampling of its conformational space, coarse-grained modeling was used to complement the atomistic picture. The coarse-grained simulations sampled a conformation that had not been observed in the all-atom simulations but that was in good agreement with a conformation previously observed in experimental data. Furthermore, our simulations predicted an α-helical content of 4.1% (experimental value: 4%). Together, our simulations represent the first effort to characterize the structure and dynamics of the full-length MeCP2 protein.

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