Investigation of the relative conformational stability of protein mutants by molecular dynamics simulation

It was the objective of this work to investigate by MD simulation the influence of experimentally verified point mutations on the structure and conformational stability of segments of the human hair monomeric IF unit as well as on their lowest aggregation level, namely the coiled coil structure. Mutations in the helix termination motif of human hair keratin gene hHb6 seem to be connected to the hereditary hair dystrophy Monilethrix. The most common mutations reported are Glu413Lys and Glu413Asp, located at the C-terminal end of the coiled coil 2B- rod domain of the IF. This study follows two approaches. First, MD simulation aims to reveal features of the dynamical behavior and the temperature dependent stability of IF segments. Secondly, a thermodynamic approach based on free energy calculations aims to reveal the energetic consequences due to amino acid mutations and to determine the relative stability of the wild type and mutated segments. The analysis of the MD trajectories shows an increase in structural destabilization with increasing temperature for all systems. In case of the coiled coil structures the temperature induced destabilization starts especially at the C-terminus. This happens for both sets of MD simulations (with cutoff method and with PME). However, the results do not put into evidence any significant differences in the dynamics and the stability of the backbones of wild type and mutated segments. Unlike this, a detailed analysis of the electrostatic interactions shows a difference between the interactions of Glu413 in the wild type coiled coil structure and Lys413 in the mutated coiled coil structure. One can presume that changing the charge from -1 (in case of Glu) to +1 (in case of Lys) leads to the observed reorientation of the side chains. However, from the MD simulation it cannot be judged how this behavior will affect the interactions within the IF, namely dimer-dimer interactions. In the second part of the thesis free energy differences between the wild type and mutated (Glu413Lys and Glu413Asp) IF systems are calculated. To this, hybrid models representing the alchemical transformation of the amino acids are created and tested in order to adequately calculate the free energy differences induced by mutations. Based on the observations of the present study, it can be speculated that higher order assembly of keratin IF is altered by Glu413Lys and, at much lower extent, by Glu413Asp mutation which may interfere with the proper dimer-dimer interactions. However, the molecular basis of the structural changes in keratin IF caused by Monilethrix can only be explained when atomic resolution detail of the dimer-dimer associations in the wild type IF becomes available

Investigation of the relative conformational stability of protein mutants by molecular dynamics simulation

It was the objective of this work to investigate by MD simulation the influence of experimentally verified point mutations on the structure and conformational stability of segments of the human hair monomeric IF unit as well as on their lowest aggregation level, namely the coiled coil structure. Mutations in the helix termination motif of human hair keratin gene hHb6 seem to be connected to the hereditary hair dystrophy Monilethrix. The most common mutations reported are Glu413Lys and Glu413Asp, located at the C-terminal end of the coiled coil 2B- rod domain of the IF. This study follows two approaches. First, MD simulation aims to reveal features of the dynamical behavior and the temperature dependent stability of IF segments. Secondly, a thermodynamic approach based on free energy calculations aims to reveal the energetic consequences due to amino acid mutations and to determine the relative stability of the wild type and mutated segments. The analysis of the MD trajectories shows an increase in structural destabilization with increasing temperature for all systems. In case of the coiled coil structures the temperature induced destabilization starts especially at the C-terminus. This happens for both sets of MD simulations (with cutoff method and with PME). However, the results do not put into evidence any significant differences in the dynamics and the stability of the backbones of wild type and mutated segments. Unlike this, a detailed analysis of the electrostatic interactions shows a difference between the interactions of Glu413 in the wild type coiled coil structure and Lys413 in the mutated coiled coil structure. One can presume that changing the charge from -1 (in case of Glu) to +1 (in case of Lys) leads to the observed reorientation of the side chains. However, from the MD simulation it cannot be judged how this behavior will affect the interactions within the IF, namely dimer-dimer interactions. In the second part of the thesis free energy differences between the wild type and mutated (Glu413Lys and Glu413Asp) IF systems are calculated. To this, hybrid models representing the alchemical transformation of the amino acids are created and tested in order to adequately calculate the free energy differences induced by mutations. Based on the observations of the present study, it can be speculated that higher order assembly of keratin IF is altered by Glu413Lys and, at much lower extent, by Glu413Asp mutation which may interfere with the proper dimer-dimer interactions. However, the molecular basis of the structural changes in keratin IF caused by Monilethrix can only be explained when atomic resolution detail of the dimer-dimer associations in the wild type IF becomes available

Benefits of Nanomedicine for Therapeutic Intervention in Malignant Diseases

Cancer remains one of the most difficult to manage healthcare problems. The last two decades have been considered the golden age of cancer research, with major breakthroughs being announced on a regular basis. However, the major problem regarding cancer treatment is the incapability to selectively target cancer cells, with certain populations of tumors still remaining alive after treatment. The main focus of researchers is to develop treatments that are both effective and selective in targeting malignant cells. In this regard, bioavailability can be increased by overcoming the biological barriers encountered in the active agent’s pathway, creating carrier vehicles that have the ability to target malignant cells and effectively release the active agent. Since its appearance, nanomedicine has provided many answers to these challenges, but still, some expectations were not satisfied. In this review, we focused on the most recent developments in targeted drug delivery. Furthermore, a summary of different types of nanoparticles used to deliver active therapeutic agents in oncology is presented, along with details on the nanodrugs that were clinically approved by the Food and Drug Administration (FDA), until April 2019