Molecular Dynamic Simulations: what can we learn about proteins using computers?



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Computational power drastically improved in the last decade which allowed many laboratories today to use molecular simulations and apply them to biological systems. This approach assists answering questions that are hard or nearly impossible to get by using “wet” laboratory techniques. Often, when the certain protein is studied, it is studied by itself without the environment. However, soluble proteins are floating in the cytoplasm is much denser than water and contains many different proteins and other agents such as ions. The presence of other crowding agents and proteins can influence protein stabilization, assist in denaturation or even alter protein secondary structure and create a new more stable conformational state with lower minimal energy. My job was to test a new model for the laboratory and find the good protein candidates for the future research work. It was satisfying to see a real-life application of the knowledge that I already had from my classes. Moreover, I had to pick up some programming skills which I had limited exposure before last summer. During my training I liked to see my own growth in amount of independent work that I was able to do. My presentation focuses on the multidisciplinary research, and my experience as an undergraduate student in an academic laboratory.