Completed notes of the course

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1 BIOMOLECULAR MODELING LABORATORY 2 LEZIONE 1 [16/09] – INTRODUCTION PROJECTS Enzyme engineering -> development of methods to improve existing enzyme or new enzyme. So one application is if we have an enzyme that catalyse a chemical reaction. Enzyme usually are very useful but also very unstable so they will last for few hour. The idea is to use comp utational modelling to generate the enzyme variants that are more stable and then go to the lab. In this way, we just prove some of them in real life in order to save time and money. Generally the work in the lab is quite expensive and time consuming. Design of self-assembling peptides -> one project in Milan is to design peptides that self-assemble. There are proteins that self -assemble in nature and they are not good , they are called amylose protein. For example the Alzheimer disease is due to the self -assemble into fibers of the a beta protein. Also the Parkinson disease is partially related to a self-assembling protein and the mad cow disease as well. However if we learn from nature how this ammino acids self -assembly we can use this tool to create for exam ple fibers or gels or particles that are made of peptides. So they are extremely biocompatible and we can use them for cell culture. So it will be very useful and interesting. Nanoplastics -> are small (5-10 nm) plastics particles that are increasingly found in the water of the oceans. The study focus on the relationship between nanoplastics and protein. They promote the self-assembly of the protein. In particular, they work as seed where a protein starts to self-assemble. So they can be related to the insurgence of disease that are related to protein self-assemble. In the study, they are using molecular modelling to understand how proteins behave in the…