Royal Institute of Technology
School of Biotechnology
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3. Macromolecular Chemistry and Biology
Important processes in materials or in real life occur at many scales. As commented above a good way to address these processes is by transcending or connecting the scales in both length and time. One way to accomplish this is to divide the system into an active site and an environment. In biology we adopt this notion to address full proteins and how proteins interact with each other.
One branch of our .macro. research aims at closing the gap between the known protein sequences and determined protein structures which has become increasingly wide. In the foreseeable future, the experimental structures of the vast majority of the known protein sequences will not be available. We model to predict protein structures to be useful for structure-based drug design and biological studies, through applying and developing various modelling approaches, such as homology modelling, loop refinement, and molecular simulation techniques. In this context we also focus on protein-ligand binding which is important for many biological processes. By applying new modelling methods to elucidate the mechanism of protein-ligand binding and binding affinities in aqueous environments we seek for new opportunities in structure-based drug design.
We also take interest in bio structures outside the human body, like carbohydrates. We here aim for understanding of the structure, self-assembly, and other properties of plant cell walls which is essential for exploring new bio-mimetic materials. We hope to identify and characterize the key factors governing the structures of cellulose fibrils and cross-linking agents, as well as their interactions. Here our tools and expertise for studying various type of interactions, catalytic reactions and general structure and dynamics, come well into play.
A particular speciality of the department is the development multiscale property methods to model the measurements of biomolecular systems, for example spin and light probes in protein pockets or in cell channels. That is we simulate NMR, IR, Vis/UV and other spectral data to .catch. parameters that characterize these systems. Molecular probes emerge here as effective tools for characterization of the micro environments in the bio-structures and in bio-imaging applications such as protein structure, drug design, and identification of diseases caused by fibril formation (for instance Alzheimer's disease) and cancer. We can here model and understand the substantial property changes that the molecular probes display by following the alternation of the molecular and electronic structure and the spectral response depending upon the nature of the environment.