Describing Methodology and Applications of an In Silico Protein Engineering Approach

Describing Methodology and Applications of an In Silico Protein Engineering Approach

Trias Thireou (National Technical University of Athens, Greece), Kostas Bethanis (Agricultural University of Athens, Greece) and Vassilis Atlamazoglou (Agricultural University of Athens, Greece)
DOI: 10.4018/978-1-60566-768-3.ch002
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This chapter presents a particular cascade of computational steps in order to build a workflow for an in silico protein engineering approach. In this respect, all available information, in order to choose and computationally implement mutations, is described, employed and monitored. Some of the prerequisites of in silico protein engineering are access to various sequence and structure molecular biology databases, software tools for three dimensional molecular visualization and manipulation, sequence and structure alignment and comparison, molecular modelling and molecular docking. The implementation of these steps is demonstrated in the context of performing mutations of particular residues on the ligand pocket of a lipocalin protein family member, to derive the desired ligand binding properties. The example chosen for inclusion introduces the reader to all of the essentials of computational protein engineering experiments. More importantly, it provides insight into understanding and properly interpreting the data produced by these methods.
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Protein Scaffolds

As mentioned above, rather than attempting to design from scratch, one can utilize a number of nature provided templates to improve on. At the very least, these templates already fulfill the criteria for stably folding proteins.

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