BioSysBio:abstracts/2007/Alfonso Jaramillo

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Computational Design of Proteins With New Functions

Author(s): A. Jaramillo
Affiliations: Ecole Polytechnique, France

Keywords: 'Synthetic Biology' 'Computational Protein Design'

Proposed Talk Abstract

In Synthetic Biology we are often confronted to the task of designing new parts and devices composed of proteins with specified functionalities that are not found in nature. We will discuss the applications of our computational protein design methodology to design proteins with new functionalities. We have developed an automated computational method that uses high-resolution protein structures together with molecular modelling techniques to simulate the result of combinatorial mutagenesis and dynamics of protein structures. We use a physical model of the protein's unfolded and folded states to rank the proteins according to their folding free energy. For that we use an all-atom force field, a high-resolution protein structure and a rotamer library. Our methodology combines the sequence and rotamer searches with the docking problem into a single combinatorial optimisation procedure to generate protein sequences and their structures, able to bind a specified molecular target. Our computational procedure can also be applied to reduce the library size in directed evolution experiments. We will discuss the applications of our methodology to design new synthetic proteins and enzymes. In particular, we have added an esterase activity into a Thioredoxin protein while maintaining its wild-type activity. We verify our predictions with experimental results.

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