05985414

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05985414 Danks, Gemma B. Stepney, Susan Caves, Leo S.D. Cotranslational protein folding with l-systems. Kampis, George (ed.) et al., Advances in artificial life. Darwin meets von Neumann. 10th European conference, ECAL 2009, Budapest, Hungary, September 13--16, 2009. Revised selected papers, Part I. Berlin: Springer (ISBN 978-3-642-21282-6/pbk). Lecture Notes in Computer Science 5777. Lecture Notes in Artificial Intelligence, 289-296 (2011). 2011 Berlin: Springer EN cotranslational protein folding L-systems

doi:10.1007/978-3-642-21283-3_36

Summary: A protein molecule adopts a specific 3D structure, necessary for its function in the cell, through a process of folding. Modelling the folding process and predicting the final fold from the unique amino acid sequence remain challenging problems. We have previously described the application of L-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a physics-based approach, using calculations of interatomic forces, and a knowledge-based approach, using data from fragments of known protein structures. Here we describe a model combining these two approaches creating an adaptive stochastic open L-systems model of protein folding. L-systems were originally developed to model growth and development. Here we also describe extensions of our L-systems models to investigate cotranslational protein folding, i.e. folding during protein biosynthesis on the ribosome, which is increasingly thought to play an important role. We demonstrate that cotranslational folding fits very naturally into the L-systems framework.