title: Towards computing with proteins.
abstract: Can proteins be used as computational devices to address difficult computational problems? In recent years there has been much interest in biological computing, that is, building a general purpose computer from biological molecules. Most of the current efforts are based on DNA because of its ability to self-hybridize. The exquisite selectivity and specificity of complex protein-based networks motivated us to suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. Such devices, powered by ATP molecules, would be able to perform, for medical applications, digital computation with natural interface to biological input conditions. We discuss how to design protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing. A solution of these elements could carry out effective computation. Finally, the model and its robustness to errors were tested in a computer simulation.
authors.affiliation: Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel. ron@biomodel.os.biu.ac.il
authors.forename: Ron
authors.initials: R
authors.lastname: Unger
authors.forename: John
authors.initials: J
authors.lastname: Moult
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D000465:Algorithms; D001185:Artificial Intelligence; D002468:Cell Physiological Phenomena; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003199:Computer Systems; D003201:Computers; D004247:DNA / Q000737:chemistry; D001330:Electronic Data Processing; D007257:Information Theory; D008432:Mathematical Computing; D008954:Models, Biological; D008962:Models, Theoretical; D016571:Neural Networks, Computer; D017711:Nonlinear Dynamics; D009693:Nucleic Acid Hybridization; D010766:Phosphorylation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D011506:Proteins; D000255:Adenosine Triphosphate; D004247:DNA