title: Protein design in biological networks: from manipulating the input to modifying the output.
abstract: Protein engineering has been an invaluable tool for the deciphering of protein folding and function and in the understanding of biological signaling networks. From an applied point of view it has been of paramount importance in biotechnological and biopharmaceutical products and applications. Traditionally, the protein engineering tools of choice were 'classical' rational design, or directed evolution-based methods. In recent years, a third tool has matured: computational protein design (CPD). In this review, we summarize the underlying principles of CPD and discuss its application for understanding and modifying biological systems. Three main applications of the use of protein design will be highlighted and reviewed: artificially rewiring of signal transduction networks, prediction and generation of large-scale in silico interaction networks and using protein design to manipulate gene expression.
authors: CRG-EMBL Systems Biology Program, Design of Biological Systems, Centre de Regulació Genòmica, 08003 Barcelona, Spain. almer.vandersloot@crg.es
authors: Almer M
authors: AM
authors: Van der Sloot
authors: Christina
authors: C
authors: Kiel
authors: Luis
authors: L
authors: Serrano
authors: Francois
authors: F
authors: Stricher
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008954:Models, Biological; D008958:Models, Molecular; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*
chemical_list: D011506:Proteins