title: Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2.
abstract: Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profitable investment, but the design of efficient biomimetic systems remains a considerable challenge. An ideal biomimetic system self-assembles in solution, binds a desired range of substrates and catalyzes reactions with turnover rates similar to the native system. To this end, tailoring catalytic functionality in engineered peptides generally requires site-directed mutagenesis or the insertion of additional amino acids, which entails an intensive search across chemical and sequence space. Here we discuss a novel strategy for the computational design of biomimetic compounds and processes that consists of a) characterization of the wild-type and biomimetic systems; b) identification of key descriptors for optimization; c) an efficient search through sequence and chemical space to tailor the catalytic capabilities of the biomimetic system. Through this proof-of-principle study, we are able to decisively understand and identify whether a given scaffold is useful, appropriate and tailorable for a given, desired task.
authors.affiliation: Department of Bioengineering, University of California, San Diego, CA, 92093, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Brunk
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland), Fax: (+41) 21 693 0320.
authors.forename: Marta A S
authors.initials: MA
authors.lastname: Perez
authors.affiliation: Department of Computer Science, Amrita School of Engineering, 560035, Bangalore, India.
authors.forename: Prashanth
authors.initials: P
authors.lastname: Athri
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland), Fax: (+41) 21 693 0320.
authors.forename: Ursula
authors.initials: U
authors.lastname: Rothlisberger
mesh_terms: D000465:Algorithms; D040761:Biomimetic Materials / Q000737:chemistry*; D002245:Carbon Dioxide / Q000737:chemistry*; D002384:Catalysis; D010455:Peptides / Q000737:chemistry* / Q000235:genetics*; D015202:Protein Engineering; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; D014867:Water; D002245:Carbon Dioxide
keywords: biomimetic systems; catalytic properties; engineered peptides; enzymes; genetic algorithms