title: Deep sequencing methods for protein engineering and design.
abstract: The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition. Examples include the creation of multiple dual-affinity Fabs targeting structurally dissimilar epitopes and engineering of a broad germline-targeted anti-HIV-1 immunogen. Additionally, we highlight the generation of enzyme fitness landscapes for conducting fundamental studies of protein behavior and evolution. We conclude with discussion of technological advances.
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States.
authors.forename: Emily E
authors.initials: EE
authors.lastname: Wrenbeck
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Faber
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States; Departments of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, United States. Electronic address: taw@egr.msu.edu.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Whitehead
mesh_terms: D000818:Animals; D018604:Epitope Mapping; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000235:genetics* / Q000276:immunology
chemical_list: D011506:Proteins