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Protein Design

Volume 1216 of the series Methods in Molecular Biology pp 161-182

Date:

Symmetric Protein Architecture in Protein Design: Top-Down Symmetric Deconstruction

  • Liam M. LongoAffiliated withDepartment of Biomedical Sciences, College of Medicine, Florida State University
  • , Michael BlaberAffiliated withDepartment of Biomedical Sciences, College of Medicine, Florida State University Email author 

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Abstract

Top-down symmetric deconstruction (TDSD) is a joint experimental and computational approach to generate a highly stable, functionally benign protein scaffold for intended application in subsequent functional design studies. By focusing on symmetric protein folds, TDSD can leverage the dramatic reduction in sequence space achieved by applying a primary structure symmetric constraint to the design process. Fundamentally, TDSD is an iterative symmetrization process, in which the goal is to maintain or improve properties of thermodynamic stability and folding cooperativity inherent to a starting sequence (the “proxy”). As such, TDSD does not attempt to solve the inverse protein folding problem directly, which is computationally intractable. The present chapter will take the reader through all of the primary steps of TDSD—selecting a proxy, identifying potential mutations, establishing a stability/folding cooperativity screen—relying heavily on a successful TDSD solution for the common β-trefoil fold.

Key words

Symmetric protein design Protein folding Protein engineering Phi-value analysis β-trefoil Protein evolution