title: Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering.
abstract: The Phox homology domain (PX domain) is a phosphoinositide-binding structural domain that is critical in mediating protein and cell membrane association and has been found in more than 100 eukaryotic proteins. The abundance of PX domains in nature offers an opportunity to redesign the protein using EvoDesign, a computational approach to design new sequences based on structure profiles of multiple evolutionarily related proteins. In this study, we report the X-ray crystallographic structure of a designed PX domain from the cytokine-independent survival kinase (CISK), which has been implicated as functioning in parallel with PKB/Akt in cell survival and insulin responses. Detailed data analysis of the designed CISK-PX protein demonstrates positive impacts of knowledge-based secondary structure and solvation predictions and structure-based sequence profiles on the efficiency of the evolutionary-based protein design method. The structure of the designed CISK-PX domain is close to the wild-type (1.54 Å in Cα RMSD), which was accurately predicted by I-TASSER based fragment assembly simulations (1.32 Å in Cα RMSD). This study represents the first successfully designed conditional peripheral membrane protein fold and has important implications in the examination and experimental validation of the evolution-based protein design approaches.
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.
authors.forename: David
authors.initials: D
authors.lastname: Shultis
authors.affiliation: Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Dodge
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA. Electronic address: zhng@umich.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D008565:Membrane Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D015202:Protein Engineering; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D008565:Membrane Proteins
keywords: Cytokine-independent survival kinase; Membrane; Phox homology; Protein design; Protein structure prediction; X-ray crystallography