title: Introduction of a polar core into the de novo designed protein Top7.
abstract: Design of polar interactions is a current challenge for protein design. The de novo designed protein Top7, like almost all designed proteins, has an entirely nonpolar core. Here we describe the replacing of a sizable fraction (5 residues) of this core with a designed polar hydrogen bond network. The polar core design is expressed at high levels in E. coli, has a folding free energy of 10 kcal/mol, and retains the multiphasic folding kinetics of the original Top7. The NMR structure of the design shows that conformations of three of the five residues, and the designed hydrogen bonds between them, are very close to those in the design model. The remaining two residues, which are more solvent exposed, sample a wide range of conformations in the NMR ensemble. These results show that hydrogen bond networks can be designed in protein cores, but also highlight challenges that need to be overcome when there is competition with solvent.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.|Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, 98195, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Basanta
authors.affiliation: Enzyme Engineering, EnzymeWorks, California, 92121.
authors.forename: Kui K
authors.initials: KK
authors.lastname: Chan
authors.affiliation: Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030.|Department of Pharmacology Baylor College of Medicine, Houston, Texas, 77030.
authors.forename: Patrick
authors.initials: P
authors.lastname: Barth
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.
authors.forename: Tiffany
authors.initials: T
authors.lastname: King
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.|Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, 60637.
authors.forename: Tobin R
authors.initials: TR
authors.lastname: Sosnick
authors.affiliation: Department of Chemistry, University of Chicago, Chicago, Illinois, 60637.
authors.forename: James R
authors.initials: JR
authors.lastname: Hinshaw
authors.affiliation: Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey, 08854.|Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.
authors.forename: Gaohua
authors.initials: G
authors.lastname: Liu
authors.affiliation: Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey, 08854.|Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.
authors.forename: John K
authors.initials: JK
authors.lastname: Everett
authors.affiliation: Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey, 08854.|Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.
authors.forename: Rong
authors.initials: R
authors.lastname: Xiao
authors.affiliation: Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey, 08854.|Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.|Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854.
authors.forename: Gaetano T
authors.initials: GT
authors.lastname: Montelione
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins
keywords: hydrogen bonds; protein NMR; protein core polar interactions; protein design; protein folding