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Protein Sci. 2016 Jul;25(7):1299-307. doi: 10.1002/pro.2899. Epub 2016 Mar 7.

Introduction of a polar core into the de novo designed protein Top7.

Basanta B1,2,3, Chan KK4, Barth P5,6,7, King T8, Sosnick TR8,9, Hinshaw JR10, Liu G11,12, Everett JK11,12, Xiao R11,12, Montelione GT11,12,13, Baker D1,2,14.

Author information

  • 1Department of Biochemistry, University of Washington, Seattle, Washington, 98195.
  • 2Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
  • 3Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, 98195, USA.
  • 4Enzyme Engineering, EnzymeWorks, California, 92121.
  • 5Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030.
  • 6Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030.
  • 7Department of Pharmacology Baylor College of Medicine, Houston, Texas, 77030.
  • 8Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.
  • 9Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, 60637.
  • 10Department of Chemistry, University of Chicago, Chicago, Illinois, 60637.
  • 11Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey, 08854.
  • 12Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.
  • 13Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey, 08854.
  • 14Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.

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.

KEYWORDS:

hydrogen bonds; protein NMR; protein core polar interactions; protein design; protein folding

PMID:
26873166
PMCID:
PMC4918430
[Available on 2017-07-01]
DOI:
10.1002/pro.2899
[PubMed - in process]
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