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Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

  1. Tobin R. Sosnickb,c,3
  1. aDepartment of Chemistry, The University of Chicago, Chicago, IL 60637;
  2. bDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;
  3. cInstitute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637;
  4. dGraduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637

  1. Edited by Ken A. Dill, Stony Brook University, Stony Brook, NY, and approved January 3, 2017 (received for review June 14, 2016)

Significance

The basis of protein-folding cooperativity and stability elicits a variety of opinions, as does the existence and importance of possible residual structure in the denatured state. We examine these issues in a protein that is striking in its dearth of hydrophobic burial and its lack of canonical α and β structures, while having a low sequence complexity with 46% glycine. Unexpectedly, the protein’s folding behavior is similar to that observed for typical globular proteins. This enigma forces a reexamination of the possible combination of factors that can stabilize a protein.

Abstract

The burial of hydrophobic side chains in a protein core generally is thought to be the major ingredient for stable, cooperative folding. Here, we show that, for the snow flea antifreeze protein (sfAFP), stability and cooperativity can occur without a hydrophobic core, and without α-helices or β-sheets. sfAFP has low sequence complexity with 46% glycine and an interior filled only with backbone H-bonds between six polyproline 2 (PP2) helices. However, the protein folds in a kinetically two-state manner and is moderately stable at room temperature. We believe that a major part of the stability arises from the unusual match between residue-level PP2 dihedral angle bias in the unfolded state and PP2 helical structure in the native state. Additional stabilizing factors that compensate for the dearth of hydrophobic burial include shorter and stronger H-bonds, and increased entropy in the folded state. These results extend our understanding of the origins of cooperativity and stability in protein folding, including the balance between solvent and polypeptide chain entropies.

Footnotes

  • ↵1Z.P.G. and M.C.B. contributed equally to this work.

  • ↵2Present address: Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea.

  • ↵3To whom correspondence may be addressed. Email: trsosnic{at}uchicago.edu or skent{at}uchicago.edu.

  • Author contributions: Z.P.G., M.C.B., B.R., S.B.H.K., and T.R.S. designed research; Z.P.G., M.C.B., W.Y., J.A.R., H.L., and T.R.S. performed research; W.Y., B.R., and S.B.H.K. contributed new reagents/analytic tools; Z.P.G., M.C.B., W.Y., J.A.R., H.L., and T.R.S. analyzed data; and Z.P.G., M.C.B., W.Y., J.A.R., S.B.H.K., and T.R.S. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1609579114/-/DCSupplemental.

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