1. Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC 506, La Jolla, California 92037, USA
2. Department of Cell Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC 506, La Jolla, California 92037, USA
3. Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
4. Department of Chemistry, Physics, and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, USA

Correspondence to: Jeffery W. Kelly¹ Email: jkelly@scripps.edu

Abstract

Backbone hydrogen bonds (H-bonds) are prominent features of protein structures; however, their role in protein folding remains controversial because they cannot be selectively perturbed by traditional methods of protein mutagenesis^{1, 2, 3}. Here we have assessed the contribution of backbone H-bonds to the folding kinetics and thermodynamics of the PIN WW domain, a small -sheet protein⁴, by individually replacing its backbone amides with esters. Amide-to-ester mutations site-specifically perturb backbone H-bonds in two ways: a H-bond donor is eliminated by replacing an amide NH with an ester oxygen, and a H-bond acceptor is weakened by replacing an amide carbonyl with an ester carbonyl^{5, 6, 7, 8, 9, 10, 11, 12, 13}. We perturbed the 11 backbone H-bonds of the PIN WW domain by synthesizing 19 amide-to-ester mutants. Thermodynamic studies on these variants show that the protein is most destabilized when H-bonds that are enveloped by a hydrophobic cluster are perturbed. Kinetic studies indicate that native-like secondary structure forms in one of the protein's loops in the folding transition state, but the backbone is less ordered elsewhere in the sequence. Collectively, our results provide an unusually detailed picture of the folding of a -sheet protein.

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