# Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics

@article{Deechongkit2004ContextdependentCO,
title={Context-dependent contributions of backbone hydrogen bonding to $\beta$-sheet folding energetics},
author={Songpon Deechongkit and Houbi Nguyen and Evan T. Powers and Philip E. Dawson and Martin Gruebele and Jeffery W. Kelly},
journal={Nature},
year={2004},
volume={430},
pages={101-105}
}
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. Here we have assessed the contribution of backbone H-bonds to the folding kinetics and thermodynamics of the PIN WW domain, a small β-sheet protein, by individually replacing its backbone amides with esters. Amide-to-ester mutations site-specifically perturb…
240 Citations

## Figures, Tables, and Topics from this paper

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain
• Chemistry, Medicine
PloS one
• 2014
Investigation of effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability finds native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding.
Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.
• Chemistry, Medicine
Proceedings of the National Academy of Sciences of the United States of America
• 2006
A comparative thermodynamic analysis of backbone hydrogen bonds in two proteins that adopt the same fold but are unrelated at the primary amino acid sequence level is reported, interpreted as evidence that the thermodynamics of backbone-backbone hydrogen-bonding interactions in a protein fold are conserved.
Understanding the mechanism of beta-sheet folding from a chemical and biological perspective.
Current perspective on how structure acquisition is influenced by the sequence is reviewed, which determines local conformational propensities and mediates the hydrophobic effect, hydrogen bonding, and analogous intramolecular interactions is reviewed.
Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states.
• Chemistry, Medicine
Journal of molecular biology
• 2006
Results reveal that backbone-backbone hydrogen bonding interactions are formed in the beta-turn and alpha-helical transition state structures of ProtL and Arc repressor, respectively; and they were not form in the intersubunit beta-sheet interface of Arc repress, a region ofArc repressor's polypeptide chain previously shown to have other non-native-like conformations in Arc's protein folding transition state.
Backbone-Backbone H-Bonds Make Context-Dependent Contributions to Protein Folding Kinetics and Thermodynamics: Lessons from Amide-to-Ester Mutations.
• Chemistry, Medicine
• 2005
The use of amide-to-ester mutation as a tool to evaluate the contribution of backbone-backbone H-bonds to protein folding kinetics and thermodynamics is reviewed.
Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations.
This study systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands, demonstrating that hydrogen bonds contribute significantly to ligand binding and specifically addresses these for PDZ domain-peptide interactions.
Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding.
• Chemistry, Medicine
Journal of the American Chemical Society
• 2012
It is shown that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-Bonds in β-hairpins are formed only after the folding transition state.
Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis.
• Chemistry, Medicine
Journal of the American Chemical Society
• 2009
It is shown, using an amide-to-ester mutation strategy, that the formation of backbone hydrogen bonds within helices is not rate-limiting in the folding of the subdomain, thereby suggesting that such hydrogen bonds are unlikely to be formed en route from the denatured to the transition state.
β-Sheet folding mechanisms from perturbation energetics
• Chemistry
• 2006
Amide backbone and sidechain mutagenesis data can be used in combination with kinetic and thermodynamic measurements to understand the energetic contributions of backbone hydrogen bonding and the
Probing Backbone Hydrogen Bonds in Proteins by Amide‐to‐Ester Mutations
• Medicine, Chemistry
Chembiochem : a European journal of chemical biology
• 2018
This minireview showcases examples of how amide‐to‐ester mutations can be used to uncover pivotal roles of backbone‐mediated hydrogen bonds in protein recognition, folding, function, and structure.

## References

SHOWING 1-10 OF 30 REFERENCES
Probing backbone hydrogen bonds in the hydrophobic core of GCN4.
• Chemistry, Medicine
Biochemistry
• 2002
The results suggest that backbone engineering through ester substitution is a useful approach for probing the relative strength of backbone hydrogen bonds.
An experimental approach to evaluating the role of backbone interactions in proteins using unnatural amino acid mutagenesis.
• Chemistry, Medicine
Biochemistry
• 1997
Comparison of the thermal stabilities of the amide- and ester-containing proteins shows that the ester substitution has a similar thermodynamic effect at all three positions, and introduction of theEster linkage in the middle of the helix, which alters two hydrogen-bonding interactions, destabilizes the protein by 1.7 kcal/mol.
Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions
• N. Ferguson, +7 authors A. Fersht
• Chemistry, Medicine
Proceedings of the National Academy of Sciences of the United States of America
• 2001
A flexible thioether linker is used as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, β-sheet protein, to extend the protein engineering method directly to secondary-structure interactions.
Design, Synthesis, and Characterization of 4-Ester CI2, a Model for Backbone Hydrogen Bonding in Protein α-Helices
• Chemistry
• 2000
The total synthesis of proteins enables unnatural groups to be incorporated into proteins to understand the molecular basis of protein stability and function. Chymotrypsin inhibitor 2 (CI2), is a
Hydrogen bonding stabilizes globular proteins.
• Chemistry, Medicine
Biophysical journal
• 1996
Experimental studies discussed here are consistent and compelling: hydrogen bonding stabilizes globular proteins.
The folding mechanism of a -sheet: the WW domain1
• Chemistry, Biology
• 2001
The location of the TS along the entropic reaction coordinate ΦT, obtained by temperature-tuning the kinetics, reveals that sufficiently destabilizing mutants in loop 2 or in the Leu7-Trp11-Tyr24-Pro37 hydrophobic cluster can cause a switch to a late TS.
Comparative analysis of two different amide-to-ester bond mutations in the beta-sheet of 4-oxalocrotonate tautomerase.
• Chemistry, Medicine
Biochemistry
• 2003
The results suggest that the two different, but structurally similar, backbone-backbone hydrogen bonds deleted in (OI2)4OT and (Oi7)4 OT make nearly equivalent contributions to the thermodynamic stability of the 4OT hexamer.
Ultrafast folding of WW domains without structured aromatic clusters in the denatured state
• Chemistry, Medicine
Proceedings of the National Academy of Sciences of the United States of America
• 2001
Folding and unfolding kinetics, studied by using rapid temperature-jump and continuous-flow techniques, show that each domain folds and unfolds very rapidly in a two-state transition through a highly compact transition state.
Stereochemical Requirements for β-Hairpin Formation: Model Studies with Four-Residue Peptides and Depsipeptides
• Chemistry
• 1996
Spectroscopic and crystallographic data are presented for a series of tetrapeptides and analogous depsipeptides that can form a minimal β-hairpin (two intramolecular hydrogen bonds). These model
Dominant forces in protein folding.
• K. Dill
• Chemistry, Medicine
Biochemistry
• 1990
The present review aims to provide a reassessment of the factors important for folding in light of current knowledge, including contributions to the free energy of folding arising from electrostatics, hydrogen-bonding and van der Waals interactions, intrinsic propensities, and hydrophobic interactions.