Contribution of hydrogen bonds to protein stability

Abstract

Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, D(DG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.

Prolyl Isomerization as a Molecular Memory in the Allosteric Regulation of the Signal Adapter Protein c-CrkII

“…The assembly with SH3N in the domain closing reaction then increases the cis content further to 86%, which requires ϳ5 kJ/mol of conformational energy. The formation of one or two extra hydrogen bonds would be sufficient to provide this energy (22). Interestingly, ligand binding shifts the cis/trans equilibrium back to ϳ40/60, similar to the ratio observed for the isolated SH3C domain.…”

Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine β-Lactamases by Relieving Steric Strain

“…Substitution of serine with a glycine residue also allows the placement of its main chain carbonyl oxygen atom in position to form an intra-helical hydrogen bond with improved distance (C=O…H-N) and angular (O…-H-N) parameters thereby further contributing to increased protein stability. 71 …”

Studying the role of cooperative hydration in stabilizing folded protein states

“…Pace et al determined the experimental folding enthalpy to be -13 kcal/mol. We have derived this second estimate from the reported folding enthalpy of −31 kcal/mol at the melting temperature of 74.4 °C and the reported heat capacity of 0.374 kcal/mol/K (Pace et al, 2014). The folding energies of villin calculated here are in reasonable agreement (Fig.…”

“…Studies on protein-folding kinetics have highlighted the importance of intermediate states (Ptitsyn et al, 1990), cooperativity (Dill et al, 1993), free energy barriers (Shastry and Roder, 1998), and folding funnels (Bryngelson et al, 1995). Studies on protein-folding thermodynamics have focused mainly on the balance between two (non-mutually exclusive) types of intermolecular interactions (Ben-Naim, 1991, Dill, 1990, Hendsch and Tidor, 1994, Lazaridis et al, 1995, Myers and Pace, 1996, Pace et al, 1996, Pace et al, 2011, Pace et al, 2014, Strickler et al, 2006):Hydrogen-bonding/polar interactions – Folded states commonly exhibit numerous hydrogen-bonding interactions between protein residues (McDonald and Thornton, 1994). However, these must compete with hydrogen-bonding interactions between the protein and the surrounding water and thus the balance of terms must be considered (Ben-Naim, 1991, Fernández et al, 2002, Fersht et al, 1985, Levy and Onuchic, 2006).…”