Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold

Abstract

Backbone-backbone hydrogen-bonding interactions are a ubiquitous and highly conserved structural feature of proteins that adopt the same fold (i.e., have the same overall backbone topology). This work addresses the question of whether or not this structural conservation is also reflected as a thermodynamic conservation. Reported here is 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. With amide-to-ester bond mutations introduced by total chemical synthesis methods, the thermodynamic consequences of backbonebackbone hydrogen-bond deletions at five different structurally equivalent positions throughout the ␤-␣-␣ fold of Arc repressor and CopG were assessed. The ester bond-containing analogues all folded into native-like three-dimensional structures that were destabilized from 2.5 to 6.0 kcal͞(mol dimer) compared with wild-type controls. Remarkably, the five paired analogues with amide-to-ester bond mutations at structurally equivalent positions were destabilized to exactly the same degree, regardless of the degree to which the mutation site was buried in the structure. The results are interpreted as evidence that the thermodynamics of backbone-backbone hydrogen-bonding interactions in a protein fold are conserved.protein mutagenesis ͉ chemical synthesis T he 30,000-plus high-resolution protein structures that have been solved to date can be grouped, according to their overall backbone topology, into a remarkably small number of protein folds (Ϸ800) (1, 2). The apparent existence of such a small number of naturally occurring protein folds has meant that a surprisingly large number of proteins, which are unrelated at the amino acid sequence level, adopt the same protein fold (i.e., fold into three-dimensional structures with the same backbone topology). Thus, nature appears to have used a number of different combinations of chemical interactions to stabilize its protein folds. However, one set of chemical interactions that are structurally conserved within a protein fold is the set of backbone-backbone hydrogen-bonding interactions that help define it. This structural conservation raises a fundamental question of whether or not the thermodynamics of backbone-backbone hydrogen-bonding interactions are also conserved in a protein fold. Such fundamental knowledge about the detailed molecular interactions that guide protein-folding reactions stands to impact a wide variety of research areas from drug discovery to theories of human evolution.The relative contributions of different backbone-backbone hydrogen-bonding interactions in protein-folding reactions have been explored in a series of recent studies on several different protein systems (3-12). These studies have typically relied on total chemical synthesis methods (13) or specialized in vitro translation techniques (14) to incorporate amide-to-ester bond mutations into the polypeptide backbone of proteins and modulate the hydrogen-bonding properties o...

Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes

“…It has been shown that electrostatic screening is the main reason for the distinct backbone conformational preferences of amino acid residues in peptides and proteins (53), the nearest neighbor effect (54), and the formation of transient β-strands in unfolded proteins (55). It has also been shown, using amide to ester mutations, that H bonds in the protein interior are stronger than those exposed to solvent (56)(57)(58).…”

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“…6,7 In this context, the computational approach must be specially highlighted, [8][9][10][11] as it can analyze this interaction individually, without considering the rest of energetic contributions ͑hydrophobicity, electrostatics, etc.͒.…”

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