The Contribution of Polar Group Burial to Protein Stability Is Strongly Context-dependent

Takano, Kazufumi; Scholtz, J. Martin; Sacchettini, James C.; Pace, C. Nick

doi:10.1074/jbc.m304177200

Cited by 58 publications

(62 citation statements)

References 58 publications

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“…are also consistent with the destabilizing effects previously noted for side-chain-backbone and side-chain-side-chain hydrogen bonds in other protein folding studies (21)(22)(23).…”

supporting

confidence: 79%

Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold

Wang

Wales

Fitzgerald

2006

Proc. Natl. Acad. Sci. U.S.A.

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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...

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“…are also consistent with the destabilizing effects previously noted for side-chain-backbone and side-chain-side-chain hydrogen bonds in other protein folding studies (21)(22)(23).…”

supporting

confidence: 79%

Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold

Wang

Wales

Fitzgerald

2006

Proc. Natl. Acad. Sci. U.S.A.

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“…Thus, a buried carboxyl group can contribute just as much to the stability of a protein as a buried aromatic group if it is hydrogen bonded and in a favorable environment. 38 This is remarkable, since the free energy change for dehydration of an Asp side-chain is 11.0 kcal mol −1 . 39 Thus, the hydrogen bonding and other interactions of the carboxyl group of Asp76 with other groups in the protein must provide over 15 kcal/mol of stabilizing free energy.…”

Section: Rnase Samentioning

confidence: 96%

Hydrogen Bonding Markedly Reduces the pK of Buried Carboxyl Groups in Proteins

Thurlkill

Grimsley

Scholtz

et al. 2006

Journal of Molecular Biology

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“…Earlier, our laboratory characterized the folding and stability of RNase Sa and several variants. 26,28,30,31,[33][34][35][36][37][38][39] The unfolding of RNase Sa and its variants is reversible and follows a two-state mechanism. The thermodynamic parameters characterizing the thermal unfolding of these variants are shown in Table 2.…”

Section: Stability Increases For the β-Turn Variants In Rnase Samentioning

confidence: 99%

Increasing Protein Conformational Stability by Optimizing β-Turn Sequence

Treviño

Schaefer

Scholtz

et al. 2007

Journal of Molecular Biology

144

128

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Protein conformational stability is an important concern in many fields. Here, we describe a strategy for significantly increasing conformational stability by optimizing beta-turn sequence. Proline and glycine residues are statistically preferred at several beta-turn positions, presumably because their unique side-chains contribute favorably to conformational stability in certain beta-turn positions. However, beta-turn sequences often deviate from preferred proline or preferred glycine. Therefore, our strategy involves replacing non-proline and non-glycine beta-turn residues with preferred proline or preferred glycine residues. Here, we develop guidelines for selecting appropriate mutations, and present results for five mutations (S31P, S42G, S48P, T76P, and Q77G) that significantly increase the conformational stability of RNase Sa. The increases in stability ranged from 0.7 kcal/mol to 1.3 kcal/mol. The strategy was successful in overlapping or isolated beta-turns, at buried (up to 50%) or completely exposed sites, and at relatively flexible or inflexible sites. Considering the significant number of beta-turn residues in every globular protein and the frequent deviation of beta-turn sequences from preferred proline and preferred glycine residues, this simple, efficient strategy will be useful for increasing the conformational stability of proteins.

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The Contribution of Polar Group Burial to Protein Stability Is Strongly Context-dependent

Cited by 58 publications

References 58 publications

Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold

Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold

Hydrogen Bonding Markedly Reduces the pK of Buried Carboxyl Groups in Proteins

Increasing Protein Conformational Stability by Optimizing β-Turn Sequence

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