Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase 1 1Edited by P. E. Wright

Baker, Brian M.; Murphy, Kenneth P.

doi:10.1006/jmbi.1997.0977

Cited by 152 publications

(192 citation statements)

References 75 publications

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“…Because of the high affinity of OMTKY3 for PPE, it is not possible to determine K experimentally in the calorimeter. The value of K has been measured from residual enzyme activity [25], and the literature value was used to determine the intrinsic ⌬GЊ and, with the fitted ⌬H Њ value, ⌬S Њ [6]. …”

Section: Resultsmentioning

confidence: 99%

“…The procedures for estimating the thermodynamics of binding from structural data have been detailed previously [6,[10][11][12] and are only summarized here. The thermodynamics calculated from the structure are expected to correspond to the intrinsic energetics, but the 'int' subscript is omitted below for clarity.…”

Section: Structural Energetics Calculationsmentioning

confidence: 99%

“…only one rotomeric state) if it is fully buried. It is assumed that the conformational entropy varies linearly with the degree of exposure of the side chain [6,11], The final term is for the mixing entropy and is simply the cratic entropy for a bimolecular association in aqueous solution [23,24]. The intrinsic ⌬GЊ of binding can be calculated as a function of temperature using equations 6-8 and the standard relationship:…”

Section: Structural Energetics Calculationsmentioning

confidence: 99%

“…The structural information required is the changes in apolar and polar accessible surface areas upon binding and, for calculating conformational entropy, the contribution of each amino acid side chain to these changes. For the binding of OMTKY3 to PPE, 1130 Å 2 of apolar surface area and 660 Å 2 of polar surface area are calculated to be buried upon formation of the complex [6]. These values, in conjunction with the identities of the amino acid side chains involved were used with equations 6-9 to estimate the intrinsic energetics of binding.…”

Section: Structural Energetics Calculationsmentioning

confidence: 99%

“…For example, disagreement between the predicted and experimental ⌬S Њ might suggest that the treatment of conformational entropy needs refinement. This paper reviews recent studies in this laboratory on the binding of a protease inhibitor, turkey ovomucoid third domain (OMTKY3), and a serine protease, porcine pancreatic elastase (PPE) [6]. We have performed structural energetics calculations using a model of the complex between these proteins and compared the predicted energetics to the experimental values determined using isothermal titration calorimetry.…”

Section: Introductionmentioning

confidence: 99%

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Structural energetics of serine protease inhibition

Murphy¹,

Baker²,

Edgcomb³

et al. 1999

Pure and App Chemis

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Abstract:We have investigated the binding of the serine protease inhibitor, turkey ovomucoid third domain (OMTKY3), to the serine protease, porcine pancreatic elastase (PPE), using isothermal titration calorimetry and structural energetics calculations. The calculations predict that the binding at 25 ЊC is characterized by a negligible ⌬H Њ, a large and positive ⌬S Њ, and a large and negative ⌬C p , resulting in a large and favorable ⌬G Њ. The experimental results indicate a significant contribution to the binding energetics from a change in the pKa of an ionizable group, presumably His57 of PPE. The resulting proton linkage is manifest in the observed ⌬H Њ and ⌬C p of binding. However, a global analysis of binding data as a function of pH, buffer, and temperature yields the intrinsic binding energetics as well as the energetics of proton binding to the ionizable group in the free and bound PPE. The experimentally determined intrinsic energetics and the calculated values are in very good agreement, suggesting that the structural energetics calculations may be a useful tool for understanding protein-protein interactions in solution.

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Section: Resultsmentioning

confidence: 99%

Section: Structural Energetics Calculationsmentioning

confidence: 99%

Section: Structural Energetics Calculationsmentioning

confidence: 99%

Section: Structural Energetics Calculationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Structural energetics of serine protease inhibition

Murphy¹,

Baker²,

Edgcomb³

et al. 1999

Pure and App Chemis

Self Cite

View full text Add to dashboard Cite

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Predicting binding energetics from structure: Looking beyond ?G�

Murphy

1999

Med. Res. Rev.

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Structure‐based design of pharmaceuticals requires the ability to predict ligand affinity based on knowledge of structure. The primary term of interest is the binding affinity constant, K, or the free energy of binding, ΔG°. It is common to attempt to predict ΔG° based on empirically derived terms which represent common contributions such as the hydrophobic effect, hydrogen bonding, and conformational entropy. Although these approaches have met with some success, when they fail it is difficult to know which parameter(s) need refinement. Confidence in these approaches is also limited by the fact that ΔG° typically is made up of compensating enthalpic and entropic terms, ΔH° and ΔS°, so that accurate prediction of a ΔG° value may be fortuitous and may not indicate a reasonable understanding of the underlying relationship between structure and affinity. This is further complicated by the fact that both ΔH° and ΔS° are strongly temperature dependent through the heat capacity change, ΔCp. In order to avoid these difficulties, we attempt to use structural data to predict ΔH°, ΔS°, and ΔCp from which ΔG° can be calculated as a function of temperature. The predictions are then compared to experimentally determined values. These calculations have been applied to several systems by ourselves and others. Systems include the binding of angiotensin II to an antibody, the dimerization of interleukin‐8, and the binding of inhibitors to aspartic and serine proteases. Overall the calculations are very successful, and suggest that our understanding of the contributions of the hydrophobic effect, hydrogen bonding, and conformational entropy are quite good. Several of these systems show a strong dependence of the binding energetics on pH, indicative of changes in proton affinity of ionizable groups upon binding. It is critical to account for these protonation contributions to the binding energetics in order to assess the reliability of any computational prediction of energetics from structure. Methods have been developed for determining the energetics of proton binding using isothermal titration calorimetry. The availability of these methods provides a means of understanding how protein structure can modify the pKa's of ionizable groups. This information will further add to our understanding of structural energetic relationships and our ability accurately to predict binding affinities. © 1999 John Wiley & Sons, Inc. Med Res Rev, 19, No. 4, 333–339, 1999.

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Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition

1999

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The principles of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) are reviewed together with the basic thermodynamic formalism on which the two techniques are based. Although ITC is particularly suitable to follow the energetics of an association reaction between biomolecules, the combination of ITC and DSC provides a more comprehensive description of the thermodynamics of an associating system. The reason is that the parameters DG, DH, DS, and DC p obtained from ITC are global properties of the system under study. They may be composed to varying degrees of contributions from the binding reaction proper, from conformational changes of the component molecules during association, and from changes in molecule/solvent interactions and in the state of protonation.

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Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase 1 1Edited by P. E. Wright

Cited by 152 publications

References 75 publications

Structural energetics of serine protease inhibition

Structural energetics of serine protease inhibition

Predicting binding energetics from structure: Looking beyond ?G�

Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition

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