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The role of conformational entropy in molecular recognition by calmodulin.

Marlow MS, Dogan J, Frederick KK, Valentine KG, Wand AJ - Nat. Chem. Biol. (2010)

Bottom Line: This view warrants a more quantitative foundation.Here we calibrate an 'entropy meter' using an experimental dynamical proxy based on NMR relaxation and show that changes in the conformational entropy of calmodulin are a significant component of the energetics of binding.These observations promote modification of our understanding of the energetics of protein-ligand interactions.

View Article: PubMed Central - PubMed

Affiliation: Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

ABSTRACT
The physical basis for high-affinity interactions involving proteins is complex and potentially involves a range of energetic contributions. Among these are changes in protein conformational entropy, which cannot yet be reliably computed from molecular structures. We have recently used changes in conformational dynamics as a proxy for changes in conformational entropy of calmodulin upon association with domains from regulated proteins. The apparent change in conformational entropy was linearly related to the overall binding entropy. This view warrants a more quantitative foundation. Here we calibrate an 'entropy meter' using an experimental dynamical proxy based on NMR relaxation and show that changes in the conformational entropy of calmodulin are a significant component of the energetics of binding. Furthermore, the distribution of motion at the interface between the target domain and calmodulin is surprisingly noncomplementary. These observations promote modification of our understanding of the energetics of protein-ligand interactions.

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Distribution of methyl symmetry axis generalized order parameters () for the target domains bound to calcium-saturated wild-type calmodulin (CaM). Determined using deuterium NMR relaxation (see Methods).
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Figure 1: Distribution of methyl symmetry axis generalized order parameters () for the target domains bound to calcium-saturated wild-type calmodulin (CaM). Determined using deuterium NMR relaxation (see Methods).

Mentions: All bound target domain methyl resonances are well resolved in 13C- NMR spectra and deuterium relaxation parameters could be measured with high precision (Supplementary Fig. 1). The degree of spatial restriction of each motional probe was assigned a number between 0, corresponding to complete isotropic disorder, and 1, corresponding to a fixed orientation within the molecular frame. This parameter is the so-called model-free squared generalized order parameter19 as it applies to the methyl symmetry axis (O2axis). A recent re-evaluation of the model-free treatment of Lipari & Szabo reinforces confidence in its robustness with respect to highly asymmetric side chain motion 20. The 80 methyl O2axis parameters from 53 residues of the target domains in the six wild-type CaM complexes are heterogeneously distributed with O2axis values ranging from 0.05 to 0.95 (Fig. 1). The distribution is non-uniform and reminiscent of the multi-modal distributions of the calmodulin component of these complexes11.


The role of conformational entropy in molecular recognition by calmodulin.

Marlow MS, Dogan J, Frederick KK, Valentine KG, Wand AJ - Nat. Chem. Biol. (2010)

Distribution of methyl symmetry axis generalized order parameters () for the target domains bound to calcium-saturated wild-type calmodulin (CaM). Determined using deuterium NMR relaxation (see Methods).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3050676&req=5

Figure 1: Distribution of methyl symmetry axis generalized order parameters () for the target domains bound to calcium-saturated wild-type calmodulin (CaM). Determined using deuterium NMR relaxation (see Methods).
Mentions: All bound target domain methyl resonances are well resolved in 13C- NMR spectra and deuterium relaxation parameters could be measured with high precision (Supplementary Fig. 1). The degree of spatial restriction of each motional probe was assigned a number between 0, corresponding to complete isotropic disorder, and 1, corresponding to a fixed orientation within the molecular frame. This parameter is the so-called model-free squared generalized order parameter19 as it applies to the methyl symmetry axis (O2axis). A recent re-evaluation of the model-free treatment of Lipari & Szabo reinforces confidence in its robustness with respect to highly asymmetric side chain motion 20. The 80 methyl O2axis parameters from 53 residues of the target domains in the six wild-type CaM complexes are heterogeneously distributed with O2axis values ranging from 0.05 to 0.95 (Fig. 1). The distribution is non-uniform and reminiscent of the multi-modal distributions of the calmodulin component of these complexes11.

Bottom Line: This view warrants a more quantitative foundation.Here we calibrate an 'entropy meter' using an experimental dynamical proxy based on NMR relaxation and show that changes in the conformational entropy of calmodulin are a significant component of the energetics of binding.These observations promote modification of our understanding of the energetics of protein-ligand interactions.

View Article: PubMed Central - PubMed

Affiliation: Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

ABSTRACT
The physical basis for high-affinity interactions involving proteins is complex and potentially involves a range of energetic contributions. Among these are changes in protein conformational entropy, which cannot yet be reliably computed from molecular structures. We have recently used changes in conformational dynamics as a proxy for changes in conformational entropy of calmodulin upon association with domains from regulated proteins. The apparent change in conformational entropy was linearly related to the overall binding entropy. This view warrants a more quantitative foundation. Here we calibrate an 'entropy meter' using an experimental dynamical proxy based on NMR relaxation and show that changes in the conformational entropy of calmodulin are a significant component of the energetics of binding. Furthermore, the distribution of motion at the interface between the target domain and calmodulin is surprisingly noncomplementary. These observations promote modification of our understanding of the energetics of protein-ligand interactions.

Show MeSH