Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein–Ligand Interactions

DeLorbe

et al. 2013

ACS Med. Chem. Lett.

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Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and tripeptides of the general form Ac-pTyr-Xaa-Asn in which the Xaa residue bears a linear alkyl chain varying in length from 1–5 carbon atoms. Binding affinity increases upon adding a methylene group to the Ala derivative, but further chain extension gives no extra enhancement in potency. The thermodynamic signatures of the ethyl and n-propyl derivatives are virtually identical as are those for the n-butyl and n-pentyl analogs. Crystallographic analysis of the complexes reveals a high degree of similarity in the structure of the domain and the bound ligands with the notable exception that there is a gauche interaction in the side chains in the bound conformations of ligands having n-propyl, n-butyl, and n-pentyl groups. However, eliminating this unfavorable interaction by introducing a Z-double bond into the side chain of the n-propyl analog does not result in an increase in affinity. Increases in the amount of nonpolar surface that is buried upon ligand binding correlate with favorable changes in ΔH°, but these are usually offset by corresponding unfavorable changes in −TΔS°; there is little correlation of ΔCp with changes in the amount of buried nonpolar surface.

contrasting

confidence: 98%

“…24 [b] Three or more experiments were performed for each ligand, and the averages are reported following normalization of the n values for each experiment by adjusting ligand concentration (See Supporting Information). Errors in the thermodynamic values were determined by the method of Krishnamurthy.…”

Section: Figurementioning

confidence: 99%

Protein–Ligand Interactions: Thermodynamic Effects Associated with Increasing the Length of an Alkyl Chain

Myslinski

DeLorbe

et al. 2013

ACS Med. Chem. Lett.

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“…During the course of studies of complexes of the Grb2-SH2 domain with ligands derived from a phosphorylated tyrosine [17], we observed domain-swapping of a Grb2-SH2 domain that was not part of a GST fusion protein. Isothermal titration calorimetry (ITC) data indicated that this dimeric form of the Grb2-SH2 domain exhibited a reduction in affinity for a Shc-derived ligand compared to the monomeric domain.…”

Section: Introductionmentioning

confidence: 99%

Structural and energetic aspects of Grb2-SH2 domain-swapping

Benfield

Whiddon

Archives of Biochemistry and Biophysics

et al. 2007

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The SH2 domain of growth factor receptor-bound protein 2 (Grb2) has been the focus of numerous studies, primarily because of the important roles it plays in signal transduction. More recently, it has emerged as a useful protein to study the consequences of ligand preorganization upon energetics and structure in protein-ligand interactions. The Grb2-SH2 domain is known to form a domain-swapped dimer, and as part of our investigations toward correlating structure and energetics in biological systems, we examined the effects that domain-swapping dimerization of the Grb2-SH2 domain had upon ligand binding affinities. Isothermal titration calorimetry was performed using Grb2-SH2 in both its monomeric and domain-swapped dimeric forms and a phosphorylated tripeptide AcNHpTyr-Val-Asn-NH 2 that is similar to the Shc sequence recognized by Grb2-SH2 in vivo. The two binding sites of domain-swapped dimer exhibited a 4-and a 13-fold reduction in ligand affinity compared to monomer. Crystal structures of peptide-bound and uncomplexed forms of Grb2-SH2 domain-swapped dimer were obtained and reveal that the orientation of residues V122, V123, and R142 may influence the conformation of W121, an amino acid that is believed to play an important role in Grb2-SH2 ligand sequence specificity. These findings suggest that domain-swapping of Grb2-SH2 not only results in a lower affinity for a Shc-derived ligand, but it may also affect ligand specificity.

“…Provided the two ligands interact in the same way with solvent and the protein ( i.e., ΔΔ H o ~ 0 kcal mol −1 ), the preorganized molecule would thus be expected to benefit from a more favorable binding free energy. However, in studies of the binding of phosphotyrosine-derived peptides to Src and Grb2 SH2 domains, we have discovered that ligand preorganization can have either favorable or unfavorable entropic consequences 3,4,5. In the general context of our interest in energetics and structure in protein-ligand interactions, we now report energetic and structural effects of introducing macrocyclic conformational constraints to preorganize Grb2 SH2 binding ligands.…”

mentioning

confidence: 97%

Thermodynamic and Structural Effects of Macrocyclic Constraints in Protein−Ligand Interactions

DeLorbe

Whiddon

et al. 2010

ACS Med. Chem. Lett.

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The thermodynamic and structural effects of macrocyclization as a tactic for stabilizing the biologically-active conformation of Grb2 SH2 binding peptides were investigated using isothermal titration calorimetry and x-ray crystallography. 23-Membered macrocycles containing the sequence pYVN were slightly more potent than their linear controls; however, preorganization did not necessarily eventuate in a more favorable binding entropy. Structures of complexes of macrocycle 7 and its acyclic control 8 are similar except for differences in relative orientations of corresponding atoms in the linking moieties of 7 and 8. There are no differences in the number of direct or water-mediated protein-ligand contacts that might account for the less favorable binding enthalpy of 7; however, an intramolecular hydrogen bond between the pY and pY+3 residues in 8 that is absent in 7 may be a factor. These studies highlight the difficulties associated with correlating energetics and structure in protein-ligand interactions.