Ligand Binding Energy and Enzyme Efficiency from Reductions in Protein Dynamics

Williams, Dudley H.; Zhou, Min; Stephens, Elaine

doi:10.1016/j.jmb.2005.11.015

Cited by 15 publications

(12 citation statements)

References 37 publications

(38 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…intermolecular hydrogen bonds. 13 Subsequently, a role for structural tightening in enzyme catalysis was supported by observed increases in amide protection factors upon binding of substrates, 27 binding of inhibitors 15 and the formation of covalent intermediates, 28 in addition to TSA binding. 14,29 However, an increase in amide protection factor induced by ligand binding is caused by one of two processes or a combination thereof.…”

Section: Discussionmentioning

confidence: 98%

Structural Tightening and Interdomain Communication in the Catalytic Cycle of Phosphoglycerate Kinase

Marston¹,

Cliff²,

Reed³

et al. 2010

Journal of Molecular Biology

View full text Add to dashboard Cite

Section: Discussionmentioning

confidence: 98%

Structural Tightening and Interdomain Communication in the Catalytic Cycle of Phosphoglycerate Kinase

Marston¹,

Cliff²,

Reed³

et al. 2010

Journal of Molecular Biology

View full text Add to dashboard Cite

“…In summary, the data for 3c and 4c provide an example of a classical enthalpy/entropy compensation. 20,21 Furthermore, differences in the solvation/desolvation properties of 3c and 4c will also have an impact on the observed thermodynamic profiles.…”

Section: Correlation Of Structural and Thermodynamic Data Of 3c/4cmentioning

confidence: 99%

“…Conversely, a binding event can be negatively cooperative when the affinity is decreased while two ligand parts experience simultaneous interactions with the protein. 11,12 This fundamental phenomenon has thus far been pragmatically ignored in favor of the simpler additivity approach, well in line with frequently applied concepts in chemistry on the basis of simple and convenient additive models.…”

Section: Introductionmentioning

confidence: 96%

“…9,10 Two ligand fragments mutually linked together into one entity can result in a ligand with a binding affinity greater than the sum of its parts. The latter situation has been defined as positively cooperative for protein-ligand interactions by Williams et al 11,12 and should be distinguished from the original definition given by Monod et al, 13 who used "cooperativity" to describe the cross-talk between multiple binding sites in protein complexes. Conversely, a binding event can be negatively cooperative when the affinity is decreased while two ligand parts experience simultaneous interactions with the protein.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

Baum¹,

Muley²,

Smolinski³

et al. 2010

Journal of Molecular Biology

145

166

View full text Add to dashboard Cite

“…This definition has been used by others in the context of protein folding (19) or ligand binding (20). We used a multiple substitution strategy previously used to identify interacting partners during protein folding (21,22).…”

Section: Calculation Of Cooperative Effectsmentioning

confidence: 99%

Cooperativity of Hydrophobic Anchor Interactions: Evidence for Epitope Selection by MHC Class II as a Folding Process

Ferrante

Gorski

2007

The Journal of Immunology

View full text Add to dashboard Cite

Peptide binding to MHC class II (MHCII) molecules is stabilized by hydrophobic anchoring and hydrogen bond formation. We view peptide binding as a process in which the peptide folds into the binding groove and to some extent the groove folds around the peptide. Our previous observation of cooperativity when analyzing binding properties of peptides modified at side chains with medium to high solvent accessibility is compatible with such a view. However, a large component of peptide binding is mediated by residues with strong hydrophobic interactions that bind to their respective pockets. If these reflect initial nucleation events they may be upstream of the folding process and not show cooperativity. To test whether the folding hypothesis extends to these anchor interactions, we measured dissociation and affinity to HLA-DR1 of an influenza hemagglutinin-derived peptide with multiple substitutions at major anchor residues. Our results show both negative and positive cooperative effects between hydrophobic pocket interactions. Cooperativity was also observed between hydrophobic pockets and positions with intermediate solvent accessibility, indicating that hydrophobic interactions participate in the overall folding process. These findings point out that predicting the binding potential of epitopes cannot assume additive and independent contributions of the interactions between major MHCII pockets and corresponding peptide side chains.

show abstract

Ligand Binding Energy and Enzyme Efficiency from Reductions in Protein Dynamics

Cited by 15 publications

References 37 publications

Structural Tightening and Interdomain Communication in the Catalytic Cycle of Phosphoglycerate Kinase

Structural Tightening and Interdomain Communication in the Catalytic Cycle of Phosphoglycerate Kinase

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

Cooperativity of Hydrophobic Anchor Interactions: Evidence for Epitope Selection by MHC Class II as a Folding Process

Contact Info

Product

Resources

About