Carbonic Anhydrase as a Model for Biophysical and Physical-Organic Studies of Proteins and Protein−Ligand Binding

Krishnamurthy, Vijay M.; Kaufman, George K.; Urbach, Adam R.; Gitlin, Irina; Gudiksen, Katherine L.; Weibel, Douglas B.; Whitesides, George M.

doi:10.1021/cr050262p

Cited by 683 publications

(829 citation statements)

References 832 publications

(2,697 reference statements)

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“…Support for this is the 5 cal/K mol increase in entropy change when allosamidin binds to ChiA-W167A compared to ChiA-WT [21]. It has been observed through NMR and ITC measurements that when the distance of the protein backbone and the ligand is extended, the entropy change rises due to an increase in protein dynamics [31][32][33].…”

Section: The -3 Subsitementioning

confidence: 96%

Substrate positioning in chitinase A, a processive chito-biohydrolase fromSerratia marcescens

et al. 2011

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a b s t r a c tThe contributions of the -3 subsite and a putative +3 subsite to substrate positioning in ChiA from Serratia marcescens have been investigated by comparing how ChiA and its -3 subsite mutant W167A interact with soluble substrates. The data show that Trp -GlcNAc stacking in the -3 subsite rigidifies the protein backbone supporting the formation of the intermolecular interaction network that is necessary for the recognition and positioning of the N-acetyl groups before the -1 subsite. The +3 subsite exhibits considerable substrate affinity that may promote endo-activity in ChiA and/or assist in expelling dimeric products from the +1 and +2 subsites during processive hydrolysis.

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Section: The -3 Subsitementioning

confidence: 96%

Substrate positioning in chitinase A, a processive chito-biohydrolase fromSerratia marcescens

et al. 2011

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“…13−15 HCA is structurally rigid and undergoes minimal (<1 Å) conformational changes upon binding of most arylsulfonamide ligands. 23 More importantly for this study of thiazole-based sulfonamide ligands, 2,4 its structural rigidity allows us to focus solely on the rearrangement of solvent within the active site of the protein, and not on contributions caused by conformational changes in the protein.…”

Section: ■ Introductionmentioning

confidence: 99%

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

et al. 2013

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ABSTRACT:The mechanism (or mechanisms) of enthalpy− entropy (H/S) compensation in protein−ligand binding remains controversial, and there are still no predictive models (theoretical or experimental) in which hypotheses of ligand binding can be readily tested. Here we describe a particularly well-defined system of protein and ligandshuman carbonic anhydrase (HCA) and a series of benzothiazole sulfonamide ligands with different patterns of fluorinationthat we use to define enthalpy/entropy (H/S) compensation in this system thermodynamically and structurally. The binding affinities of these ligands (with the exception of one ligand, in which the deviation is understood) to HCA are, despite differences in fluorination pattern, indistinguishable; they nonetheless reflect significant and compensating changes in enthalpy and entropy of binding. Analysis reveals that differences in the structure and thermodynamic properties of the waters surrounding the bound ligands are an important contributor to the observed H/S compensation. These results support the hypothesis that the molecules of water filling the active site of a protein, and surrounding the ligand, are as important as the contact interactions between the protein and the ligand for biomolecular recognition, and in determining the thermodynamics of binding.

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“…In this study, we used site-directed mutagenesis to rearrange water filling the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1), a structurally rigid protein [16] . We combined isothermal titration calorimetry (ITC), X-ray crystallography, and molecular dynamics simulations to determine-and subsequently rationalize-the repercussions of those perturbations for the thermodynamics of HCAII-ligand association.…”

Section: Introductionmentioning

confidence: 99%

Water‐Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

Fox

Kang

Sastry³

et al. 2017

Angew Chem Int Ed

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This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein–ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water‐mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy‐driven or entropy‐driven. Our findings highlight a possible asymmetry in protein–ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.

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Carbonic Anhydrase as a Model for Biophysical and Physical-Organic Studies of Proteins and Protein−Ligand Binding

Cited by 683 publications

References 832 publications

Substrate positioning in chitinase A, a processive chito-biohydrolase fromSerratia marcescens

Substrate positioning in chitinase A, a processive chito-biohydrolase fromSerratia marcescens

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

Water‐Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

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