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

Baum, Bernhard; Muley, Laveena; Smolinski, Michael; Heine, A.; Hangauer, David; Klebe, G.

doi:10.1016/j.jmb.2010.02.007

Cited by 144 publications

(171 citation statements)

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“…It has been suggested by Laskowski and coworkers (70) that one element responsible for the predictably additive behavior in serine protease-canonical inhibitor association is a lock and key rather than induced fit mode of molecular recognition. Dynamical properties also appear to play an important role in cooperativity between functional groups in protein-small molecule ligand binding (73). Thus, it is possible that the conformational adjustments required at the mesotrypsin⅐inhibitor interface, suggestive of an induced fit mechanism of recognition, lead to more complex energetic relationships between individual residues than are seen in most other canonical inhibitor complexes.…”

Section: Discussionmentioning

confidence: 99%

“…Our diffraction data were collected at 100 K, where motions are considerably reduced, but we would expect that flash cooling will generate a frozen static picture of protein dynamics under ambient conditions (73). The four copies of the mesotrypsin⅐APPI complex in the crystal differ considerably in their average B-factors, with the chain A⅐chain E complex possessing the lowest B-factors whereas the chain D⅐chain H complex possesses much higher B-factors throughout; however, the trends described here and plotted for the chain A⅐chain E complex in Fig.…”

Section: The Inhibitor Scaffold Is a Major Determinant Of Inhibitor Smentioning

confidence: 99%

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Determinants of Affinity and Proteolytic Stability in Interactions of Kunitz Family Protease Inhibitors with Mesotrypsin

Salameh

Soares

Navaneetham

et al. 2010

Journal of Biological Chemistry

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An important functional property of protein protease inhibitors is their stability to proteolysis. Mesotrypsin is a human trypsin that has been implicated in the proteolytic inactivation of several protein protease inhibitors. We have found that bovine pancreatic trypsin inhibitor (BPTI), a Kunitz protease inhibitor, inhibits mesotrypsin very weakly and is slowly proteolyzed, whereas, despite close sequence and structural homology, the Kunitz protease inhibitor domain of the amyloid precursor protein (APPI) binds to mesotrypsin 100 times more tightly and is cleaved 300 times more rapidly. To define features responsible for these differences, we have assessed the binding and cleavage by mesotrypsin of APPI and BPTI reciprocally mutated at two nonidentical residues that make direct contact with the enzyme. We find that Arg at P 1 (versus Lys) favors both tighter binding and more rapid cleavage, whereas Met (versus Arg) at P 2 favors tighter binding but has minimal effect on cleavage. Surprisingly, we find that the APPI scaffold greatly enhances proteolytic cleavage rates, independently of the binding loop. We draw thermodynamic additivity cycles analyzing the interdependence of P 1 and P 2 substitutions and scaffold differences, finding multiple instances in which the contributions of these features are nonadditive. We also report the crystal structure of the mesotrypsin⅐APPI complex, in which we find that the binding loop of APPI displays evidence of increased mobility compared with BPTI. Our data suggest that the enhanced vulnerability of APPI to mesotrypsin cleavage may derive from sequence differences in the scaffold that propagate increased flexibility and mobility to the binding loop.

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Section: Discussionmentioning

confidence: 99%

Section: The Inhibitor Scaffold Is a Major Determinant Of Inhibitor Smentioning

confidence: 99%

Determinants of Affinity and Proteolytic Stability in Interactions of Kunitz Family Protease Inhibitors with Mesotrypsin

Salameh

Soares

Navaneetham

et al. 2010

Journal of Biological Chemistry

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“…17 Yet changes in this interaction do not explain all observed non-additivity levels, and other changes in interactions with protein residues occur across the entire binding site. Therefore coupling between the X=NH 3 + and R 1 substituents is the result of an energetic balance between numerous interactions, whose final outcome depends non-trivially on the precise chemical nature of R 1 .…”

Section: Resultsmentioning

confidence: 97%

“…54 Alternatively the larger R 1 substituents push the ligand slightly away from the S3 pocket, causing a shortening of the hydrogen-bond distances between the extra amino group of the 5 series ligands and the backbone carbonyl of Gly216, and one of the ligands amide carbonyl and Gly216 backbone NH. 17 Clarification was sought by extracting the contribution of protein-ligand interaction energies to the non-additivity levels from the computed trajectories (equation 6). The thrombin binding site was partitioned in four groups that contact different sections of the ligands ( Figure 10A).…”

Section: Docking Energies Overall Correlate Poorly But Show Trends Wmentioning

confidence: 99%

“…A detailed study of non-additivity of functional group contributions to protein-ligand interactions was reported by Baum et al 17 The work featured isothermal titration calorimetry (ITC) measurements and crystallographic analyses of the enzyme thrombin in complex with different series of congeneric inhibitors. Structurally the ligand binding site in thrombin presents three sub-pockets illustrated in Figure 1A.…”

Section: Introductionmentioning

confidence: 99%

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