Differential binding energy: a detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors

Morgan, P Bradley; Scholtz, J. Martin; Ballinger, Marcus; Zipkin, Ilan D.; Bartlett, Paul A.

doi:10.1021/ja00001a043

Cited by 199 publications

(127 citation statements)

References 2 publications

(5 reference statements)

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“…Water-accessible surface area (A21 Change from phosphonamidate to phosphinate Two independently determined experimental values for ZGP(C)LL were reported at almost the same time, and both claimed to be accurate to 10%. Our AAGe/e agrees with that of Grohelny et al (1989), whereas Merz and Kollman's (1989) FEP calculation closely predicted that of Morgan et al (1991). Morgan et al attributed the difference to the different salt concen- Table 2.…”

supporting

confidence: 81%

“…In particular, the positive charges on Zn and Arg 203, which are not the acceptors, contribute significantly to the hydrogen bonds between two amides of ZGPLL and the thermolysin. Morgan et al, 1991). It has been shown that modifications on X or Y yield uniform binding constant changes for those inhibitors with identical R. In particular, the average binding energy change between phosphonamidates and phosphonates is 4.0 * 0.1 kcal/mol.…”

mentioning

confidence: 99%

“…Grohelny et al (1989) proposed that the basicities of the inhibitors and a much smaller H-bond energy of 1.5 kcal/mol are responsible for the loss of binding affinity in going from phosphonamidates to phosphonates. Although Morgan et al (1991) showed that the basicities of another series of phosphorus-containing inhibitors are not critical to the binding, a final conclusion has not been reached due to the lack of relevant experiments and, perhaps, of more convincing theoretical calculation as well. …”

mentioning

confidence: 99%

“…As Bartlett and Marlow (1987) indicated, the modification of the P1' and P2' NH produces no, or few, complications from conformational strain and entropy, or any energetic change associated with the release of binding waters, making this system ideal for FDPB study. Furthermore, the FDPB calculation scheme is essentially identical to the thermodynamic cycle used in the binding mechanistic studies (Bartlett & Marlowe, 1987;Morgan et al, 1991). We are able to extract the relevant energies to compare with the experiments and provide qualitative estimates.…”

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confidence: 99%

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Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method

Shen

Wendoloski

1995

Protein Science

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Zinc endopeptidase thermolysin can be inhibited by a series of phosphorus-containing peptide analogues, CbzGly-$(PO2)-X-Leu-Y-R (ZGP(X)L(Y)R), where X = NH, 0, or CH2; Y = NH or 0; and R = Leu, Ala, Gly, Phe, H , or CH3. The affinity correlation as well as an X-ray crystallography study suggest that these inhibitors bind to thermolysin in an identical mode. In this work, we calculate the electrostatic binding free energies for a series of 13 phosphorus-containing inhibitors with modifications at X, Y, and R moieties using finite difference solution to the Poisson-Boltzmann equation. A method has been developed to include the solvation entropy changes due to binding different ligands to a macromolecule. We demonstrate that the electrostatic energy and empirically derived solvation entropy can account for most of the binding energy differences in this series. By analyzing the binding contribution from individual residues, we show that the energy of a hydrogen bond is not confined to the donor and acceptor. In particular, the positive charges on Zn and Arg 203, which are not the acceptors, contribute significantly to the hydrogen bonds between two amides of ZGPLL and the thermolysin. Morgan et al., 1991). It has been shown that modifications on X or Y yield uniform binding constant changes for those inhibitors with identical R. In particular, the average binding energy change between phosphonamidates and phosphonates is 4.0 * 0.1 kcal/mol. These correlations, as well as an X-ray crystallography study Tronrud et al., 1987;Matthews, 1988), suggest that these inhibitors bind to thermolysin in an identical mode.Previous theoretical studies focused on the variation of the X moiety of these inhibitors. Bash et al. (1987) and Merz and Kollman (1989) carried out free energy perturbation (FEP) simulations for ZGP(X)LL with thermolysin. The good agreement between the calculations and experiments indicates that the solvation of the inhibitors and the interaction between the X moiety and a hydrogen bond (H-bond) acceptor of the enzyme are two primary determinants of the binding affinity difference. Through a qualitative analysis, Bartlett and Marlowe (1987) suggested that the intrinsic H-bond energy for phosphonamidates Reprint requests to: Jian Shen at his present address: Marion Merre11 Dow, lnc., 2110 East Galbraith Road, P.O. Box 156300, Cincinnati, is significantly higher than the observed binding energy change of 4 kcal/mol from the PI' NH to 0 substitution. However, the calculated solvation energies as well as the interpretation were challenged by partition coefficient and pK, measurements. Grohelny et al. (1989) proposed that the basicities of the inhibitors and a much smaller H-bond energy of 1.5 kcal/mol are responsible for the loss of binding affinity in going from phosphonamidates to phosphonates. Although Morgan et al. (1991) showed that the basicities of another series of phosphorus-containing inhibitors are not critical to the binding, a final conclusion has not been reached due to the lack of relevant ...

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confidence: 81%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method

Shen

Wendoloski

1995

Protein Science

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“…44 -48). Some caveolin-2 is found in caveolae, in association with caveolin-1, but even in these cases, most of the caveolin-2 detected by immunofluorescence resides in the Golgi complex (45)(46)(47). A recent study showed co-localization of human group V sPLA 2 with caveolin-2 in punctate domains in the macrophage-like cell line p388D1 (49).…”

Section: Localization Of Hgiia In Hek293 Cells By Immunofluorescence-mentioning

confidence: 99%

Arachidonic Acid Release from Mammalian Cells Transfected with Human Groups IIA and X Secreted Phospholipase A2 Occurs Predominantly during the Secretory Process and with the Involvement of Cytosolic Phospholipase A2-α

Mounier

Ghomashchi

Lindsay

et al. 2004

Journal of Biological Chemistry

137

147

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Stable expression of human groups IIA and X secreted phospholipases A 2 (hGIIA and hGX) in CHO-K1 and HEK293 cells leads to serum-and interleukin-1␤-promoted arachidonate release. Using mutant CHO-K1 cell lines, it is shown that this arachidonate release does not require heparan sulfate proteoglycan-or glycosylphosphatidylinositol-anchored proteins. It is shown that the potent secreted phospholipase A 2 inhibitor Me-Indoxam is cell-impermeable. By use of Me-Indoxam and the cellimpermeable, secreted phospholipase A 2 trapping agent heparin, it is shown that hGIIA liberates free arachidonate prior to secretion from the cell. With hGX-transfected CHO-K1 cells, arachidonate release occurs before and after enzyme secretion, whereas all of the arachidonate release from HEK293 cells occurs prior to enzyme secretion. Immunocytochemical studies by confocal laser and electron microscopies show localization of hGIIA to the cell surface and Golgi compartment. Additional results show that the interleukin-1␤-dependent release of arachidonate is promoted by secreted phospholipase A 2 expression and is completely dependent on cytosolic (group IVA) phospholipase A 2 . These results along with additional data resolve the paradox that efficient arachidonic acid release occurs with hGIIAtransfected cells, and yet exogenously added hGIIA is poorly able to liberate arachidonic acid from mammalian cells.Phospholipases A 2 (PLA 2 s) 1 are a class of enzymes that release fatty acids from the sn-2 position of glycero-phospholipids. Biomedical interest in these enzymes stems from the finding that the liberation of arachidonic acid for the biosynthesis of the eicosanoids (prostaglandins, leukotrienes, and others) is mediated in mammalian cells by one or more PLA 2 s. Current evidence favors a role for cytosolic phospholipase A 2 -␣ (cPLA 2 -␣, also known as group IVA PLA 2 ) as a major component of the arachidonate releasing signal transduction pathway (1-3). Mammals also contain a large number of secreted phospholipases A 2 (sPLA 2 s) (4, 5), and the possible participation of these enzymes in arachidonate release is under active investigation. For example, group V sPLA 2 is present in the macrophage-like cell line p388D1 and contributes a portion of the arachidonate released in response to lipopolysaccharide (6). Exogenous addition of groups V and X sPLA 2 s to a variety of mammalian cells leads to arachidonate release (7-10). There is some evidence to suggest that the action of cPLA 2 -␣ is a prerequisite for sPLA 2 function in cells (11,12) and even for the vice versa scenario (13-15), but such cross-talk between PLA 2 s remains poorly understood.To assess the arachidonate releasing capacity of PLA 2 s in mammalian cells, CHO and HEK293 cell lines that stably express the various enzymes have been established (16 -20). The behavior of human group IIA (hGIIA) and human group X (hGX) sPLA 2 s when transfected in HEK293 and CHO cells has been extensively studied. hGIIA is secreted from HEK293 cells, and most of the extracellular enzyme is a...

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Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy

Shen¹,

Wendoloski²

1996

J. Comput. Chem.

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Differential binding energy: a detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors

Cited by 199 publications

References 2 publications

Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method

Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method

Arachidonic Acid Release from Mammalian Cells Transfected with Human Groups IIA and X Secreted Phospholipase A2 Occurs Predominantly during the Secretory Process and with the Involvement of Cytosolic Phospholipase A2-α

Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy

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