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Mohammadi M, Shareghi B, Akbar Saboury A. Comparative studies on the interaction of spermidine with carboxypeptidase A using multispectroscopic and docking methods. Int J Biol Macromol 2020; 147:821-831. [PMID: 31751718 DOI: 10.1016/j.ijbiomac.2019.09.242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 10/25/2022]
Abstract
Carboxypeptidase A (CPA) (EC 3.4.17.1) is one of the main members of the M14 family that release one amino acid from the C-terminal region of the polypeptides at each time. The purpose of the present study was to study the effect of spermidine (NH2(CH2)3NH(CH2)4NH2) on the conformation, thermal stability, and activity of native CPA from bovine pancreas, by employing ultraviolet-visible (UV-Vis) spectroscopy, intrinsic fluorescence, thermal stability, circular dichroism (CD), kinetic techniques and molecular docking. It was found that the decrease in the CPA, UV-Vis absorption could be due to the formation of the CPA-spermidine complexes. The results of fluorescence spectroscopic measurements at the temperatures of 308 and 318 K also revealed that spermidine had the capability to quench the intrinsic fluorescence of CPA with the static mode. Further, the thermodynamic parameters, (Gibbs free-energy, enthalpy and entropy changes) showed that the binding process of spermidine to CPA was spontaneous and the main force in stabilizing the complex was the van der Waals and hydrogen interactions, along with the molecular docking results. In addition, CD spectra and fluorescence results revealed that spermidine had a partial effect on the CPA structure, leading to some changes in its secondary structure. The Tm studies of the CPA-spermidine complex also indicated that the Tm values were enhanced with increasing the spermidine concentration. Kinetic studies further showed that by spermidine binding, the Vmax value and activity of the enzyme were increased.
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Affiliation(s)
- Mozhgan Mohammadi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Mohammadi M, Shareghi B, Akbar Saboury A, Farhadian S. Spermine as a possible endogenous allosteric activator of carboxypeptidase A: multispectroscopic and molecular simulation studies. J Biomol Struct Dyn 2019; 38:101-113. [DOI: 10.1080/07391102.2019.1567387] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mozhgan Mohammadi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
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Citri N. Conformational adaptability in enzymes. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 37:397-648. [PMID: 4632894 DOI: 10.1002/9780470122822.ch7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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4
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Han MS, Ryu CH, Chung SJ, Kim DH. A novel strategy for designing irreversible inhibitors of metalloproteases: acetals as latent electrophiles that interact with catalytic nucleophile at the active site. Org Lett 2000; 2:3149-52. [PMID: 11009368 DOI: 10.1021/ol006346w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new strategy for design of irreversible inactivators for carboxypeptidase A (CPA), a prototypic zinc protease, has been developed by exploiting the property of acetals to generate an oxacarbenium ion intermediate in the conversion into the corresponding carbonyl compounds. The design strategy is exemplified by 2-benzyl-5-alkyl-3,5-dioxapentanoic acids (1a-c). Interestingly, (R)-1b is slightly more potent than an (S)-1b as an inactivator of CPA.
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Affiliation(s)
- M S Han
- Center for Biofunctional Molecules and Department of Chemistry, Pohang University of Science and Technology, San 31 Hyojadong, Pohang 790-784, Korea
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Mock WL, Wang L. Synergistic inhibition of carboxypeptidase A by zinc ion and imidazole. Biochem Biophys Res Commun 1999; 257:239-43. [PMID: 10092540 DOI: 10.1006/bbrc.1999.0440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Zinc ion in solution yields a 560-fold enhancement in the kinetic inhibition of carboxypeptidase A by the simple heterocycle imidazole, behavior attributed to formation of a ternary complex of the three species. However, the effect is partially negated by formation of less-inhibitory Zn2+(C3H4N2)2-4 coordination complexes, providing for the enzyme an anomalous profile of catalytic rate versus imidazole concentration.
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Affiliation(s)
- W L Mock
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, USA.
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Zenchenko TA, Morozov VN. Mechanical deformation enhances catalytic activity of crystalline carboxypeptidase A. Protein Sci 1995; 4:251-7. [PMID: 7757013 PMCID: PMC2143058 DOI: 10.1002/pro.5560040211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A new approach for investigating mechano-chemical interactions in enzymes is described. The catalytic activity of crystalline crosslinked enzymes subjected to uniaxial deformation has been measured. Extension of monoclinic P2(1) crystals of carboxypeptidase A along the [010] direction leads to a many-fold increase in catalytic esterase activity with no changes in the effective Michaelis constant. This increase is interpreted as due to liberation of conformational mobility associated with catalytic activity of the enzyme in the deformed crystal.
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Affiliation(s)
- T A Zenchenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region
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7
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Abstract
ADP-ribosylation reaction, that is the transfer of the ADP-ribose moiety of NAD+ to acceptor protein, is catalyzed by two classes of ADP-ribosyltransferases, i.e., poly(ADP-ribose) synthetase and mono(ADP-ribosyl)transferases. These two types differ not only in the number of transferring ADP-ribose units but also in the acceptor amino acid(s) and protein. Their inhibitors, particularly those of poly(ADP-ribose) synthetase, have been successfully employed in studies on biological functions of the enzymes and other related fields of research. Recently, we found many potent and specific inhibitors of poly(ADP-ribose) synthetase, and broadened their chemical as well as biochemical variety. More recently, we found several potent inhibitors of arginine-specific mono(ADP-ribosyl)transferases and activators of poly(ADP-ribose) synthetase.
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Affiliation(s)
- M Banasik
- Department of Clinical Science and Laboratory Medicine, Kyoto University Faculty of Medicine, Japan
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8
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Latent inhibitors Part 10. The inhibition of carboxypeptidase a by tetrapeptide analogues based on 1-aminocyclopropane carboxylic acid. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)85539-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Kemp A, Tedford C, Suckling CJ. Substrate activated time dependent inhibition of carboxypeptidase a by aminocyclopropane carboxylic acid derivatives and analogues. Bioorg Med Chem Lett 1991. [DOI: 10.1016/s0960-894x(01)80465-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Kojro E, Willhardt I, Römbach A, Grzonka Z, Hermann P. Tetrazole analogs of amino acids as constituents of modifiers of carboxypeptidase A catalysis. FEBS Lett 1987; 212:83-6. [PMID: 3803610 DOI: 10.1016/0014-5793(87)81561-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The action of substrate analogs containing the tetrazolyl group instead of the C-terminal carboxy group on the peptidase activity of carboxypeptidase A is studied. The analogs compete with the substrate for the secondary binding site thus showing activation phenomena.
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Schäffer A, Auld DS. Activity of copper-substituted carboxypeptidase A toward oligopeptides and depsipeptides. Biochemistry 1986; 25:2476-9. [PMID: 3013305 DOI: 10.1021/bi00357a028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cu(II)-substituted carboxypeptidase A catalyzes the hydrolysis of oligopeptides and their depsipeptide (ester) analogues. Stopped-flow fluorescence assays demonstrate that relative to the zinc enzyme the Cu enzyme can have kcat/Km values up to 24% toward esters but only up to 2.5% toward the corresponding peptides. Adding Zn(II) to the copper enzyme reveals a slow exchange process that correlates with an increase in peptidase activity and with changes in the Cu(II) electron paramagnetic resonance spectra. Low concentrations of 1,10-phenanthroline (OP) (0.1-2.5 microM) markedly increase activity toward furanacryloyl-Phe-Phe (up to 8% of the zinc enzyme), but higher concentrations inhibit, resulting in complete inhibition at 0.8 mM OP. The non-metal-binding, hydrophobic analogues m- and p-phenanthroline are only activators of peptide hydrolysis, even at 1 mM. Activation is likely due to a modifier binding to a hydrophobic locus and either displacing an inhibitory peptide binding mode or inducing a conformational change in the active site.
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Cleaver JE, Borek C, Milam K, Morgan WF. The role of poly(ADP-ribose) synthesis in toxicity and repair of DNA damage. Pharmacol Ther 1985; 31:269-93. [PMID: 3939630 DOI: 10.1016/0163-7258(85)90026-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Danner J, Somerville JE, Truner J, Dunn BM. Multiple binding sites of carboxypeptidase B: the evaluation of dissociation constants by quantitative affinity chromatography. Biochemistry 1979; 18:3039-45. [PMID: 37894 DOI: 10.1021/bi00581a020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Chemical modifications of the subtilisins with special reference to the binding of large substrates. A review. ACTA ACUST UNITED AC 1976. [DOI: 10.1007/bf02906260] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Spilburg CA, Bethune JL, Vallee BL. The physical state dependence of carboxypeptidase Aalpha and Agamma kinetics. Proc Natl Acad Sci U S A 1974; 71:3922-6. [PMID: 4530272 PMCID: PMC434298 DOI: 10.1073/pnas.71.10.3922] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Spectrochemical probes have demonstrated that the conformations of carboxypeptidase A (EC 3.4.12.2) differ in solution and in the crystalline state. Detailed kinetic studies of carboxypeptidase A(alpha) and A(gamma) crystals and solutions now show that the physical state of the enzyme is also a critical parameter that affects the function of the A(alpha) and A(gamma) enzymes in the same manner. The kinetic profiles and the corresponding kinetic constants of substrate hydrolysis are, therefore, important functional indices of the known conformational differences of the enzyme in these two physical states. The complex kinetic behavior of this enzyme, however, precludes meaningful comparisons of activity measurements for crystals and solutions obtained at only one substrate concentration. Underlying differences in varying substrate-inhibiting or -activating binding modes can result in either high or low activity ratios, concealing the true, functional consequences of the change in physical state. Thus, for all substrates examined, crystallization of the enzyme markedly reduces catalytic efficiency, k(cat), from 20- to 1000-fold. Equally as important, the substrate inhibition, apparent in solution for some di- and depsipeptides, is abolished with crystals, while for longer substrates the normal solution kinetics may acquire activation with the crystals. Hypothetical modes of substrate-enzyme interaction, generated by superimposing substrate models on the crystal structure of carboxypeptidase to simulate kinetics in solution, have failed to detect both of these changes, which affect inhibitory or activating binding modes. The only structure of carboxypeptidase yet published and that of its functionally inert complex with the pseudosubstrate, glycyl-L-tyrosine, derive from a unique form of carboxypeptidase A(alpha) crystals. These crystals differ from all others with regard both to their spectral properties and activity toward carbobenzoxy-glycyl-L-phenylalanine, which is 30% of that in solution, though the significance of this value cannot be gauged without knowledge of the relevant kinetic constants. The rapidly accumulating evidence for functional and conformational differences between crystals and solutions and the recent stress on the nonproductive aspects of the carboxypeptidase A(alpha)-glycyl-L-tyrosine complex, based on 30% site occupancy, suggest that the functional implications of its structural features require reevaluation.
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18
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Bodlaender P. Functional effects of reducing and carboxymethylating the single disulfide bond in bovine carboxypeptidase A. Arch Biochem Biophys 1974; 164:456-9. [PMID: 4477700 DOI: 10.1016/0003-9861(74)90055-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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Lange LG, Auld DS, Riordan JF. Substrate enantiomers. Modifiers of carboxypeptidase A activity. Biochemistry 1974; 13:1983-6. [PMID: 4858174 DOI: 10.1021/bi00706a031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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20
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Schechter I, Zazepizki E. On the mechanism of acceleration of carboxypeptidase A activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 18:469-73. [PMID: 5101751 DOI: 10.1111/j.1432-1033.1971.tb01265.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Quiocho FA, Lipscomb WN. Carboxypeptidase A: a protein and an enzyme. ADVANCES IN PROTEIN CHEMISTRY 1971; 25:1-78. [PMID: 4946703 DOI: 10.1016/s0065-3233(08)60278-8] [Citation(s) in RCA: 305] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Navon G, Shulman RG, Wyluda BJ, Yamane T. Nuclear magnetic resonance study of the binding of fluoride ions to carboxypeptidase A. J Mol Biol 1970; 51:15-30. [PMID: 5529708 DOI: 10.1016/0022-2836(70)90266-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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23
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Auld DS, Vallee BL. Kinetics of carboxypeptidase A. II. Inhibitors of the hydrolysis of oligopeptides. Biochemistry 1970; 9:602-9. [PMID: 5461217 DOI: 10.1021/bi00805a022] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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26
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Adelman RC, Lacko AG. The inhibition of bovine pancreatic carboxypeptidase A by dihydroxyacetone phosphate. Biochem Biophys Res Commun 1968; 33:596-601. [PMID: 5726178 DOI: 10.1016/0006-291x(68)90337-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Vallee BL, Riordan JF, Bethune JL, Coombs TL, Auld DS, Sokolovsky M. A model for substrate binding and kinetics of carboxypeptidase A. Biochemistry 1968; 7:3547-56. [PMID: 5681464 DOI: 10.1021/bi00850a032] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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