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Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities.

Bioconjugate chemistry

Zhou Y, Liu B, Yang R, Liu J.
PMID: 29172463
Bioconjug Chem. 2017 Dec 20;28(12):2903-2909. doi: 10.1021/acs.bioconjchem.7b00673. Epub 2017 Dec 06.

Using nanomaterials to mimic the function of protein enzymes is an interesting idea. Many nanomaterials have a similar size as enzymes and they also possess catalytic activity. Over the past decade, a surge of nanozyme work has emerged, likely...

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Zhou Y, Liu B, Yang R, et al. Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities. Bioconjug Chem. 2017;28(12):2903-2909doi: 10.1021/acs.bioconjchem.7b00673.
Zhou, Y., Liu, B., Yang, R., & Liu, J. (2017). Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities. Bioconjugate chemistry, 28(12), 2903-2909. https://doi.org/10.1021/acs.bioconjchem.7b00673
Zhou, Yibo, et al. "Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities." Bioconjugate chemistry vol. 28,12 (2017): 2903-2909. doi: https://doi.org/10.1021/acs.bioconjchem.7b00673
Zhou Y, Liu B, Yang R, Liu J. Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities. Bioconjug Chem. 2017 Dec 20;28(12):2903-2909. doi: 10.1021/acs.bioconjchem.7b00673. Epub 2017 Dec 06. PMID: 29172463.
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Tracing metabolic pathways from enzyme data.

Biochimica et biophysica acta

McDonald AG, Tipton KF, Boyce S.
PMID: 19563919
Biochim Biophys Acta. 2009 Sep;1794(9):1364-71. doi: 10.1016/j.bbapap.2009.06.015. Epub 2009 Jun 27.

The IUBMB Enzyme List is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was never designed for activities such as pathway tracing, which have become increasingly...

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McDonald AG, Tipton KF, Boyce S. Tracing metabolic pathways from enzyme data. Biochim Biophys Acta. 2009;1794(9):1364-71doi: 10.1016/j.bbapap.2009.06.015.
McDonald, A. G., Tipton, K. F., & Boyce, S. (2009). Tracing metabolic pathways from enzyme data. Biochimica et biophysica acta, 1794(9), 1364-71. https://doi.org/10.1016/j.bbapap.2009.06.015
McDonald, Andrew G, et al. "Tracing metabolic pathways from enzyme data." Biochimica et biophysica acta vol. 1794,9 (2009): 1364-71. doi: https://doi.org/10.1016/j.bbapap.2009.06.015
McDonald AG, Tipton KF, Boyce S. Tracing metabolic pathways from enzyme data. Biochim Biophys Acta. 2009 Sep;1794(9):1364-71. doi: 10.1016/j.bbapap.2009.06.015. Epub 2009 Jun 27. PMID: 19563919.
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Continuous micro-production using enzymatic reaction and online monitoring.

Chimia

Moser R, Chappuis T, Vanoli E, Crelier S, Naef O.
PMID: 21197844
Chimia (Aarau). 2010;64(11):799-802. doi: 10.2533/chimia.2010.799.

A micro-reactor coupled to a microfluidic system and an online UV/VIS spectrometer is described. The enzymatic reaction studied is the hydrolysis of the N-benzoyl-L-tyrosine ethyl ester (BTEE) to N-benzoyl-L-tyrosine (BT) and ethanol, catalyzed by chymotrypsin. The production is online...

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Moser R, Chappuis T, Vanoli E, et al. Continuous micro-production using enzymatic reaction and online monitoring. Chimia (Aarau). 2010;64(11):799-802doi: 10.2533/chimia.2010.799.
Moser, R., Chappuis, T., Vanoli, E., Crelier, S., & Naef, O. (2010). Continuous micro-production using enzymatic reaction and online monitoring. Chimia, 64(11), 799-802. https://doi.org/10.2533/chimia.2010.799
Moser, Regula, et al. "Continuous micro-production using enzymatic reaction and online monitoring." Chimia vol. 64,11 (2010): 799-802. doi: https://doi.org/10.2533/chimia.2010.799
Moser R, Chappuis T, Vanoli E, Crelier S, Naef O. Continuous micro-production using enzymatic reaction and online monitoring. Chimia (Aarau). 2010;64(11):799-802. doi: 10.2533/chimia.2010.799. PMID: 21197844.
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iPath2.0: interactive pathway explorer.

Nucleic acids research

Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P.
PMID: 21546551
Nucleic Acids Res. 2011 Jul;39:W412-5. doi: 10.1093/nar/gkr313. Epub 2011 May 05.

iPath2.0 is a web-based tool (http://pathways.embl.de) for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various chemical compounds and edges represent...

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Yamada T, Letunic I, Okuda S, et al. iPath2.0: interactive pathway explorer. Nucleic Acids Res. 2011;39:W412-5doi: 10.1093/nar/gkr313.
Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., & Bork, P. (2011). iPath2.0: interactive pathway explorer. Nucleic acids research, 39W412-5. https://doi.org/10.1093/nar/gkr313
Yamada, Takuji, et al. "iPath2.0: interactive pathway explorer." Nucleic acids research vol. 39 (2011): W412-5. doi: https://doi.org/10.1093/nar/gkr313
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Res. 2011 Jul;39:W412-5. doi: 10.1093/nar/gkr313. Epub 2011 May 05. PMID: 21546551; PMCID: PMC3125749.
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Kinetic analysis of the transient phase and steady state of open multicyclic enzyme cascades.

Acta biochimica Polonica

Varón R, Havsteen BH, Valero E, Molina-Alarcón M, García-Cánovas F, García-Moreno M.
PMID: 16086076
Acta Biochim Pol. 2005;52(4):765-80. Epub 2005 Aug 05.

This paper presents a kinetic analysis of the whole reaction course, i.e. of both the transient phase and the steady state, of open multicyclic enzyme cascade systems. Equations for fractional modifications are obtained which are valid for the whole...

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Varón R, Havsteen BH, Valero E, et al. Kinetic analysis of the transient phase and steady state of open multicyclic enzyme cascades. Acta Biochim Pol. 2005;52(4):765-80
Varón, R., Havsteen, B. H., Valero, E., Molina-Alarcón, M., García-Cánovas, F., & García-Moreno, M. (2005). Kinetic analysis of the transient phase and steady state of open multicyclic enzyme cascades. Acta biochimica Polonica, 52(4), 765-80.
Varón, Ramón, et al. "Kinetic analysis of the transient phase and steady state of open multicyclic enzyme cascades." Acta biochimica Polonica vol. 52,4 (2005): 765-80.
Varón R, Havsteen BH, Valero E, Molina-Alarcón M, García-Cánovas F, García-Moreno M. Kinetic analysis of the transient phase and steady state of open multicyclic enzyme cascades. Acta Biochim Pol. 2005;52(4):765-80. Epub 2005 Aug 05. PMID: 16086076.
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Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies.

Analytical chemistry

Munge B, Liu G, Collins G, Wang J.
PMID: 16013886
Anal Chem. 2005 Jul 15;77(14):4662-6. doi: 10.1021/ac050132g.

Signal amplification using enzyme multilayers on carbon nanotube (CNT) templates is shown to yield a remarkably sensitive electrochemical detection of proteins and nucleic acids. The electrostatic layer-by-layer (LBL) self-assembly onto CNT carriers maximizes the ratio of enzyme tags per...

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Munge B, Liu G, Collins G, et al. Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies. Anal Chem. 2005;77(14):4662-6doi: 10.1021/ac050132g.
Munge, B., Liu, G., Collins, G., & Wang, J. (2005). Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies. Analytical chemistry, 77(14), 4662-6. https://doi.org/10.1021/ac050132g
Munge, Bernard, et al. "Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies." Analytical chemistry vol. 77,14 (2005): 4662-6. doi: https://doi.org/10.1021/ac050132g
Munge B, Liu G, Collins G, Wang J. Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies. Anal Chem. 2005 Jul 15;77(14):4662-6. doi: 10.1021/ac050132g. PMID: 16013886.
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Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements.

The journal of physical chemistry. B

Alberty RA.
PMID: 19159341
J Phys Chem B. 2009 Jan 29;113(4):1225-31. doi: 10.1021/jp8080436.

Rapid-equilibrium rate equations are derived for the five different mechanisms for the enzymatic catalysis of A + B + C --> products using a computer. These rate equations are used to determine the minimum number of velocities required to...

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Alberty RA. Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements. J Phys Chem B. 2009;113(4):1225-31doi: 10.1021/jp8080436.
Alberty, R. A. (2009). Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements. The journal of physical chemistry. B, 113(4), 1225-31. https://doi.org/10.1021/jp8080436
Alberty, Robert A. "Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements." The journal of physical chemistry. B vol. 113,4 (2009): 1225-31. doi: https://doi.org/10.1021/jp8080436
Alberty RA. Determination of kinetic parameters of enzyme-catalyzed reaction a + B + C --> products with the minimum number of velocity measurements. J Phys Chem B. 2009 Jan 29;113(4):1225-31. doi: 10.1021/jp8080436. PMID: 19159341; PMCID: PMC2654092.
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Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction.

Computational biology and chemistry

Srividhya J, Mourão MA, Crampin EJ, Schnell S.
PMID: 19945917
Comput Biol Chem. 2010 Feb;34(1):11-8. doi: 10.1016/j.compbiolchem.2009.10.007. Epub 2009 Oct 31.

The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of...

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Srividhya J, Mourão MA, Crampin EJ, et al. Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction. Comput Biol Chem. 2009;34(1):11-8doi: 10.1016/j.compbiolchem.2009.10.007.
Srividhya, J., Mourão, M. A., Crampin, E. J., & Schnell, S. (2010). Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction. Computational biology and chemistry, 34(1), 11-8. https://doi.org/10.1016/j.compbiolchem.2009.10.007
Srividhya, Jeyaraman, et al. "Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction." Computational biology and chemistry vol. 34,1 (2010): 11-8. doi: https://doi.org/10.1016/j.compbiolchem.2009.10.007
Srividhya J, Mourão MA, Crampin EJ, Schnell S. Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction. Comput Biol Chem. 2010 Feb;34(1):11-8. doi: 10.1016/j.compbiolchem.2009.10.007. Epub 2009 Oct 31. PMID: 19945917.
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[Determination of various enzyme activities of human pancreatic tissue].

Arzneimittel-Forschung

DIOGUARDI N, SECCHI GC, AGOSTONI A.
PMID: 13816887
Arzneimittelforschung. 1960 Jun;10:448-50.

No abstract available.

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DIOGUARDI N, SECCHI GC, AGOSTONI A. [Determination of various enzyme activities of human pancreatic tissue]. Arzneimittelforschung. 1960;10:448-50
DIOGUARDI, N., SECCHI, G. C., & AGOSTONI, A. (1960). [Determination of various enzyme activities of human pancreatic tissue]. Arzneimittel-Forschung, 10448-50.
DIOGUARDI, N, et al. "[Determination of various enzyme activities of human pancreatic tissue]." Arzneimittel-Forschung vol. 10 (1960): 448-50.
DIOGUARDI N, SECCHI GC, AGOSTONI A. [Determination of various enzyme activities of human pancreatic tissue]. Arzneimittelforschung. 1960 Jun;10:448-50. German. PMID: 13816887.
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Kinetic modeling as a tool to integrate multilevel dynamic experimental data.

Methods in molecular biology (Clifton, N.J.)

Mogilevskaya E, Bagrova N, Plyusnina T, Gizzatkulov N, Metelkin E, Goryacheva E, Smirnov S, Kosinsky Y, Dorodnov A, Peskov K, Karelina T, Goryanin I, Demin O.
PMID: 19597787
Methods Mol Biol. 2009;563:197-218. doi: 10.1007/978-1-60761-175-2_11.

The metabolic networks are the most well-studied biochemical systems, with an abundance of in vitro and in vivo data available for quantitative estimation of its kinetic parameters. In this chapter, we present our approach to developing mathematical description of...

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Mogilevskaya E, Bagrova N, Plyusnina T, et al. Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods Mol Biol. 2009;563:197-218doi: 10.1007/978-1-60761-175-2_11.
Mogilevskaya, E., Bagrova, N., Plyusnina, T., Gizzatkulov, N., Metelkin, E., Goryacheva, E., Smirnov, S., Kosinsky, Y., Dorodnov, A., Peskov, K., Karelina, T., Goryanin, I., & Demin, O. (2009). Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods in molecular biology (Clifton, N.J.), 563197-218. https://doi.org/10.1007/978-1-60761-175-2_11
Mogilevskaya, Ekaterina, et al. "Kinetic modeling as a tool to integrate multilevel dynamic experimental data." Methods in molecular biology (Clifton, N.J.) vol. 563 (2009): 197-218. doi: https://doi.org/10.1007/978-1-60761-175-2_11
Mogilevskaya E, Bagrova N, Plyusnina T, Gizzatkulov N, Metelkin E, Goryacheva E, Smirnov S, Kosinsky Y, Dorodnov A, Peskov K, Karelina T, Goryanin I, Demin O. Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods Mol Biol. 2009;563:197-218. doi: 10.1007/978-1-60761-175-2_11. PMID: 19597787.
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Metabolic control and its analysis. Extensions to the theory and matrix method.

European journal of biochemistry

Sauro HM, Small JR, Fell DA.
PMID: 3569295
Eur J Biochem. 1987 May 15;165(1):215-21. doi: 10.1111/j.1432-1033.1987.tb11214.x.
Free Article

The matrix algebra procedure for determining the flux control coefficients of enzymes in metabolic pathways has been extended to allow determination of the concentration control coefficients. Although it is shown that the procedure is essentially unchanged in most cases,...

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Sauro HM, Small JR, Fell DA. Metabolic control and its analysis. Extensions to the theory and matrix method. Eur J Biochem. 1987;165(1):215-21doi: 10.1111/j.1432-1033.1987.tb11214.x.
Sauro, H. M., Small, J. R., & Fell, D. A. (1987). Metabolic control and its analysis. Extensions to the theory and matrix method. European journal of biochemistry, 165(1), 215-21. https://doi.org/10.1111/j.1432-1033.1987.tb11214.x
Sauro, H M, et al. "Metabolic control and its analysis. Extensions to the theory and matrix method." European journal of biochemistry vol. 165,1 (1987): 215-21. doi: https://doi.org/10.1111/j.1432-1033.1987.tb11214.x
Sauro HM, Small JR, Fell DA. Metabolic control and its analysis. Extensions to the theory and matrix method. Eur J Biochem. 1987 May 15;165(1):215-21. doi: 10.1111/j.1432-1033.1987.tb11214.x. PMID: 3569295.
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Switching mechanism of a cyclic enzyme system: role as a "chemical diode".

Bio Systems

Okamoto M, Sakai T, Hayashi K.
PMID: 3689885
Biosystems. 1987;21(1):1-11. doi: 10.1016/0303-2647(87)90002-5.

We previously showed with computer simulations that cyclic enzyme systems play a role in metabolic switching events. In the present study, the detailed switching mechanism was investigated by clarifying the relationship between the switching mode and the phase-difference of...

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Okamoto M, Sakai T, Hayashi K. Switching mechanism of a cyclic enzyme system: role as a "chemical diode". Biosystems. 1987;21(1):1-11doi: 10.1016/0303-2647(87)90002-5.
Okamoto, M., Sakai, T., & Hayashi, K. (1987). Switching mechanism of a cyclic enzyme system: role as a "chemical diode". Bio Systems, 21(1), 1-11. https://doi.org/10.1016/0303-2647(87)90002-5
Okamoto, M, et al. "Switching mechanism of a cyclic enzyme system: role as a "chemical diode"." Bio Systems vol. 21,1 (1987): 1-11. doi: https://doi.org/10.1016/0303-2647(87)90002-5
Okamoto M, Sakai T, Hayashi K. Switching mechanism of a cyclic enzyme system: role as a "chemical diode". Biosystems. 1987;21(1):1-11. doi: 10.1016/0303-2647(87)90002-5. PMID: 3689885.
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Showing 1 to 12 of 75 entries