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ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.

Bevc S, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D - PLoS ONE (2011)

Bottom Line: We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions.ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme.ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Chemistry, Ljubljana, Slovenia.

ABSTRACT
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.

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Related in: MedlinePlus

Cholinesterase reaction with a substrate.The reaction scheme and the corresponding differential equations were created by ENZO. Substrate (butyrylthiocholine) bound to the peripheral anionic site is denoted by “S” on the left of the label name (e.g., SE, SES, SEA, SEAS). When bound to the catalytic anionic site, the “S” is placed on the right of the name (e.g., ES, SES, EAS SEAS). Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The acyl group is denoted by A.
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pone-0022265-g008: Cholinesterase reaction with a substrate.The reaction scheme and the corresponding differential equations were created by ENZO. Substrate (butyrylthiocholine) bound to the peripheral anionic site is denoted by “S” on the left of the label name (e.g., SE, SES, SEA, SEAS). When bound to the catalytic anionic site, the “S” is placed on the right of the name (e.g., ES, SES, EAS SEAS). Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The acyl group is denoted by A.

Mentions: The active site in cholinesterases is relatively large and a second substrate molecule can bind to the PAS with the affinity of k7/k6 = k9/k8 = k15/k14 at different times before the turnover of the first substrate is completed at the CAS [14]. In Figure 8, substrate bound to the PAS is denoted by “S” on the left of E e.g., SE. When bound to the CAS, the “S” is placed on the right, e.g., ES. Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The release of the acyl group (A) is unimportant, and is therefore omitted. In the case of butyrylcholinesterase (BChEs) a second substrate molecule, bound to PAS, enhances both the acylation as well as the deacylation steps, shown in Figure 8 as SES→SEA and SEA→SE, respectively. Thus k11>k5 and k10>k4. All this information can be easily drawn by ENZO as the comprehensive reaction scheme shown in Figure 8 [15] and subsequently the experimental data can be evaluated by fitting the parameters of the corresponding differential equations.


ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.

Bevc S, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D - PLoS ONE (2011)

Cholinesterase reaction with a substrate.The reaction scheme and the corresponding differential equations were created by ENZO. Substrate (butyrylthiocholine) bound to the peripheral anionic site is denoted by “S” on the left of the label name (e.g., SE, SES, SEA, SEAS). When bound to the catalytic anionic site, the “S” is placed on the right of the name (e.g., ES, SES, EAS SEAS). Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The acyl group is denoted by A.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139599&req=5

pone-0022265-g008: Cholinesterase reaction with a substrate.The reaction scheme and the corresponding differential equations were created by ENZO. Substrate (butyrylthiocholine) bound to the peripheral anionic site is denoted by “S” on the left of the label name (e.g., SE, SES, SEA, SEAS). When bound to the catalytic anionic site, the “S” is placed on the right of the name (e.g., ES, SES, EAS SEAS). Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The acyl group is denoted by A.
Mentions: The active site in cholinesterases is relatively large and a second substrate molecule can bind to the PAS with the affinity of k7/k6 = k9/k8 = k15/k14 at different times before the turnover of the first substrate is completed at the CAS [14]. In Figure 8, substrate bound to the PAS is denoted by “S” on the left of E e.g., SE. When bound to the CAS, the “S” is placed on the right, e.g., ES. Covalent acyl-enzyme is represented by EA and P is the first product (thiocholine) released upon enzyme acylation. The release of the acyl group (A) is unimportant, and is therefore omitted. In the case of butyrylcholinesterase (BChEs) a second substrate molecule, bound to PAS, enhances both the acylation as well as the deacylation steps, shown in Figure 8 as SES→SEA and SEA→SE, respectively. Thus k11>k5 and k10>k4. All this information can be easily drawn by ENZO as the comprehensive reaction scheme shown in Figure 8 [15] and subsequently the experimental data can be evaluated by fitting the parameters of the corresponding differential equations.

Bottom Line: We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions.ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme.ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Chemistry, Ljubljana, Slovenia.

ABSTRACT
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.

Show MeSH
Related in: MedlinePlus