Name: hot biological catalysis: isothermal titration calorimetry to characterize enzymatic reactions
Uploaded: 2014-04-04T13:45:00
Description: Watch this Scientific Journal Video about Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions at JoVE.com

The Specialty Fertilizer Products Company (SFP) is acknowledged for providing the funds necessary for this study.

1. Preparing Samples
<ol>
	<li>Prepare 2 ml of enzyme solution and 0.5 ml of substrate solution for each experimental run. Dilute concentrated stock solutions of enzyme and substrate in buffer solutions having identical composition to minimize the heat of dilution and mixing during the substrate addition.
	<ol>
		<li>Choose the buffer conditions that are adequate to prevent pH change during experiment. For example, 20 mM HEPES pH 7 is adequate for measurements at neutral pH. 
		NOTE: If proton exchange is...

<ol>
	<li>Leavitt, S., Freire, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+measurement+of+protein+binding+energetics+by+isothermal+titration+calorimetry.">Direct measurement of protein binding energetics by isothermal titration calorimetry.</a> Curr. Opin. Struct. Biol. 11, 560-566 (2001).</li><li>Ladbury, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+isothermal+titration+calorimetry+in+the+biological+sciences:+things+are+heating+up!+BioTechniques.">Application of isothermal titration calorimetry in the biological sciences: things are heating up! BioTechniques.</a> 37, 885-887 (2004).</li><li>Zambelli, B., Bellucci, M., Danielli, A., Scarlato, V., Ciurli, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Ni2++binding+properties+of+Helicobacter+pylori+NikR.">The Ni2+ binding properties of Helicobacter pylori NikR.</a> Chem. Commun. , 3649-3651 (2007).</li><li>Zambelli, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-affinity+Ni2++binding+selectively+promotes+binding+of+Helicobacter+pylori+NikR+to+its+target+urease+promoter.">High-affinity Ni2+ binding selectively promotes binding of Helicobacter pylori NikR to its target urease promoter.</a> J. Mol. Biol. 383, 1129-1143 (2008).</li><li>Duff, M. R., Grubbs, J., Howell, E. 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J., Gomez, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzyme+kinetics+determined+using+calorimetry:+a+general+assay+for+enzyme+activity.">Enzyme kinetics determined using calorimetry: a general assay for enzyme activity.</a> Anal. Biochem. 296, 179-187 (2001).</li><li>Bianconi, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calorimetry+of+enzyme-catalyzed+reactions.">Calorimetry of enzyme-catalyzed reactions.</a> Biophys. Chem. 126, 59-64 (2007).</li><li>Demarse, N. A., Killian, M. C., Hansen, L. D., Quinn, C. 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O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Nickel and its surprising impact in nature. 2, 241-278 (2007).</li><li>Zambelli, B., Musiani, F., Benini, S., Ciurli, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemistry+of+Ni2++in+urease:+sensing,+trafficking,+and+catalysis.">Chemistry of Ni2+ in urease: sensing, trafficking, and catalysis.</a> Acc. Chem. Res. 44, 520-530 (2011).</li><li>Zonia, L. E., Stebbins, N. E., Polacco, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Essential+role+of+urease+in+germination+of+nitrogen-limited+Arabidopsis+thaliana+seeds.">Essential role of urease in germination of nitrogen-limited Arabidopsis thaliana seeds.</a> Plant Physiol. 107, 1097-1103 (1995).</li><li>Follmer, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insights+into+the+role+and+structure+of+plant+ureases.">Insights into the role and structure of plant ureases.</a> Phytochemistry. 69, 18-28 (2008).</li><li>Sumner, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+isolation+and+crystallization+of+the+enzyme+urease.">The isolation and crystallization of the enzyme urease.</a> J. Biol. Chem. 69, 435-441 (1926).</li><li>Krajewska, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ureases+I.+Functional,+catalytic+and+kinetic+properties:+A+review.">Ureases I. Functional, catalytic and kinetic properties: A review.</a> J. Mol. Cat. B. 59, 9-21 (2009).</li><li>Callahan, B. P., Yuan, Y., Wolfenden, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+burden+borne+by+urease.">The burden borne by urease.</a> J. Am. Chem. Soc. 127, 10828-10829 (2005).</li><li>Krajewska, B., van Eldik, R., Brindell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temperature-+and+pressure-dependent+stopped-flow+kinetic+studies+of+jack+bean+urease.+Implications+for+the+catalytic+mechanism.">Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism.</a> J. Biol. Inorg. Chem. 17, 1123-1134 (2012).</li><li>Hausinger, R. P., Karplus, P. A., Huber, R., Poulos, T., Wieghardt, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Handbook of Metalloproteins. , 867-879 (2001).</li><li>Goldberg, R., Kishore, N., Lennen, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamic+quantities+for+the+ionization+reactions+of+buffers.">Thermodynamic quantities for the ionization reactions of buffers.</a> J. Phys. Chem. Ref. Data. 31, 231-370 (2002).</li><li>Baumann, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advantages+of+isothermal+titration+calorimetry+for+xylanase+kinetics+in+comparison+to+chemical-reducing-end+assays.">Advantages of isothermal titration calorimetry for xylanase kinetics in comparison to chemical-reducing-end assays.</a> Anal. Biochem. 410, 19-26 (2011).</li><li>Noske, R., Cornelius, F., Clarke, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigation+of+the+enzymatic+activity+of+the+Na+,K+-ATPase+via+isothermal+titration+microcalorimetry.">Investigation of the enzymatic activity of the Na+,K+-ATPase via isothermal titration microcalorimetry.</a> Biochim. Biophys. Acta. 1797, 1540-1545 (2010).</li><li>Harmon, K. M., Niemann, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+competitive+inhibition+of+the+urease-catalyzed+hydrolysis+of+urea+by+phosphate.">The competitive inhibition of the urease-catalyzed hydrolysis of urea by phosphate.</a> J. Biol. Chem. 177, 601-605 (1949).</li><li>Benini, S., Rypniewski, W. R., Wilson, K. S., Ciurli, S., Mangani, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure-based+rationalization+of+urease+inhibition+by+phosphate:+novel+insights+into+the+enzyme+mechanism.">Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism.</a> J. Biol. Inorg. Chem. 6, 778-790 (2001).</li><li>Segel, I. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Enzyme kinetics: behavior and analysis of rapid equilibrium and steady-state enzyme systems. , (1993).</li></ol>

Significance of ITC to study enzymatic activity with respect to existing methods
In addition to its classical applications to study binding equilibria, isothermal titration calorimetry provides a reliable and fast method to characterize enzymatic reactions in solution using the heat of reaction as a probe, without requiring system modification or labeling. The kinetic parameters kcat and KM are usually obtained through a set of time cour...

Quantitative determination of biochemical reactions provides insights into the biological processes at the basis of life. Calorimetry offers a label-free methodology to quantitatively characterize virtually every chemical reaction in solution. This technique measures the heat released or absorbed over time, and is therefore a universal detection system and a very convenient methodology to quantify the amount of reacting molecules (i.e. binding thermodynamics), as well as to measure the reaction rate (i.e. kinetics). In particular, isothermal titration calorimetry (ITC) has been adopted as method of choice to characterize the thermodynamics of biomolecular equilibria, involving protein-ligand, protein-protein, protein-metal ions and protein-DNA interactions1-6. In addition, the ability of ITC to provide kinetic information makes it a very powerful system to measure enzyme catalysis, although the potential of this application is still underestimated7-9.
The Michaelis-Menten equation10 is a quantitative description of enzymatic reactions, as it provides a relationship between the reaction rate and the substrate concentration, depending on two kinetic parameters: the Michaelis constant (KM) and the catalytic rate constant (kcat). The kcat/KM ratio is referred as the catalytic efficiency of an enzyme. In practice, determination of KM and kcat for a specific reaction provides a complete description of the catalysis.
In a typical enzymatic reaction (Figure 1), a substrate (S) interacts with the enzyme (E) forming the enzyme-substrate (ES) complex, which is subsequently activated into the transition state (ES*). The latter is converted into the enzyme-product (EP) complex that eventually dissociates. These steps are described by the following reaction.
<img fo:content-width="2in" src="/files/ftp_upload/51487/51487eq1.jpg" width="197" /> (1)
where k1 is the rate constant for the formation of the ES complex, k-1 is the rate constant for the dissociation of the ES complex, while kcat is the catalytic rate constant or turnover number.
According to the Michaelis-Menten equation10, the rate of the reaction can be calculated as:
<img fo:content-width="1.5in" src="/files/ftp_upload/51487/51487eq2.jpg" width="144" /> (2)
in which KM = (k-1 + kcat)/k1 and kcat = vmax/[E], with vmax being the maximal velocity reached when all enzyme is bound to the substrate.
The isothermal titration calorimeter is the instrument used in this study to characterize the enzymatic hydrolysis of urea. This instrument is made of an adiabatic shield containing two coined-shaped cells (Figure 1). These are connected to the outside with narrow access tubes. The sample cell (ca. 1.4 ml) is loaded with the enzyme solution, while the reference cell is generally filled with water or with the solvent used for the analysis. A rotating syringe with a long needle and a stir paddle attached, usually containing ca. 0.3 ml of substrate solution, is mounted on the sample cell. A thermoelectric device measures the difference of temperature between the sample and the reference cell and, using a &#8220;cell feedback network&#8221;, it maintains this difference at zero by adding or subtracting heat. During the experiment, the substrate is injected into the enzyme solution at a constant chosen temperature. When the enzymatic reaction takes place, the amount of heat released or absorbed is proportional to the number of substrate molecules that are converted into product molecules. In addition, the rate of heat flow is directly related to the rate of the reaction. The measured data, appearing as a deviation of the heat trace from initial baseline (Figure 1), represent the thermal power (&#956;cal/sec) supplied by the instrument to the sample cell, which is proportional to the heat flow occurring in the sample cell over time.
<img alt="Figure 1" fo:content-width="5in" src="/files/ftp_upload/51487/51487fig1highres.jpg" width="500" /> 
Figure 1. Schematic representation of isothermal titration calorimeter to study enzymatic reactions. An enzymatic reaction occurring upon titration of the substrate (in the injection syringe) into the enzyme solution (in the sample cell) results in a change of the thermal power released by the calorimeter, needed to keep the difference of temperature between the sample cell and the reference cell constant. <a href="https://www.jove.com/files/ftp_upload/51487/51487fig1highres.jpg" target="_blank">Click here to view larger image.</a>
Overall, the heat change (Q) is proportional to the molar enthalpy of the reaction (&#916;H) and the number of moles of product generated (n), which in turn is given by the total volume times the concentration:
<img fo:content-width="2in" src="/files/ftp_upload/51487/51487eq3.jpg" width="200" /> (3)
The product formation over time (dP/dt), which corresponds to the reaction rate, can thus be related to the amount of heat generated over the same time (dQ/dt) through the relation:
<img fo:content-width="2in" src="/files/ftp_upload/51487/51487eq4.jpg" width="150" /> (4)
According to this equation, in order to obtain a Michaelis-Menten plot it is necessary to measure i) the total molar enthalpy &#916;H, and ii) the heat flow dQ/dt at different substrate concentrations. Usually, this is performed in two different experiments: in the first experiment (Method 1, M1), the substrate is injected into the enzyme solution and the heat for complete substrate conversion is measured; in the second experiment (Method 2, M2), multiple injections of substrate are performed and the rate of heat production is measured at different substrate concentrations. These two sets of data are sufficient to derive the kinetic parameters KM and kcat.
In the present article, a general protocol to determine the kinetic parameters for enzymatic reactions performed using ITC is described. We applied the method to urea hydrolysis by Canavalia ensiformis urease, as a reference system. The good agreement between the results obtained using this method and the data reported in literature demonstrates the reliability of this approach.

<table border="0" cellpadding="0" cellspacing="0" width="796">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;">HEPES</td>
			<td style="width:111px;">Sigma</td>
			<td style="width:119px;">H3375</td>
			<td style="width:323px;">dissolving in water and adjusting pH with NaOH</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;">TRIZMA-Base</td>
			<td style="width:111px;">Sigma</td>
			<td style="width:119px;">T1503</td>
			<td>dissolving in water and adjusting pH with HCl</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;">Sodium dihydrogen phosphate</td>
			<td style="width:111px;">Riedel-de-Haen</td>
			<td style="width:119px;">4270</td>
			<td>dissolving in water</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;">Sodium phosphate dibasic</td>
			<td style="width:111px;">Riedel-de-Haen</td>
			<td style="width:119px;">30427</td>
			<td>dissolving in water</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;">Urea</td>
			<td style="width:111px;">Sigma</td>
			<td style="width:119px;">U4128</td>
			<td>dissolving in water at 40 &#176;C</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:245px;">Canavalia ensiformis urease (type C-3)</td>
			<td style="width:111px;">Sigma</td>
			<td style="width:119px;">U0251</td>
			<td>dissolving in 20 mM HEPES pH 7 and stored at -80 &#176;C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:245px;"></td>
			<td style="width:111px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:245px;">VP-ITC on Origin 7.0</td>
			<td style="width:111px;">MicroCal (GE Healthcare)</td>
			<td style="width:119px;">SYS13901</td>
			<td>instrument&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:245px;">VPViewer2000 1.30.00 on Origin 7.0</td>
			<td style="width:111px;">MicroCal (GE Healthcare)</td>
			<td style="width:119px;"></td>
			<td>data acquisition software supplied with the instrument</td>
		</tr>
	</tbody>
</table>

hot biological catalysis: isothermal titration calorimetry to characterize enzymatic reactions

Isothermal titration calorimetry (ITC) is a well-described technique that measures the heat released or absorbed during a chemical reaction, using it as an intrinsic probe to characterize virtually every chemical process. Nowadays, this technique is extensively applied to determine thermodynamic parameters of biomolecular binding equilibria. In addition, ITC has been demonstrated to be able of directly measuring kinetics and thermodynamic parameters (kcat, KM, &#916;H) of enzymatic reactions, even though this application is still underexploited. As heat changes spontaneously occur during enzymatic catalysis, ITC does not require any modification or labeling of the system under analysis and can be performed in solution. Moreover, the method needs little amount of material. These properties make ITC an invaluable, powerful and unique tool to study enzyme kinetics in several applications, such as, for example, drug discovery.
In this work an experimental ITC-based method to quantify kinetics and thermodynamics of enzymatic reactions is thoroughly described. This method is applied to determine kcat and KM of the enzymatic hydrolysis of urea by Canavalia ensiformis (jack bean) urease. Calculation of intrinsic molar enthalpy (&#916;Hint) of the reaction is performed. The values thus obtained are consistent with previous data reported in literature, demonstrating the reliability of the methodology.

Urease (EC 3.5.1.5; urea amidohydrolase) is a multisubunit nickel-containing enzyme found in archea, bacteria, unicellular eukaryotes and plants. This protein acts in the last step of organic nitrogen mineralization, catalyzing the hydrolysis of urea to ammonia and carbamate, which spontaneously decomposes to give a second molecule of ammonia and bicarbonate (Equation 6)12.
<img fo:content-width="4in" src="/files/ftp_upload/51487/51487eq6.jpg" width="450" /> (6)...

Watch this Scientific Journal Video about Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions at JoVE.com

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions

Isothermal titration calorimetry measures heat flow released or absorbed in chemical reactions. This method can be used to quantify enzyme-catalysis. In this paper, the protocol for instrumental setup, experiment running, and data analysis is generally described, and applied to the characterization of enzymatic urea hydrolysis by jack bean urease.

Isothermal titration calorimetry (ITC) is a well-described technique that measures the heat released or absorbed during a chemical reaction, using it as ...

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