Name: the determination of protease specificity in mouse tissue extracts by maldi-tof mass spectrometry: manipulating ph to cause specificity changes
Uploaded: 2018-05-25T13:30:00
Description: Watch this Scientific Journal Video about The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes at JoVE.com

This work was supported in part by the Nihon Pharmaceutical University Research Grant from Nihon Pharmaceutical University (2016) and the MEXT KAKENHI Grant Number JP17854179.

Animal experimental protocols were approved by the Nihon Pharmaceutical University&#39;s ethics committee and performed in accordance with the guidelines for the Care and Use of Laboratory Animals of the Nihon Pharmaceutical University. The protocol has been adjusted for tissue extracts derived from ICR&#160;mice. ICR mice were purchased from Nippon SLC Ltd. (Shizuoka, Japan)
1. Preparation of the Iminobiotin-labeled Substrate
The substrate undergoes solid-phase synth...

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This protocol uses MALDI-TOF mass spectrometry to identify protease specificity in crude samples derived from tissue extracts and may easily be scaled up for multiple sample processing. In particular, we manipulated pH to cause a change in substrate specificity.
The avidin-biotin complex (ABC) method, which has been widely used in biochemistry due to its binding specificity, was utilized in our protocol. Due to the strong affinity of ABC, the binding of avidin to biotin is almost irreversible....

Proteases regulate physiological processes by cleaving proteins, and the initiation of protease activity at specific times and locations is regulated1. It is therefore important to identify the expression and activity of tissues that are locally regulated, and to develop a novel method to detect proteases. The method proposed in this study aims to identify protease specificity in parallel to detecting proteases.
There are some methods for detecting protease specificity. The azocasein method is well-known for its use in the detection of proteases2 but is limited in its ability to obtain further information. Zymography is another comprehensive protease detection method that can be used to determine the molecular weight of proteases3, but it cannot be used to examine substrate specificity. Protease specificity can be determined by spectrometric assays, using substrates such as p-nitroanilide4, and fluorometric assays, using coumarin substrates5 or Fluorescence Resonance Energy Transfer (FRET) assays6. These methods enable single-specificity detection of substrates contained in a single well. In the present study, the protease specificity of tissue extracts is examined under various conditions, as these extracts contain multiple proteases. Protease activity is regulated by several factors, including pH, coenzymes, prosthetic groups, and ion strength. Recently, proteomics-based methods have been used to identify protease specificity; for example, the method reported by Biniossek et al.7 uses the proteome to determine substrate specificity even in crude extracts and allows accurate determination of the cleavage activity of proteases that recognize multiple amino acid sequences8. However, this method is not suitable for the analysis of numerous samples. In contrast, our method enables the simultaneous processing of multiple samples, and the use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry for sample analysis facilitates rapid and easy detection of the cleaved substrates.
This paper outlines a method to evaluate protease specificity by using MALDI-TOF mass spectrometry to measure the molecular weight of unique substrates. The molecular forms of cleaved substrates, along with their theoretical molecular weights, are shown in Figure 1 and Table 1. Previous studies have used substrates containing polyglycine spacers and biotin9; however, these substrates are flawed because the polyglycine sequence may be cleaved by enzymes that recognize the glycine sequence. Additionally, the high affinity between avidin and biotin may lead to a low recovery rate. To improve upon these drawbacks, in this study we synthesized a unique substrate, which was composed of polyethylene glycol (PEG), iminobiotin, and an amino acid that could identify the cleavage site (Figure 1). To discriminate between amino acids of similar molecular weights, D-serine was added between the PEG spacer and the amino acid at the cleaved site.
The N-terminal of the substrate was labeled with iminobiotin, which enables affinity purification from crude samples. The use of iminobiotin instead of biotin is critical; biotin has a strong affinity with avidin, which results in low recovery rates of biotin-labeled substrates from avidin resin, while iminobiotin&#39;s affinity for avidin can be altered by pH. Iminobiotin-labeled substrates will bind to avidin in conditions above pH 9, while avidin releases iminobiotin-labeled substrates in conditions below pH 4. Therefore, iminobiotin was used for affinity purification10. In summary, we describe a detailed protocol for detecting protease specificity using unique substrates.

<table>
	<tbody>
		<tr>
			<td>Fmoc-NH-SAL Resin(-[2,4-Dimethoxyphenyl-N-(9-fluorenylmethoxycarbonyl)aminomethyl]phenoxy resin)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00102</td>
			<td></td>
		</tr>
		<tr>
			<td>N,N-dimethylformamide (DMF)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00185</td>
			<td></td>
		</tr>
		<tr>
			<td>piperidine</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00176</td>
			<td></td>
		</tr>
		<tr>
			<td>trinitrobenzenesulfonic acid (TNBS)</td>
			<td>WAKO Chemical</td>
			<td>209-1483</td>
			<td></td>
		</tr>
		<tr>
			<td>O-(6-Chloro-1H-benzotriazol-1-yl)-N,N,N&#39;,N&#39;-tetramethyluronium hexafluorophosphate (HCTU)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00067</td>
			<td></td>
		</tr>
		<tr>
			<td>1-Hydroxy-1H-benzotriazole,monohydrate (HOBt)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00014</td>
			<td></td>
		</tr>
		<tr>
			<td>diisopropylethylamine (DIPEA)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00030</td>
			<td></td>
		</tr>
		<tr>
			<td>triisopropylsilane (TIS)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00170</td>
			<td></td>
		</tr>
		<tr>
			<td>ethanedithiol (EDT)</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td>A00057</td>
			<td></td>
		</tr>
		<tr>
			<td>trifluoroacetic acid (TFA)</td>
			<td>Millipore</td>
			<td>S6612278 403</td>
			<td></td>
		</tr>
		<tr>
			<td>acetonitrile</td>
			<td>Kokusan Chemical</td>
			<td>2153025</td>
			<td></td>
		</tr>
		<tr>
			<td>C18 cartridge column</td>
			<td>Waters</td>
			<td>WAT051910</td>
			<td></td>
		</tr>
		<tr>
			<td>poly(oxyethylene) octylphenyl ether</td>
			<td>WAKO Chemical</td>
			<td>168-11805</td>
			<td>Triton X-100</td>
		</tr>
		<tr>
			<td>mixing homogenizer</td>
			<td>Kinematica</td>
			<td>PT3100</td>
			<td>polytron homogenizer</td>
		</tr>
		<tr>
			<td>Coomassie Brilliant Blue (CBB) -G250</td>
			<td>Nakarai Chemical</td>
			<td>094-09</td>
			<td></td>
		</tr>
		<tr>
			<td>glycerol</td>
			<td>Nakarai Chemical</td>
			<td>170-18</td>
			<td></td>
		</tr>
		<tr>
			<td>N-tosyl-L-phenylalanine chloromethyl ketone (TPCK)-trypsin</td>
			<td>Sigma-Aldrich</td>
			<td>T1426</td>
			<td></td>
		</tr>
		<tr>
			<td>dimethyl sulfoxide (DMSO)</td>
			<td>WAKO Chemical</td>
			<td>043-07216</td>
			<td></td>
		</tr>
		<tr>
			<td>streptavidin sepharose</td>
			<td>GE Healthcare</td>
			<td>17-511-01</td>
			<td></td>
		</tr>
		<tr>
			<td>ZipTipC18</td>
			<td>Millipore</td>
			<td>ZTC18S096</td>
			<td></td>
		</tr>
		<tr>
			<td>&#945;-cyano-4-hydroxycinnamic acid (CHCA)</td>
			<td>Sigma-Aldrich</td>
			<td>C2020</td>
			<td></td>
		</tr>
		<tr>
			<td>MALDI-TOF mass spectrometry</td>
			<td>Bruker Daltonics, Germany</td>
			<td>autoflex</td>
			<td></td>
		</tr>
		<tr>
			<td>2-iminobiotin</td>
			<td>Sigma-Aldrich</td>
			<td>I4632</td>
			<td></td>
		</tr>
		<tr>
			<td>Fmoc-amino acids</td>
			<td>Watanabe Chemical Co., Ltd.</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

the determination of protease specificity in mouse tissue extracts by maldi-tof mass spectrometry: manipulating ph to cause specificity changes

Proteases have several biological functions, including protein activation/inactivation and food digestion. Identifying protease specificity is important for revealing protease function. The method proposed in this study determines protease specificity by measuring the molecular weight of unique substrates using Matrix-assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry. The substrates contain iminobiotin, while the cleaved site consists of amino acids, and the spacer consists of polyethylene glycol. The cleaved substrate will generate a unique molecular weight using a cleaved amino acid. One of the merits of this method is that it may be carried out in one pot using crude samples, and it is also suitable for assessing multiple samples. In this article, we describe a simple experimental method optimized with samples extracted from mouse lung tissue, including tissue extraction, placement of digestive substrates into samples, purification of digestive substrates under different pH conditions, and measurement of the substrates&#39; molecular weight using MALDI-TOF mass spectrometry. In summary, this technique allows for the identification of protease specificity in crude samples derived from tissue extracts using MALDI-TOF mass spectrometry, which may easily be scaled up for multiple sample processing.

Evaluation of the method for identification of protease specificity by model protease
The efficiency of this system was evaluated using TPCK-trypsin and V8 protease, whose substrate specificities were obtained. TPCK-trypsin and V8 protease were estimated to cleave the amino acid sequence at the C-terminal of the lysine and arginine residues, and at the carboxy side of the aspartic acid and glutamic acid residues, respectively. <str...

Watch this Scientific Journal Video about The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes at JoVE.com

The Determination of Protease Specificity in Mouse Tissue Extracts by MALDI-TOF Mass Spectrometry: Manipulating PH to Cause Specificity Changes

Here, we present a protocol to determine protease specificity in crude mouse tissue extracts using MALDI-TOF spectrometry.

Proteases have several biological functions, including protein activation/inactivation and food digestion. Identifying protease specificity is important ...

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