如何预测蛋白质泛素化位点

如何预测蛋白质泛素化位点

How to predict ubiquitination sites on proteins

       泛素化是指泛素（一类低分子量的蛋白质）分子在一系列特殊的酶作用下对靶蛋白进行特异性修饰的过程。该过程具体如下：在ATP水解供能的情况下，酶E1粘附在泛素分子尾部的半胱氨酸（Cys）残基上激活泛素，接着活化酶E1将激活的泛素分子转移到结合酶E2上，随后，E2和连接酶E3共同识别靶蛋白并对其进行泛素化修饰。泛素化通过调控蛋白质降解、活性、相互作用以及亚细胞定位来影响众多生理过程。在研究蛋白质泛素化之前，如果能先预测蛋白质泛素化位点，后面的研究将事半功倍。本文将讲解如何预测蛋白质泛素化位点。

Ubiquitination refers to the specific modification of target proteins by ubiquitin (a type of low molecular weight protein) molecules under a series of special enzyme actions. The specific process is as follows: activating enzyme E1 adheres to the cysteine (Cys) residue at the tail of the ubiquitin molecule to activate ubiquitin using energy from ATP hydrolysis. Then E1 transfers the activated ubiquitin molecule to conjugating enzyme E2. Subsequently, E2 and ligase E3 jointly recognize the target protein and modify it with ubiquitination. Ubiquitination affects numerous physiological processes by regulating protein degradation, activity, interactions, and subcellular localization. If protein ubiquitination sites could be predicted, subsequent research would be twice as efficient. This article shows how to predict ubiquitination sites on proteins.

利用GPS (Group-based Prediction System)-Uber (Ubiquitn-protein ligase Enzymes-substrate relationship prediction) 预测蛋白质泛素化位点步骤如下：

The steps for predicting ubiquitination sites on proteins by GPS (Group-based Prediction System)-Uber (Ubiquitn-protein ligase Enzymes-substrate relationship prediction) are as follows:

1 从https://gpsuber.biocuckoo.cn/index.php网址进入GPS-Uber

1 Enter GPS-Uber from https://gpsuber.biocuckoo.cn/index.php

2     点击“WEB SERVER”

2 Click “WEB SERVER”

3 以FASTA格式输入蛋白质（人DICER1）序列

3 Enter protein sequence (Human DICER1) in FASTA format

4 选择预测类型（一般预测或E3特异性预测）以及阈值，提交

4 Select the prediction type (general prediction or E3-specific prediction) and threshold, submit

5 查看结果

5 View results

此外，还可以用UbiBrowser 3.0预测介导靶蛋白质泛素化的连接酶E3或者连接酶E3的底物，步骤如下：

Besides, ligase E3 mediating ubiquitination of targeted proteins or substrate of ligase E3 could be predicted by UbiBrowser 3.0, and steps are as follows:

1 从http://ubibrowser.bio-it.cn/ubibrowser_v30/网址进入UbiBrowser 3.0

1 Enter UbiBrowser 3.0 from http://ubibrowser.bio-it.cn/ubibrowser_v30/

2输入蛋白质名称（DICER1），数据库ID或FASTA格式的蛋白质序列

2 Input the protein name (DICER1), database ID or protein sequence in FASTA format

3 选择过程（泛素化）

3 Select the process （Ubquitination）

4 选择蛋白质类型“底物”

4 Select the query protein as “Substrate”

5 选择物种（人）

5 Select species (H.sapiens)

5 点击“Protein-Centric Interaction Browse”

5 Click “Protein-Centric Interaction Browse”

6 继续

6 Continue

7 查看结果

7 View results

8 输入蛋白质名称（CBL），数据库ID或FASTA格式的蛋白质序列

8 Input the protein name (CBL), database ID or protein sequence in FASTA format

9 选择过程（泛素化）

9 Select the process （Ubquitination）

10 选择蛋白质类型“连接酶E3”

10 Select the query protein as “Ubiquitin ligase (E30”

11 选择物种（人）

12 Select species (H.sapiens)

13 点击“Protein-Centric Interaction Browse”

13 Click “Protein-Centric Interaction Browse”

14 继续

14 Continue

15 查看结果

15 View results

另外，还可以利用BioGRID查询已知的蛋白质泛素化位点，步骤如下：

Additionally, BioGRID also could be used to query known ubiquitination sites on proteins, and steps are as follows:

1从https://thebiogrid.org/网址进入BioGRID

1 Enter BioGRID from https://thebiogrid.org/

2输入蛋白质名称（DICER1），选择物种（人类），搜索

2 Input the protein name (DICER1)，select an organism (Homo sapiens), search

3点击“PTM sites”查看结果

3 Click “PTM sites” to view results

也可以利用UniProt查询已知的蛋白质泛素化位点，步骤如下：

UniProt could be used to query known ubiquitination sites on proteins as well, and steps are as follows:

1从https://www.uniprot.org/网址进入UniProt

1 Enter UniProt from https://www.uniprot.org/

2选择“UniProtKB”，输入蛋白质名称（DICER1），搜索

2 Select “UniProtKB”, input the protein name (DICER1)，search

3选择“DICER_HUMAN”，点击

3 Select “DICER_HUMAN”, click

4点击“PTM/Processing”，查看结果

4 Click “PTM/Processing”, view results