1、一个离子通道蛋白,从N端到C端,查询哪个数据库可以知道从哪个氨基酸到哪个氨基酸是哪个Domain?***What do you mean by 'domain' here? How do you know it is an iron channel? I mean by experiment or by prediction? I guess it is the latter. Then it should match with some known structure (homologues). 那段跨膜?*** The transmembrane domain can be predicted by many Topology prediction software, like TMHMM2.0. 那段是胞内段/胞外段链接区?** Also by TMHMM or equivalent programs. But again this is only PREDICTION.
SMART等都是预测蛋白结构域。但如果是结构域、蛋白晶体已很明了的已知蛋白,到哪个数据库去查询呢? *** What do you mean? Known structures can be searched at cuturl('www.pdb.org.') Membrane protein structure can be searched at a database specific for membrane proteins. cuturl('www.mpdb.ul.ie')
2、像下面所附图,是否有现成数据库可以直接查询输出?
如果没有现成数据库,那么:用什么软件来画出?有没有专用的离子通道蛋白结构示意图作图软件?(PhotoShop等大众化画图软件慢慢折腾应该也能画出,但直觉告诉我们,国外作者应该不是用的它)
Search for topology map drawing. I can not remember the site now but I have seen one. You can generate a 'snake' like map but not something like you cited above. If you go to the paper and if it did not tell you what program was used, it is likely the map is generated by something like microsoft powpoint, i.e., not something complicated.
Sorry about the English... Only machine I can use at this moment...作者: 算盘阿星 时间: 2013-12-21 09:17
amberly, thank you for your reply. You have a good command of English.
Domain means 结构域 in Chinese, which is commponent of transmembrane channel structure as to ion channel protein.
The protein I am concerned with is one of sodium channel ones, surely belonging to ion channel family. And its function and crystal strunture are all well known, not needed to make prediction any more.
Topology of proteins can tell us their spatial structures, but can't supply the information on its transmembrane configuration with respect to channel forming.
Thanks for telling me websites cuturl('www.pdb.org') and cuturl('www.mpdb.ul.ie.') I used them to perform my searching. However, cuturl('www.pdb.org') gives only result of topology of protein, while cuturl('www.mpdb.ul.ie') gives no records.
The picture I pasted above was captured from the protein's whole illustration, i.e. it's only a part of it, much more complicated. Therefor, Powerpoint of MS Office and the like are not capable of performing the task.
More answers are expected to solute the problem. 作者: fqswdzd 时间: 2013-12-21 09:18
amberly, thank you for your reply. You have a good command of English.
Domain means 结构域 in Chinese, which is commponent of transmembrane channel structure as to ion channel protein.
The protein I ...
Thanks.. I have not figured out the problem with the new Ubuntu so I can still only type English. Sorry
Yes I know what 'domain' means but not sure what you meant here.
I get lost by reading the whole post now. It seems that you want to know a way to draw a cartoon representing a known structure?
I have not done that myself but I am sure the Powerpoint can do such a drawing cited above. It just shows the number of hilices, the disulf bond, the loops and the membrane (lipid bilayer).
If you want to generate a more acurate picture you may consider using pymol. It is free and you can make it in a way that simplify everything (side chain, for example), because the pdb id is available.
I guess you won't need the following information since it is a solved structure. But I still put them for your information
cuturl('http://blanco.biomol.uci.edu/mptopo/')
cuturl('http://blanco.biomol.uci.edu/mpex/')
cuturl('http://icb.med.cornell.edu/crt/RbDe/RbDe.html')
By the way what is the protein?
Have fun作者: remenb 时间: 2013-12-21 09:18
If you want to generate a more acurate picture you may consider using pymol. It is free and you can make it in a way that simplify everything (side chain, for example), because the pdb id is available.
By the way what is the protein?
相关疾病:
电击伤
(不好意思,我是做临床的,对生物医学的基础理论、database等的东西知道的很有限。可能问的问题有些很初级,让行家们见笑了)
谢谢amberly版主的回复。
1、我想要画的是一个已知蛋白:人类的电压门控钠离子通道蛋白SCN1A (Sodium channel protein type 1 subunit alpha),附图是国外综述文献上对这个通道蛋白的示意图,我就是想弄明白:这样的示意图他们到底是怎么create出来的?!
2、在UniProt上查这个蛋白编号,UniProtKB/Swiss-Prot P35498 (SCN1A_HUMAN),可是PDB数据库用SCN1A或者Sodium channel protein type 1 subunit alpha作为Keyword来搜,搜索出来的净是些毫不相关的东西啊?这个数据库要怎么搜啊?SCN1A这个蛋白的PDB ID在哪里找?
3、此外我们都注意到,国外文献关于信号转导、信号通路,常有非常复杂精美的示意图,我不知道是不是用类似软件画出来的?如果是,那么以后在自己的文章上也可以自己作图了。
4、搜找了一下pymol,主页是不是cuturl('http://www.pymol.org/')? 好像是要付费的啊!点击Download没有反应。amberly版主如果有的话可否分享一份?