Re: [ccp4bb] modeling flexible ends on proteins
Hi, For loops, there are servers like SuperLooper http://bioinf-applied.charite.de/superlooper/ ModLoop http://modbase.compbio.ucsf.edu/modloop/ FALC-Loop http://falc-loop.seoklab.org/ (seems to be down) If you want model flexible region itself, there is a program called flexible-meccano. http://www.ibs.fr/science-213/scientific-output/software/flexible-meccano?la ng=en Cheers, Min-Kyu | -Original Message- | From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of | Tommi Kajander | Sent: Wednesday, October 22, 2014 8:43 AM | To: CCP4BB@JISCMAIL.AC.UK | Subject: [ccp4bb] modeling flexible ends on proteins | | Hi All, | | Would anyone know a software to model (just with some kind of random | coil) the amino acid chain for the assumed flexible disorderd regions | between domains, or at one end of protein? just for illustrative purposes. | | Thanks! | Tommi
Re: [ccp4bb] nmr blog
You can check the following site. http://qa.nmrwiki.org/ http://nmrwiki.org/wiki/index.php?title=Blogs +--+ Cho, Min-Kyu Postdoctoral scholar Dept. of Biochemistry (Sanders lab.) Vanderbilt University School of Medicine, Nashville, TN Phone: 615-936-3757 | -Original Message- | From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of | Luthra,Amit | Sent: Thursday, March 22, 2012 1:36 PM | To: CCP4BB@JISCMAIL.AC.UK | Subject: [ccp4bb] nmr blog | | Is any NMR blog available for discussion? | | | Amit Luthra, Ph.D. | Post-Doctoral Fellow | The Radolf Laboratory | Department of Medicine | University of Connecticut Health Center | | [e] aut...@uchc.edumailto:aut...@uchc.edu | [p] 860/ 679 - 8390 | [w] http://spirocheteresearch.uchc.edu/
[ccp4bb] My protein precipitates at r.t and dissolves at 4 oC
Hi all, I have a homotetrameric coiled-coil domain sample with 45aa per each. While I store this sample at 4oC, the sample looks clear w/o any particles. But when I took out the sample to my bench at r.t, I can see there are precipitates (as stack of needle like particles) at the bottom of the tube after several hours. Interestingly, when I put it back into 4oC fridge, the precipitates disappeared and the solution turned into clear again. Does anyone have knowledge of such behavior of any protein? I appreciate any information related. Min-Kyu
Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC
I am using KPi buffer at pH 5.5, 100mM KCl, 2mM beta-mercaptoethanol, 0.02% NaN3. Yes, I agree I should check CD melting curve to see temperature preference of my protein. Min-Kyu | -Original Message- | From: Kevin Jin [mailto:kevin...@gmail.com] | Sent: Monday, March 12, 2012 11:16 AM | To: Min-Kyu Cho | Cc: CCP4BB@jiscmail.ac.uk | Subject: Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 | oC | | Which kind of buffer you use? If it is Tris, then temperature change will | cause pH change. | | Actually, this is a good way for crystallization. | | Kevin | | On Mon, Mar 12, 2012 at 9:02 AM, Min-Kyu Cho min-kyu@live.com wrote: | Hi all, | | I have a homotetrameric coiled-coil domain sample with 45aa per each. | While I store this sample at 4oC, the sample looks clear w/o any | particles. But when I took out the sample to my bench at r.t, I can | see there are precipitates (as stack of needle like particles) at the | bottom of the tube after several hours. Interestingly, when I put it | back into 4oC fridge, the precipitates disappeared and the solution | turned into clear again. | | Does anyone have knowledge of such behavior of any protein? I | appreciate any information related. | | Min-Kyu
Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC
Hi Kevin, Could you tell me more detail about beta-mercaptoethanol problem? Min-Kyu | -Original Message- | From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of | Kevin Jin | Sent: Monday, March 12, 2012 3:32 PM | To: CCP4BB@JISCMAIL.AC.UK | Subject: Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 | oC | | I remember I saw the similar problem caused by beta-mercaptoethanol. | | | Kevin | | | On Mon, Mar 12, 2012 at 1:29 PM, Artem Evdokimov | artem.evdoki...@gmail.com wrote: | Could be one of those weird behaviors displayed by detergents where | cloud point anomalously changes with temperature... | | Artem | | On Mar 12, 2012 1:11 PM, Min-Kyu Cho min-kyu@live.com wrote: | | I am using KPi buffer at pH 5.5, 100mM KCl, 2mM beta-mercaptoethanol, | 0.02% NaN3. | | Yes, I agree I should check CD melting curve to see temperature | preference of my protein. | | Min-Kyu | | | -Original Message- | | From: Kevin Jin [mailto:kevin...@gmail.com] | | Sent: Monday, March 12, 2012 11:16 AM | | To: Min-Kyu Cho | | Cc: CCP4BB@jiscmail.ac.uk | | Subject: Re: [ccp4bb] My protein precipitates at r.t and dissolves | at 4 | | oC | | | | Which kind of buffer you use? If it is Tris, then temperature | change will | | cause pH change. | | | | Actually, this is a good way for crystallization. | | | | Kevin | | | | On Mon, Mar 12, 2012 at 9:02 AM, Min-Kyu Cho | min-kyu@live.com | wrote: | | Hi all, | | | | I have a homotetrameric coiled-coil domain sample with 45aa per | each. | | While I store this sample at 4oC, the sample looks clear w/o any | | particles. But when I took out the sample to my bench at r.t, I | can | | see there are precipitates (as stack of needle like particles) | at the | | bottom of the tube after several hours. Interestingly, when I | put it | | back into 4oC fridge, the precipitates disappeared and the | solution | | turned into clear again. | | | | Does anyone have knowledge of such behavior of any protein? I | | appreciate any information related. | | | | Min-Kyu
