[ccp4bb] zalman 3d monitors

[Brett, Thomas]

Hi all:
I have a Zalman ZM-M240W 3D monitor that just burned out and I want to replace 
it. I remember at one time that it was difficult to buy these monitors in the 
US. Is that still the case? I bought this one a good 5-6 years back and am 
hoping to replace it with another Zalman, unless there is another option that 
people are using now that works well with Coot and Pymol. Where can one buy the 
Zalman monitors or is there another option that the community likes now?
thanks in advance,
-Tom

[ccp4bb] bluetooth monitor

[Brett, Thomas]

Hi all:
I was wondering if anyone had economical suggestions on a bluetooth LED or LCD 
monitor. I would like to have a wall mounted monitor that one could easily 
connect laptops and imacs to for structure display, doing tutorials on building 
into maps, etc. 
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

[ccp4bb] shape complimentarity for small molecule

[Brett, Thomas]

Hi all:
If have used SC previously to calculate shape complimentarity for 
macromolecular complexes. Can this also be used to calculate shape 
complimentarity for a (say) protein/small molecule inhibitor complex? Or is 
there some other metric/software that can/should be used to quantitate how well 
a small molecule fits a pocket?
thanks
-tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?

[Brett, Thomas]

Look at AP-2 alpha-appendage. And for that matter, the beta appendage too. 
Alpha appendage binds ~30 different proteins using two sites on one domain.

J Biol Chem. 2004 Oct 29;279(44):46191-203. Epub 2004 Aug 2.
Dual engagement regulation of protein interactions with the AP-2 adaptor alpha 
appendage.
Mishra SK, Hawryluk MJ, Brett TJ, Keyel PA, Dupin AL, Jha A, Heuser JE, Fremont 
DH, Traub LM.

Structure. 2002 Jun;10(6):797-809.
Accessory protein recruitment motifs in clathrin-mediated endocytosis.
Brett TJ, Traub LM, Fremont DH.


Mol Biol Cell. 2008 Dec;19(12):5309-26. Epub 2008 Oct 8.
The AP-2 adaptor beta2 appendage scaffolds alternate cargo endocytosis.
Keyel PA, Thieman JR, Roth R, Erkan E, Everett ET, Watkins SC, Heuser JE, Traub 
LM.

-Tom
Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radisky, Evette 
S., Ph.D. [radisky.eve...@mayo.edu]
Sent: Tuesday, August 23, 2011 9:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Is there a protein that it could interact with different 
proteins by the same part?

This is very common among the small GTP-binding proteins of the Ras
superfamily.  For an interesting analysis (although doubtless there are
lots of more recent examples) you might look at:
Corbett and Alber, TIBS 26 (12) 710-716 (2001)

Evette S. Radisky, Ph.D.
Assistant Professor
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm 310
4500 San Pablo Road
Jacksonville, FL 32224
(904) 953-6372

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Yamei Yu
Sent: Tuesday, August 23, 2011 9:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Is there a protein that it could interact with
different proteins by the same part?

HI all,

We know one protein can interact with different partners by different
domains or different parts. Is there a protein that it could interact
with different proteins by the same part (maybe the same part but in
different conformations?)? Thank you in advance!!

yamei

Re: [ccp4bb] mutation and minimization

[Brett, Thomas]

On a similar extension to this topic, is there a good software out there for 
doing these kinds of modifications and minimizations for protein structures 
with chemicals entities (i.e., protein/inhibitor complexes). What I am looking 
to do is take a protein/inhbitor complex and add chemical modifications onto 
the inhibitor and see how they fit. so a little minimization/relaxation of the 
surrounding protein would be nice. It there a freely available software that 
will allow something like this, if not what commercial packages are 
cheapest/best at this? Thanks and sorry for hijacking this thread.
-tom

Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Pettersen 
[p...@cgl.ucsf.edu]
Sent: Friday, May 13, 2011 2:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] mutation and minimization

On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote:

Hey all,

I would like to introduce point mutations in a structure and quickly
(and dirtily) minimize the new residue.  (Best rotamer dependent on
local environment, or the like.)  What are simple approaches that don't
involve VMD/NAMD or some such overkill.

Chimera is pretty good for this.  It has a Rotamer tool for making the 
substitution based on Dunbrack or Richardson libraries, and can screen based on 
probability / H-bonds formed / steric clashes:

http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html

You can then use Chimera's Minimize Structure tool to minimize the side chain 
and/or the local environment or, if you're feeling frisky, the whole protein:

http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html

--Eric


Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

Chimera home page:  www.cgl.ucsf.edu/chimera

[ccp4bb] off topic: protease identification

[Brett, Thomas]

Hi all:
I was wondering if anyone had any tips on identifying proteases. I have a 
protein for which I know the proteolytic cleavage site. What are the best ways 
to identify the protease that does the cutting either:
1) bioinformatically (i.e., a good database to search using the cleavage site 
or a consensus)
2) experimentally (some engineered substrate to trap/identify the substrate or 
any other method?)
Thanks in advance 
-Tom

Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/

[ccp4bb] off-topic replay: glycerol in protein stock solutions

[Brett, Thomas]

Hi guys:
I know this has been asked before, but I want to get (current) opinions and 
observations once again. Every once in a while, you work with a protein that 
needs to have a little something added to the buffer to keep it soluble. The 
most common trick is addition of glycerol (usually 5-10%). I'm looking for 
general observations on this. I was of the opinion that this was usually a bad 
thing to do with protein stock that you intend to cyrstallize because glycerol 
will coat the protein in a non-homogeneous manner and make your homogeneous 
protein prep heterogeneous (in a way). Or do people usually have good luck 
crystallizing proteins that have to be stored in some glycerol? Or is there a 
better additive? Also, when having to use glycerol, do you put it on your 
sizing columns, etc? I am concerned with putting glycerol on my columns I may 
never be able to completely wash it away. What are your thoughts, community?
thanks in advance,
-tom

[ccp4bb] phosphatase construct

[Brett, Thomas]

Hello:
I am making a kinase in e.coli that seems to autophosphorylate itself a bit, 
which makes it difficult to get a pure homogeneous sample for crystallization. 
I would like to use a phosphatase to remove the abberant phosphorylation. I 
have seen lambda phosphatase used for this type of thing in the past, but 
buying it is pricey. Does anyone have a e coli construct for this or some other 
phosphatase or perhaps another suggested solution to this dilema? thanks in 
advance.
-Tom 

[ccp4bb] protein dimensions

[Brett, Thomas]

Hi all:
Is there program or utility out there that will give maximum protein dimensions 
(length and width) from the pdb file? I'm sure there is, just curious what 
people use.
Thanks,
-Tom

[ccp4bb] Postdoctoral position at Washington University in St. Louis

[Brett, Thomas]

POSTDOCTORAL POSITION IN STRUCTURAL BIOLOGY
WASHINGTON UNIVERSITY SCHOOL OF MEDICINE, ST. LOUIS MO

An NIH-funded Postdoctoral position is immediately available to study the 
structure and function of proteins involved in obstructive pulmonary diseases 
(asthma and COPD). These proteins represent key therapeutic targets for the 
treatment of asthma and COPD. This work will be done in collaboration with 
individuals in the Pulmonary Division.

Our lab is located in the Department of Internal Medicine (Pulmonary Division) 
and has state-of-the-art equipment for protein expression and purification as 
well as direct access to crystallization robotics in addition to 
instrumentation for protein characterization (CD, MALS, AUC) and probing 
protein-protein interactions (ITC, SPR). Instrumentation for in-house X-ray 
data collection is available, and we have frequent access to synchrotron sites 
(either directly or via remote data collection). Excellent computation 
facilities are available.

Enthusiastic and self-motivated individuals with (or expecting) a PhD in 
Biochemistry or a related discipline are encouraged to apply. The ideal 
candidate will have extensive experience in all aspects of protein expression, 
purification, characterization and crystallization. Experience in X-ray 
crystallography and the use of biophysical methods to characterize 
protein-protein interactions as well as cell-binding assays would be 
advantageous but not required as training can be provided. Must have a strong 
interest in the biology of human diseases. This is an excellent position for a 
structural biologist wanting to learn more about chronic inflammatory diseases 
or (vice versa) an individual with experience in inflammatory disease research 
wanting to learn structural biology. Excellent oral and written communication 
skills are required.  

Interested candidates are encouraged to apply or inquire by submitting (via 
email) a curriculum vitae (including a summary of research experience and 
interests, and contact information for 2-3 references) to Tom J. Brett:

tbr...@wustl.edu

http://brettlab.dom.wustl.edu/

Contact Info:
Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110

[ccp4bb] homology modelling using sequence alignment

[Brett, Thomas]

Dear all:
I am trying to create a homology model of a coiled-coil for use in molecular 
replacement. I have a template poly-ala coiled coil that I like to use, so that 
is fine. I want to thread my sequence onto the helix and am trying to find a 
server/easy program that will do this. I want to use a hand made alignment so 
that I can create 7 models shifted by residue (to be complete). Really all this 
should need is a template pdb and the sequence alignment. What are peoples 
favorite servers/easy programs for this? I have been trying to use the WHAT IF 
server and the SCWRL3 server, but WHAT IF isn't working for me (it just spits 
out the template pdb with the original sidechains that were pruned to poly ala 
built back in- is it because I am using a mac?) and scwrl keeps crashing with 
python errors (has anyone got the scwrl server to work?). Apologies for the off 
topic. Thanks in advance,
-Tom


Tom J. Brett, PhD
Assistant Professor of Medicine 
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110

Re: [ccp4bb] Cryoprotection in > 3M ammonium sulfate

[Brett, Thomas]

Or saturated LiSO4 works too. Should work in this case.
-Tom

Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110

From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Savvas Savvides 
[savvas.savvi...@ugent.be]
Sent: Wednesday, August 19, 2009 11:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Cryoprotection in > 3M ammonium sulfate

Hi Brenda
Try > 3M ammonium sulfate itself! We have tried that with great succes by
cryo-cooling xtals grown at 3.2M AS straight out of their crystallization
drops. You can consult the "M&M" section in Kyndt J. et al Biochemistry 2007
Jan 9;46(1):95-105 for a more detailed description of what we did.

Best of luck
Savvas


Savvas Savvides
L-ProBE, Unit for Structural Biology
Ghent University
K.L. Ledeganckstraat 35
9000 Ghent, BELGIUM
office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19
Email: savvas.savvi...@ugent.be
http://www.lprobe.ugent.be/xray.html



-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Schulman, Brenda
Sent: Wednesday, August 19, 2009 6:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Cryoprotection in > 3M ammonium sulfate

Hello!

I would be grateful for suggestions on cryoprotectants for crystals growing
in > 3M ammonium sulfate.

Thanks!

Brenda


Email Disclaimer:  www.stjude.org/emaildisclaimer





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[ccp4bb] imosflm with multiple data sets

[Brett, Thomas]

I am an imosflm novice and have a relatively simple question. I have a 360 deg 
data set collected in two swathes of 180 deg (one with phi=0 and omega going 
0-180 and the second with phi = 180 and omega going 0-180). What is the easiest 
way to process the two datasets using a matching orientation matrix (or one 
rotated by 180 deg as it were) so that all the data can be merged together. Is 
there an easy way to do it in imosflm or must one process the two sets 
separately and then manipulate later with pointless before scalling and merging 
everything together?
Thanks in advance.
-Tom

Tom J. Brett, PhD
Assistant Professor of Medicine 
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110

[ccp4bb] John Stezowski 1942-2007

[Brett, Thomas]

Crystallographic Community:

It is with deep regret that I must report the untimely passing of a valued
member of the crystallographic community, Professor John J. Stezowski.  John
was a Professor of Chemistry at the University of Nebraska from 1991 up until
the time of his passing. John began his academic career at the University of
Stuttgart where he was a faculty member for many years before moving to
Nebraska.  While at Stuttgart, John spent many summers at Fox Chase Cancer
Center as a sabbatical scientist.  As a leader in the crystallographic
community, John (along with Bill Duax and Judith Flippen-Anderson)
established the IUCr Commission on Small Molecules (now called the Commission
on Chemical Crystallography) and served as its first chair.  He also lead a
group that arranged a special IUCr symposium in China in 1986 that featured
Dorothy Hodgkin, Bill Lipscomb, Herb Hauptman, and Jack Dunitz as plenary
lecturers at John's request.  While at Nebraska, John launched a highly
successful program in chemical and protein crystallography.

I apologize for the off-topic post, but this bulletin board has become the
most effective way to get in touch with the crystallographic community at
large.  I am in the process of trying to compile a tribute to John for the
ACA Reflexions newsletter, and would appreciate any input of John's
accomplishments or any personal reflections.  For example, I know he was
editor of a european crystallography journal for some time, just not sure
which one. I would encourage those who knew John to leave a message on his
guestbook linked from here:

http://www.chem.unl.edu/dept/stezowskimemorial.shtml

If anyone has any info for me, please contact me directly at:

[EMAIL PROTECTED]


Thanks,
-Tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110